{"paper_id":"12ef52c2-7da5-4d4c-b8b5-cb1b53cdb12e","body_text":"Comparative Multi-Omics Analysis Reveals Systems-Level Molecular Dysfunctions Underlying Salt Sensitivity in Solanum lycopersicum | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Comparative Multi-Omics Analysis Reveals Systems-Level Molecular Dysfunctions Underlying Salt Sensitivity in Solanum lycopersicum Tushar Ahmed Shishir, Sultan Shanneedh Quader, Inshera Ahmed, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7277116/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Background Soil salinity threatens over 20% of global cultivated land and is projected to affect 50% of arable areas by 2050, posing critical challenges to food security. While Arabidopsis thaliana exhibits moderate salt tolerance through well-characterized mechanisms including the SOS signaling pathway, economically vital crops like Solanum lycopersicum (tomato) demonstrate extreme salt sensitivity despite possessing orthologs of key salt tolerance genes. Understanding the molecular determinants underlying this species-specific salt tolerance disparity is essential for developing rational crop improvement strategies. Results Through comprehensive multi-layered silico analysis of 14 curated salt tolerance genes, we revealed complex evolutionary patterns underlying salt sensitivity of tomato. Four critical genes (NHX2, WRKY8, MYB74, CHX17) were completely lost in tomato, while five others underwent expansion but with compromised functionality. Noticeably, key regulatory genes exhibited opposite transcriptional responses under salt stress. HAK5 showed robust induction in Arabidopsis (+3.42 LogFC) but repression in tomato (-0.36 LogFC), while SOS3 demonstrated strong activation in Arabidopsis (+2.26 LogFC) versus downregulation in tomato (-0.27 LogFC). Promoter analysis revealed 3 to 6 fold depletion of stress-responsive cis-elements in tomato genes, with WRKY motifs showing the greatest disparity. Structural modeling identified significant conformational divergence in critical proteins, including increased disorder in tomato SOS1 and loss of transmembrane domain in SOS2. Evolutionary analysis revealed positive selection in expanded gene families, indicating adaptive evolution that paradoxically correlates with reduced salt tolerance. Conclusions Tomato's salt sensitivity results from systems-level dysfunction involving coordinated gene loss, structural protein divergence, transcriptional network remodeling, and regulatory element depletion rather than simple absence of salt tolerance machinery. These findings necessitate a paradigm shift from gene complementation approaches toward comprehensive systems-level engineering strategies for enhancing crop salt tolerance, providing a mechanistic framework for developing salt-tolerant crops essential for future food security. Salt Tolerance Comparative Genomics Crop Improvement Transcriptional Regulation SOS Pathway Evolutionary Selection Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Background Soil salinity represents one of the most formidable abiotic stress factors threatening agricultural productivity worldwide, affecting over 20% of cultivated land and causing substantial crop yield losses [ 1 – 3 ]. The accumulation of excessive salts, particularly sodium (Na⁺) and chloride (Cl⁻) ions, disrupts cellular ion homeostasis, induces osmotic stress, and triggers oxidative damage, ultimately limiting plant growth and development [ 4 , 5 ]. Salinization is estimated to impact 50% of all arable land by 2050. This environmental challenge poses an existential threat to global food security, particularly in the context of a growing world population and climate change intensification [ 6 – 8 ]. Evolutionarily, plants have evolved sophisticated and diverse mechanisms to cope with salinity stress, primarily for maintaining optimal cytosolic Na⁺/K⁺ ratios through coordinated physiological and molecular responses [ 4 , 5 ]. These adaptive strategies include multiple interconnected processes, including the exclusion of Na⁺ from root tissues, compartmentalization of toxic ions into vacuoles, synthesis of compatible osmolytes, and activation of antioxidant defense systems [ 1 , 4 ]. The molecular foundation of plant salt tolerance has been extensively characterized through decades of research, revealing complex regulatory networks that compose these multifaceted responses to saline environments [ 9 , 10 ]. Arabidopsis thaliana , a model dicotyledonous plant, has emerged as the paradigmatic system for understanding plant salt tolerance mechanisms [ 11 , 12 ]. Despite being classified as a glycophyte with moderate salt sensitivity, Arabidopsis possesses a comprehensive genetic toolkit for salt stress response, arranged around the well-characterized Salt Overly Sensitive (SOS) signaling pathway [ 9 , 11 ]. This regulatory network, including the plasma membrane Na⁺/H⁺ antiporter SOS1, the serine/threonine kinase SOS2, and the calcium-binding protein SOS3, controls critical ion transport processes that prevent toxic Na⁺ accumulation in photosynthetic tissues [ 4 , 9 ]. Additional key components include the high-affinity K⁺ transporter HKT1, which retrieves Na⁺ from the xylem, and the vacuolar Na⁺/H⁺ exchanger NHX1, which facilitates Na⁺ sequestration [ 4 , 9 ]. The extensive characterization of these molecular mechanisms in Arabidopsis has provided fundamental insights into the genetic basis of plant salt tolerance and established a comprehensive framework for understanding glycophyte responses to salinity stress [ 10 , 13 ]. In contrast to the relative salt tolerance exhibited by Arabidopsis , many economically vital crop species demonstrate significantly higher sensitivity to saline conditions, resulting in substantial agricultural losses and food security concerns [ 14 , 15 ]. Solanum lycopersicum (tomato), one of the world's most important horticultural crops, exemplifies this agricultural challenge as a salt-sensitive species that tolerates only moderate salinity levels (EC ~ 2.5 dS m⁻¹) before experiencing severe yield reductions [ 14 , 15 ]. Tomato's salt sensitivity is persistent across all developmental stages, from germination and seedling establishment to reproductive maturity, with root systems being particularly vulnerable to elevated salt concentrations [ 14 , 16 ]. This increased sensitivity is particularly concerning, given projections that tomato yields may decrease by 50% by 2050 due to salt stress alone, highlighting the urgent need to understand the molecular basis of crop salt sensitivity [ 17 ]. The differences in salt tolerance among model plants like Arabidopsis and economically important crops such as tomato presents a compelling scientific paradox. They possess orthologs of key salt tolerance genes, including components of the SOS pathway, HKT transporters, and NHX exchangers, yet exhibit different physiological responses to salinity stress [ 10 , 14 ] which indicates salt tolerance differences may arise from subtle variations in gene copy number, protein sequences, regulatory control mechanisms, or system-level integration of stress response pathways rather than the complete absence of tolerance machinery [ 10 , 13 ]. Comparative genomic and transcriptomic analyses between salt-tolerant and salt-sensitive species have revealed that halophytes often constitutively express stress-response genes that are only induced under salt stress in glycophytes, indicating fundamental differences in gene regulation rather than gene presence [ 10 , 13 ]. The evolutionary and functional divergence of orthologous salt tolerance genes across plant species represents a critical knowledge gap that limits our understanding of crop salt sensitivity and limits efforts to develop salt-tolerant varieties [ 18 , 19 ]. Recent advances in comparative genomics, transcriptomics, and systems biology approaches have provided powerful tools to dissect these complex relationships and identify the molecular determinants of species-specific salt tolerance [ 20 , 21 ]. However, comprehensive comparative studies that integrate genomic architecture, protein structure-function relationships, evolutionary selection pressures, and gene expression dynamics between model tolerant species and sensitive crops remain limited. Understanding the specific genetic and molecular mechanisms underlying the differential salt tolerance between Arabidopsis and tomato is therefore essential for developing rational strategies to enhance crop salt tolerance through breeding, biotechnology, or agronomic interventions. Such knowledge could inform targeted approaches to improve salt tolerance in tomato and other sensitive crops, potentially through gene editing, transgenic approaches, or marker-assisted breeding programs that leverage favorable alleles or regulatory elements from tolerant species [ 18 , 22 ]. Furthermore, elucidating the evolutionary forces that have shaped salt tolerance mechanisms could provide insights into the adaptive potential of crop species and guide conservation and utilization of genetic resources for future agricultural sustainability [ 21 , 23 ]. Therefore, the present study addresses this critical knowledge gap by conducting a comprehensive multi-layered in silico investigation to elucidate the divergent salt tolerance mechanisms between Arabidopsis thaliana and Solanum lycopersicum . Through integrative analyses including comparative genomics, protein structural modeling, evolutionary selection analysis, regulatory element analysis and transcriptomic profiling, this research aims to identify the molecular determinants of species-specific salt tolerance and provide systematic insights into crop salt sensitivity. The findings from this work will contribute to our fundamental understanding of plant salt tolerance evolution and provide a foundation for developing enhanced salt tolerance in economically important crop species. Materials and Methods Data Acquisition and Curation Reference genomes, proteomes, and coding sequences for Arabidopsis thaliana (TAIR10) and Solanum lycopersicum (SL3.0) were obtained from NCBI RefSeq [ 24 ]. Salt-tolerance genes in A. thaliana were curated via literature review and categorized into two groups Core and Secondary. Core seven proteins with primary roles in Na⁺ transport and signaling and six Secondary protein representing upstream regulators and transport families. Synteny and Collinearity Analysis Large-scale chromosomal conservation was analyzed using MCScanX [ 25 ]. An all-vs-all BLASTp search (E-value < 1e − 10 ) was performed between the two proteomes. The BLAST results, along with simplified GFF files containing gene coordinate information, were used as input for MCScanX to identify collinear blocks between the two genomes. Orthologous Gene Identification To identify the corresponding tomato orthologs for the curated Arabidopsis genes, the complete proteomes of both species were analyzed using OrthoVenn3 web server using the Orthofinder algorithm [ 26 ]. The software performs an all-vs-all protein sequence comparison to cluster genes into orthologous families. The resulting Orthologous groups were parsed to create a map connecting the curated Arabidopsis proteins to their Solanum counterparts. Phylogenetic Analysis For each Core gene family, protein sequences of all members from both species were extracted based on the OrthoVenn3 results. Multiple sequence alignments were generated using MAFFT (v7.490) [ 27 ] with default parameters. The resulting alignments were trimmed using TrimAl (v1.4) [ 28 ] to remove poorly aligned regions. Maximum-likelihood phylogenetic trees were then constructed using IQ-TREE (v2.2.0) [ 29 ] with the best-fit substitution model automatically determined by ModelFinder [ 30 ] and branch support assessed with 1,000 ultrafast bootstrap. Protein Domain Analysis Protein domain architecture was analyzed using the InterProScan web server [ 31 ]. The resulting domain annotations were compared between orthologous groups to identify any gain, loss, or truncation of functional domains in the tomato lineage. Selection Pressure (Ka/Ks) Analysis The ratio of nonsynonymous to synonymous substitution rates (Ka/Ks) was calculated to determine the selection pressure on tomato genes. Protein orthologs were aligned using MAFFT and corresponding CDS alignments were generated with pal2nal.pl, and Ka/Ks ratios were computed using KaKs_Calculator [ 32 ]. Promoter and Cis-Regulatory Element Analysis Isolated the 2000 bp region upstream of each annotated start codon using the BEDTools suite to investigate regulatory architecture [ 33 ], guided by genome GFF3 annotation files. PlantPAN 4.0 [ 34 ] was used to scan these promoter sequences for known plant transcription factor binding sites. Later, four major cis-element families (ABRE [bZIP], DRE/CRT [AP2/ERF], MYB, WRKY W-box) were systematically analyzed for each orthologous gene pair. Differential Gene Expression Analysis Publicly available RNA-Seq datasets for salt stress were selected and analyzed with GEO2R of the NCBI Gene Expression Omnibus (GEO) [ 35 ]. The datasets used were GSE193762 for A. thaliana and GSE106149 for S. lycopersicum . The provided Log2 Fold Change (LogFC) values were used for the comparison. Protein Structure Prediction and Comparison Three-dimensional protein structures of selected proteins were predicted using AlphaFold3 [ 36 ]. Structural alignments and similarity metrics (RMSD, TM-score) were calculated with TM-align [ 37 ]. Results Comparative Genomic Landscape The genomes of A. thaliana and S. lycopersicum exhibit significant differences in scale and complexity. The tomato genome, at approximately 950 Mb, is roughly seven times larger than the compact 135 Mb Arabidopsis genome. This expansion is reflected in the chromosome number, with Solanum having 12 pairs compared to the 5 chromosomes of Arabidopsis . Despite this size difference, the number of protein-coding genes is comparable, with tomato encoding approximately 31,760 genes and Arabidopsis encoding around 27,000. An initial analysis of orthologous protein clusters revealed a substantial core of 11,582 shared protein families, alongside 1,605 clusters unique to Arabidopsis and 1,521 unique to tomato (Fig. 1 ). Synteny analysis further revealed extensive chromosomal rearrangement since the divergence of species, indicating that the genomic context of conserved genes has been significantly altered (Fig. 2 ). Orthologous Remodeling of Salt Stress Signaling Components in Solanum lycopersicum To investigate the evolutionary conservation of the salt tolerance machinery between Arabidopsis thaliana and Solanum lycopersicum , we performed targeted orthologous mapping of 13 curated Arabidopsis proteins associated with salt stress responses. The resulting comparative framework clarifies a complex evolutionary landscape marked by conserved core transporters, lineage-specific gene expansions, and selective gene loss, indicative of substantial reconfiguration of the tomato salt tolerance network (Table 1 ). Of the seven Core proteins identified in Arabidopsis , six retained orthologs in tomato, including plasma membrane Na⁺/H⁺ antiporter SOS1 (NP_001234698.2), high-affinity K⁺/Na⁺ transporter HKT1 (NP_001289833.1), vacuolar H⁺-pyrophosphatase AVP1 (NP_001307479.1), serine/threonine kinase SOS2 (NP_001234210.1, XP_069147947.1), and vacuolar exchanger NHX1 (NP_001233885.2, XP_010324159.1, XP_025884695.1). Notably, the Ca²⁺ sensor SOS3, serine kinase SOS2 and vacuolar exchanger NHX1 exhibited orthologous expansion in tomato. In contrast, NHX2 was absent in the tomato genome, suggesting a gene loss event or functional divergence compensated by NHX1 paralogs. Table 1 Orthologous mapping of salt tolerance genes. The analysis reveals selective gene loss in tomato, particularly for transcriptional regulators WRKY8, MYB74, and the vacuolar exchanger NHX2. Group Gene Name Arabidopsis ID Protein Function Tomato Ortholog ID Core SOS1 NP_178307.2 Membrane Na+/H + Antiporter NP_001234698.2 Core SOS2 NP_198391.1 Serine/Threonine Kinase NP_001234210.1, XP_069147947.1 Core SOS3 NP_001190377.1, NP_001331302.1, NP_001331303.1, NP_001331304.1, NP_197815.1 Calcium-Binding Protein (Sensor) NP_001234705.1, XP_025885582.1, XP_025885583.1, XP_025885584.1, XP_069150952.1, XP_069150953.1 Core HKT1 NP_567354.1 High-Affinity K+/Na + Transporter NP_001289833.1 Core NHX1 NP_198067.1 Vacuolar Na+/H + Exchanger NP_001233885.2, XP_010324159.1, XP_025884695.1 Core NHX2 NP_187154.1 Vacuolar Na+/H + Exchanger No Ortholog Found Core AVP1 NP_173021.1 Vacuolar H+-Pyrophosphatase NP_001307479.1 Secondary WRKY8 NP_199447.1 WRKY Transcription Factor No Ortholog Found Secondary MYB74 NP_192419.1 MYB Transcription Factor No Ortholog Found Secondary CTR1 NP_195993.1, NP_850760.1 Serine/Threonine Kinase NP_001234454.1, XP_025888482.1 Secondary GSO1 NP_193747.2 Leucine-Rich Repeat Kinase XP_004239381.1 Secondary HAK5 NP_567404.1 High-Affinity K + Transporter NP_001234372.2, XP_069147902.1 Secondary CHX17 NP_194101.1, NP_001328705.1 Cation/H + Exchanger No Ortholog Found Among the six secondary components, evolutionary outcomes were more variable. While CTR1 and HAK5 demonstrated moderate expansion, WRKY8, MYB74, and CHX17 does not have orthologs in tomato, pointing to potential lineage-specific transcriptional rewiring. GSO1 was conserved as a single-copy ortholog, indicating preservation of peptide-mediated signaling in root architecture. Phylogenetic Analysis Reveals Divergent Evolution of Key Salt Tolerance Gene Families in Tomato To further investigate the lineage-specific expansions and losses observed in our ortholog mapping, we constructed maximum-likelihood phylogenetic trees for three core salt tolerance gene families, SOS3 (calcium sensor), NHX (vacuolar Na⁺/H⁺ exchangers), and SOS2 (serine/threonine kinase). These trees reveal distinct evolutionary trajectories in Solanum lycopersicum compared to Arabidopsis thaliana and provide structural insights into the remodeling of signaling pathways connected to salt stress. The phylogenetic reconstruction of the SOS3 family (Fig. 3 A) discloses a pronounced expansion in tomato, consistent with the six co-orthologs identified earlier. The tree topology shows a divergence into two strongly supported clades. One clade group all five Arabidopsis SOS3 paralogs. The second clade comprises the tomato orthologs and no Arabidopsis members. The extended branch length (0.13301) separating these clades suggests an ancient duplication event exclusive to the tomato lineage. This divergence indicates the emergence of SOS3 families in S. lycopersicum , which may confer distinct calcium-sensing roles or regulatory specificities under salinity stress. The NHX phylogeny (Fig. 3 B) provides clear divergence events in tomato. The tree separates into two clades with strong bootstrap support. The first clade contains Arabidopsis NHX1 (NP_198067.1) alongside the NHX2 protein from Arabidopsis (NP_187154.1). The second clade includes all three tomato orthologs, with no Arabidopsis representatives. The absence of tomato proteins in the NHX2 clade, coupled with a long branch between NHX1 and NHX2 clusters, indicates that tomato lost the NHX2 sub-family following an ancient duplication event. This loss may reduce vacuolar buffering redundancy and alter the ionic sequestration dynamics compared to Arabidopsis . On the other hand, the SOS2 tree (Fig. 3 C) exhibits a simpler evolutionary pattern. The Arabidopsis SOS2 kinase (NP_198391.1) appears on an isolated branch, whereas the two tomato co-orthologs cluster tightly in a sister clade. The short internal branch length (0.01745) between these tomato sequences suggests a relatively recent duplication. Given their proximity and lack of divergence, the tomato SOS2 paralogs likely retain redundant or overlapping functional roles in the phosphorylation cascade of the salt stress response. Core Domain Architectures Are Broadly Conserved with Specific Divergence in Regulatory Paralogs To understand the molecular foundations behind the contrasting salt tolerance observed in the resilient Arabidopsis thaliana and the sensitive Solanum lycopersicum , a comprehensive comparative analysis of their protein architectures associated with salt stress response was then conducted. The results reveal that although the core biochemical framework is broadly conserved between the two species, distinct structural deviations, particularly in membrane topology and intrinsic disorder of key regulatory proteins, combined with the complete absence of certain gene families in tomato, likely contribute to its pronounced sensitivity to salinity (Tables 2 & 3 , Supplementary file 1). Across essential gene families, domain architectures were largely preserved. Proteins from both species retained canonical motifs such as Na⁺/H⁺ exchangers, H⁺-pyrophosphatases, cation transporters, and EF-hand calcium-binding domains (Table 2 ). Transmembrane regions showed high similarity, suggesting that membrane insertion and transport functions are largely intact. However, subtle structural distinctions may hold functional significance. For instance, tomato SOS1 exhibited a higher proportion of disordered regions (11.47%) relative to Arabidopsis (6.02%), potentially influencing its regulatory plasticity. Arabidopsis SOS2 harbored an additional transmembrane domain and a cytoplasmic localization signal absent in tomato homologs, which may alter its intracellular signaling dynamics. The SOS3 family presents another layer of divergence. Although tomato paralogs retain dual EF-hand motifs, the presence of six variants compared to five in Arabidopsis points to possible functional diversification or subfunctionalization. Similarly, tomato HKT1 features an extra transporter domain and more transmembrane regions than its Arabidopsis counterpart, suggesting at differences in ion selectivity or regulation under saline conditions. Above all, a major deviation was the complete absence of NHX2 in tomato (Fig. 4 ). While Arabidopsis NHX2 showed high structural similarity to NHX1, including 13 TM regions and a conserved exchanger domain, no orthologous protein was identified in tomato (Fig. 3 , Table 2 ). NHX2 is known to contribute significantly to vacuolar Na⁺ compartmentalization under salt stress, and its absence may reduce ion buffering capacity in tomato. Table 2 Comparative architectural analysis of Core proteins Gene Species Accession Class Domains/ Motifs #Dom TM IDR (%) CytD ExtD AVP1 Arabidopsis thaliana NP_173021.1 Vacuolar H+-pyrophosphatase H + pyrophosphatase 1 13 0 7 7 Solanum lycopersicum NP_001307479.1 Vacuolar H+-pyrophosphatase H + pyrophosphatase 1 13 0 7 7 HKT1 Arabidopsis thaliana NP_567354.1 Potassium/sodium transporter Cation transporter 1 8 0 5 4 Solanum lycopersicum NP_001289833.1 Potassium/sodium transporter Cation transporter 2 10 0 6 5 NHX1 Arabidopsis thaliana NP_198067.1 Sodium/H + exchanger Na+/H + exchanger 1 13 0 7 7 Solanum lycopersicum NP_001233885.2 Sodium/H + exchanger Na+/H + exchanger 1 12 2, 8.77% 6 7 Solanum lycopersicum XP_010324159.1 Sodium/H + exchanger Na+/H + exchanger 1 12 2, 8.77% 6 7 XP_025884695.1 Sodium/H + exchanger Na+/H + exchanger 1 12 2, 8.77% 6 7 NHX2 Arabidopsis thaliana NP_187154.1 Sodium/H + exchanger Na+/H + exchanger 1 13 0 7 7 Solanum lycopersicum Absent in Solanum lycopersicum SOS1 Arabidopsis thaliana NP_178307.2 Sodium/H + antiporter Na+/H + exchanger 1 13 4, 6.02% 7 7 Solanum lycopersicum NP_001234698.2 Sodium/H + antiporter Na+/H + exchanger 1 13 3, 11.47% 7 7 SOS2 Arabidopsis thaliana NP_198391.1 Calcium-dependent protein kinase NAF domain, Protein kinase 2 1 0 1 1 Solanum lycopersicum NP_001234210.1 Calcium-dependent protein kinase NAF domain, Protein kinase 2 0 0 0 0 XP_069147947.1 Calcium-dependent protein kinase NAF domain, Protein kinase 2 0 0 0 0 SOS3 Arabidopsis thaliana NP_197815.1 Calcineurin B-like protein EF-hand domain 2 0 0 0 0 Solanum lycopersicum NP_001234705.1 Calcineurin B-like protein EF-hand domain 2 0 0 0 0 XP_025885582.1 Calcineurin B-like protein EF-hand domain 2 0 0 0 0 XP_025885583.1 Calcineurin B-like protein EF-hand domain 2 0 0 0 0 XP_025885584.1 Calcineurin B-like protein EF-hand domain 2 0 0 0 0 XP_069150952.1 Calcineurin B-like protein EF-hand domain 2 0 0 0 0 XP_069150953.1 Calcineurin B-like protein EF-hand domain 2 0 0 0 0 #Dom – Number of domains/motifs; TM – Transmembrane regions; IDR (%) – No of Intrinsically disordered regions and % coverage; CytD – Cytoplasmic domains; ExtD – Extracellular domains. While the core machinery remains largely intact, notable architectural differences among regulatory and transport proteins appear to further distinguish the salt response capabilities of tomato. For example, the CTR1 protein in Arabidopsis exhibits substantially higher disorder (15.23%) than its tomato counterparts (5–6%), possibly reflecting greater flexibility in assembling or modulating signaling complexes. Both species maintain well-conserved GSO1 orthologs, with complete LRR and kinase domains and matching topological features, suggesting preserved function. In contrast, tomato HAK5 variants display fewer transmembrane regions and greater variability across intracellular and extracellular segments, features that may compromise their transport efficiency. Table 3 Comparative architectural analysis of Secondary proteins. Gene Species Accession Class Domains/ Motifs #Dom TM IDR (%) CytD ExtD CTR1 Arabidopsis thaliana NP_195993.1 Serine/threonine protein kinase EDR1/CTR1 peptidase-like, Protein kinase 2 0 4, 15.23% 0 0 Solanum lycopersicum NP_001234454.1 Serine/threonine protein kinase EDR1/CTR1 peptidase-like, Protein kinase 2 0 2, 5.26% 0 0 Solanum lycopersicum XP_025888482.1 Serine/threonine protein kinase EDR1/CTR1 peptidase-like, Protein kinase 2 0 2, 5.98% 0 0 GSO1 Arabidopsis thaliana NP_193747.2 LRR receptor-like kinase Leucine-rich repeat (LRR), Protein kinase 13 1 0 1 1 Solanum lycopersicum XP_004239381.1 LRR receptor-like kinase Leucine-rich repeat (LRR), Protein kinase 13 1 0 1 1 HAK5 Arabidopsis thaliana NP_567404.1 High-affinity potassium transporter K + transporter domains 2 12 4, 9.68% 7 6 Solanum lycopersicum NP_001234372.2 High-affinity potassium transporter K + transporter domains 2 12 2, 8.65% 7 6 Solanum lycopersicum XP_069147902.1 High-affinity potassium transporter K + transporter domains 2 10 2, 9.97% 6 5 MYB74 Arabidopsis thaliana NP_192419.1 MYB transcription factor MYB DNA-binding 2 0 0 0 0 Solanum lycopersicum Absent in Solanum lycopersicum WRKY8 Arabidopsis thaliana NP_199447.1 WRKY transcription factor WRKY DNA-binding 1 0 3, 29.75% 0 0 Solanum lycopersicum Absent in Solanum lycopersicum CHX17 Arabidopsis thaliana NP_194101.1 Cation/H + antiporter Plant cation/H + antiporter 3 12 0 6 7 Solanum lycopersicum Absent in Solanum lycopersicum #Dom – Number of domains/motifs; TM – Transmembrane regions; IDR (%) – No of Intrinsically disordered regions and % coverage; CytD – Cytoplasmic domains; ExtD – Extracellular domains. Most noticeably, the absence of entire gene families in tomato presents a undeniable explanation for its weakened tolerance to salt stress (Fig. 4 ). Tomato lacks orthologs for key transcription factors such as WRKY8 and MYB74, as well as the cation exchanger CHX17 (Table 3 ). The loss of WRKY8 is especially consequential since its Arabidopsis homolog contains a substantial intrinsically disordered region (20.75%), indicating a role as a central regulatory hub. Without these transcriptional activators, tomatoes may be failing to initiate critical downstream protective responses that are active in Arabidopsis under saline conditions. Positive Selection Drives Functional Innovation in Expanded Tomato Gene Families To quantitatively assess the evolutionary forces shaping salt tolerance in tomato, we calculated the non-synonymous to synonymous substitution rate (Ka/Ks) for each orthologous group. The comparative analysis revealed a clear contradiction in selective pressure. While single copy orthologs exhibit strong purifying selection consistent with functional conservation, expanded gene families in tomato demonstrate Ka/Ks ratios exceeding 1.0, indicating adaptive evolution through positive selection (Table 4 , Fig. 5 ). Table 4 Evolutionary selection analysis of orthologous gene pairs. Ka/Ks ratios for salt tolerance gene families indicating the mode of selection pressure. Positive selection (Ka/Ks > 1.0) is observed in expanded families NHX1 and SOS3, while purifying selection characterizes conserved single-copy genes, suggesting different evolutionary constraints on gene families. Group Gene Family Avg. Ka/Ks Value Inferred Mode of Selection Core NHX1 1.6735 Positive Selection Core SOS3 1.0924 Positive Selection Core SOS2 0.8538 Near-Neutral Evolution Core HKT1 0.4793 Purifying Selection Core SOS1 0.3671 Purifying Selection Core AVP1 0.2764 Purifying Selection Core NHX2 N/A Gene Loss Secondary CTR1 0.1283 Strong Purifying Selection Secondary HAK5 0.6450 Purifying Selection Secondary GSO1 0.5538 Purifying Selection Secondary WRKY8 N/A Gene Loss Secondary CHX17 N/A Gene Loss Secondary MYB74 N/A Gene Loss Salt tolerance genes with conserved copy number between Arabidopsis and tomato, including SOS1, HKT1, AVP1, CTR1, and GSO1, exhibited Ka/Ks ratios significantly below 1.0. These values indicate ongoing purifying selection against deleterious mutations, consistent with critical physiological roles and functional stability. The lowest Ka/Ks value was observed in CTR1 (0.1283), suggesting intense selective constraint on this ethylene pathway regulator. Similarly, core ion transporters like SOS1 (0.3671) and HKT1 (0.4793) showed strong conservation, reinforcing their indispensable roles in Na⁺ exclusion and K⁺ homeostasis. In contrast, the two tomato gene families that underwent marked expansion, NHX1 and SOS3, exhibited Ka/Ks ratios of 1.6735 and 1.0924, respectively. These values surpass the neutral threshold (Ka/Ks > 1.0), supporting the inference of positive selection driving diversification. Elevated substitution rates suggest that amino acid changes in these gene copies are being favored, reflecting neofunctionalization or enhanced regulatory flexibility to cope with complex salt stress conditions. This finding is particularly prominent in the NHX1 vacuolar transporter group, where paralog expansion coincides with signatures of adaptive evolution. Likewise, the SOS3 calcium sensor family includes paralogs which are under positive selection, indicating concurrent evolutionary innovation. Moreover, four orthologous groups, NHX2, WRKY8, CHX17, and MYB74, showed complete absence in tomato, consistent with gene loss events. The lack of selective retention suggests that these genes were not under strong purifying selection in the tomato lineage, allowing functional redundancy or dispensability to drive genome streamlining. Together, these data suggest a compensatory evolutionary mechanism in tomato. The loss of transcriptional regulators and redundant transporters may have created selective pressure that favored the expansion and rapid divergence of key effector proteins. Moreover, the higher Ka/Ks values in NHX1 and SOS3 orthologs indicate a mode of adaptive response, where gene family expansion facilitates flexible and robust salt stress responses. Divergent Promoter Architecture in Tomato Orthologs Then we analyzed their promoter regions for the presence of key stress-responsive cis-regulatory elements, to investigate the regulatory potential of the curated genes. The analysis revealed a plain and consistent pattern, the promoters of Arabidopsis salt-tolerance genes are significantly enriched with binding sites for bZIP (ABRE), AP2/ERF (DRE), MYB, and WRKY transcription factors compared to their tomato orthologs (Table 5 , Fig. 6 , Supplementary file 1). Table 5 Promoter Cis-regulatory element analysis. Quantitative comparison of stress-responsive transcription factor binding sites in promoter regions of orthologous genes. 3 to 6 fold reduction in motif density in tomato compared to Arabidopsis , indicates compromised transcriptional responsiveness to salt stress. Gene Family Arabidopsis thaliana Solanum lycopersicum ID bZIP AP2/ERF MYB WRKY Ortholog(s) ID bZIP AP2/ERF MYB WRKY SOS1 NP_178307.2 11 9 15 7 NP_001234698.2 2 3 4 1 SOS2 NP_198391.1 8 14 10 5 NP_001234210.1, XP_069147947.1 1, 3 2, 5 3, 3 0, 1 SOS3 NP_197815.1 6 11 9 4 NP_001234705.1, XP_025885582.1, XP_025885583.1, XP_025885584.1, XP_069150952.1, XP_069150953.1 3, 2, 2, 4, 1, 3 5, 4, 3, 6, 2, 4 4, 3, 3, 5, 2, 2 1, 1, 0, 2, 0, 1 HKT1 NP_567354.1 14 16 18 9 NP_001289833.1 3 4 5 2 NHX1 NP_198067.1 9 12 11 6 NP_001233885.2, XP_010324159.1, XP_025884695.1 4, 3, 3 5, 6, 5 6, 4, 5 2, 1, 1 AVP1 NP_173021.1 7 8 6 3 NP_001307479.1 1 2 2 0 CTR1 NP_195993.1 10 13 12 8 NP_001234454.1, XP_025888482.1 2, 4 3, 6 4, 5 1, 2 GSO1 NP_193747.2 12 15 14 7 XP_004239381.1 4 5 6 1 HAK5 NP_567404.1 11 14 13 10 NP_001234372.2, XP_069147902.1 3, 2 4, 3 5, 4 2, 1 Counts for tomato orthologs are listed in the same order as their IDs. The results reveal a consistent and substantial reduction in cis-element density within tomato promoters compared to their Arabidopsis counterparts (Table 5 ). Genes such as SOS1 and HKT1, which maintain strict one-to-one orthologous relationships and highly conserved protein domains, display blunt differences in regulatory potential. The promoter of AtHKT1 contained 14 ABRE and 16 DRE motifs, whereas its tomato ortholog possessed only 3 and 4, respectively. Similarly, the promoter of AtSOS1 harbored 42 total stress-responsive elements, compared to just 10 in its tomato counterpart. This trend persists across expanded tomato families, including SOS3 and NHX1. Despite their duplication, the average number of cis-regulatory motifs per tomato promoter remains notably lower than that of the single Arabidopsis homolog. For example, while AtSOS3 includes 6 ABREs and 11 DREs, the tomato paralogs range from 1 to 4 ABREs and 2 to 6 DREs, suggesting functional divergence in transcriptional regulation rather than compensation through promoter complexity. Promoters of secondary regulators also show parallel reductions, with CTR1, GSO1, and HAK5 orthologs exhibiting diminished motif presence across all categories. This global decline in regulatory element abundance suggests that transcriptional activation under salt stress may be substantially weaker or delayed in tomato, regardless of ortholog conservation at the coding level. These findings highlight a critical mechanistic constraint that tomato’s salt sensitivity may result not only from gene loss or domain divergence, but also from depleted regulatory elements that weaken inducible gene expression. Transcriptomic Evidence of a Blunted Salt Stress Response in S. lycopersicum Salt-responsive gene expression profiles using publicly available RNA-Seq datasets were then analyzed to evaluate the transcriptional consequences of the observed genomic and regulatory divergence. Comparative analysis across the curated gene families revealed a pronounced differential response where Arabidopsis thaliana consistently upregulated key stress-associated genes, whereas orthologous genes in Solanum lycopersicum displayed limited induction or were not expressed under the tested salt stress conditions (Table 6 ; Fig. 7 ). Table 6 Comparative Log2 Fold Change (LogFC) of gene expression under salt stress based on corrected data. The analysis reveals opposite regulatory responses for key genes like HAK5 and SOS3, highlighting species-specific transcriptional dysfunction in tomato. Gene Family A. thaliana Avg. LogFC S. lycopersicum Avg. LogFC Fold Change Difference HAK5 3.42 -0.36 3.78 CHX17 2.32 Not Expressed - SOS3 2.26 -0.27 2.53 SOS2 1.05 -0.06 1.11 HKT1 0.98 0.05 0.93 NHX2 0.43 0.04 0.39 SOS1 0.04 0.15 -0.11 NHX1 0.08 Not Expressed - CTR1 -0.53 0.23 -0.76 GSO1 -0.60 Not Expressed - AVP1 -0.14 Not Expressed - WRKY8 -0.09 Not Expressed - MYB74 -0.08 Not Expressed - A higher gene expression difference was observed for upstream regulators of the SOS pathway. SOS3, a calcium sensor critical for salt signaling, was strongly induced in A. thaliana (+ 2.26), but downregulated in tomato (–0.27). Its downstream kinase SOS2 followed a similar trend, with high induction in Arabidopsis (+ 1.05) and negligible activation in tomato (–0.06) (Fig. 7 ). The Na⁺ transporter HKT1 was also markedly upregulated in A. thaliana (+ 0.98), while remaining largely unresponsive in tomato (+ 0.05). Moreover, HAK5, a high-affinity K⁺ transporter central to ionic homeostasis, showed robust induction in Arabidopsis (+ 3.42) but was repressed in tomato (–0.36). Conversely, SOS1 exhibited low expression in both species. Furthermore, tomato orthologs of key regulatory and transport genes, including CHX17, NHX1, GSO1, AVP1, WRKY8, and MYB74, were found not expressed, which indicates transcriptional silencing or expression below detection thresholds (Table 6 ). Structural Deviation in Key Salt Transporter Conformations Finally, to assess whether sequence-level variation in salt-responsive genes translates into structural divergence, we modeled and compared the structures of core salt-tolerance proteins between Arabidopsis thaliana and their orthologs in Solanum lycopersicum . These orthologous pairs from Arabidopsis thaliana and Solanum lycopersicum reveal a spectrum of conservation and deviation in three-dimensional architecture, providing insight into functional evolution across lineages (Fig. 8 ). Structurally, AVP1 exhibits near-perfect conservation (90% identity, RMSD = 1.53 Å, TM-score = 0.98), reflecting strong purifying selection likely driven by its essential role in proton transport and vacuolar function. This high-fidelity alignment suggests that AVP1’s attributes, including domain folding and membrane integration, are evolutionarily stable between species. NHX1 (75% identity, RMSD = 2.52 Å, TM-score = 0.92) and SOS3 (73% identity, RMSD = 2.00 Å, TM-score = 0.83) also demonstrate retained core architecture, although with moderate loop-level deviations. These minor topological shifts, particularly in SOS3's calcium-binding EF-hand motifs, may confer species-specific tuning of ion sensing and regulatory feedback under saline stress. Conversely, tomato orthologs of HKT1, SOS1, and SOS2 exhibit substantial structural remodeling. HKT1 shows the lowest sequence identity among the set (49%) yet retains a relatively high TM-score (0.88), indicating fold preservation despite notable RMSD (2.59 Å). Structural displacement in helices and loop regions, critical for ion selectivity and passage, suggests impaired channel function in tomato, potentially explaining compromised salt uptake efficiency. SOS1 (61% identity, RMSD = 4.19 Å, TM-score = 0.77) demonstrates the most noticeable conformational divergence, with widespread distortion across interfacial helices and domain junctions. These deviations may undermine its Na⁺ extrusion capability, aligning with previously reported salt sensitivity in tomato. Similarly, SOS2 (62% identity, RMSD = 4.12 Å, TM-score = 0.80) shows slight displacement and loop remodeling that could weaken phosphorylation dynamics and signal relay efficiency under stress conditions. Discussion Our comprehensive multi-layered analysis reveals that salt sensitivity of tomato plants results from coordinated systems-level dysfunction rather than the simple absence of individual salt tolerance genes. This paradigm challenges the traditional view that salt tolerance differences between species arise primarily from gene presence or absence [ 38 , 39 ]. The identification of four completely lost gene families (NHX2, WRKY8, MYB74, CHX17) combined with structural and regulatory deterioration of conserved components establishes a novel framework for understanding crop salt sensitivity at the molecular level. The loss of NHX2 in tomato represents a critical gap in vacuolar ion sequestration capacity. In Arabidopsis , NHX2 functions synergistically with NHX1 to maintain ionic homeostasis under salt stress [ 2 ]. The absence of this buffering redundancy in tomatoes likely compromises the plant's ability to manage cytosolic Na⁺ concentrations effectively. The complete absence of transcriptional regulators WRKY8 and MYB74 in tomato suggests fundamental rewiring of salt stress gene expression networks. The dramatic reduction in WRKY motif density in tomato promoters provides molecular evidence for this transcriptional network breakdown ([ 40 ]. Our protein structural analysis reveals a paradoxical relationship between positive selection and functional deterioration in expanded tomato gene families. The NHX1 and SOS3 families, both showing Ka/Ks ratios > 1.0 indicative of positive selection, simultaneously exhibit structural features associated with reduced functionality. The increased disorder content in tomato SOS1 and loss of transmembrane domains in SOS2 suggest that adaptive evolution in tomato has proceeded along a route that compromises salt tolerance rather than enhancing it. This phenomenon may reflect relaxed selection pressure on salt tolerance during tomato domestication, where breeding focused on fruit quality and yield rather than stress tolerance [ 40 ]. The 3 to 6 fold reduction in stress-responsive cis-element density in tomato promoters represents a systems-level collapse of transcriptional responsiveness to salt stress. This regulatory element depletion affects all major stress-responsive transcription factor binding sites [ 38 ]. The HAK5 potassium transporter exemplifies this regulatory dysfunction, showing robust salt-induced expression in Arabidopsis but repression in tomato. HAK5 is crucial for maintaining cytosolic K⁺/Na⁺ ratios under salt stress, and its inappropriate downregulation in tomato likely contributes significantly to salt sensitivity [ 38 ]. Our computational predictions provide a foundation for experimental validation through transgenic complementation studies and CRISPR/Cas9-mediated precision editing. Priority targets include NHX2 complementation, reducing disordered regions in tomato SOS1, and engineering promoters to increase cis-element density. Recent advances in CRISPR-based editing have successfully generated multi-stress tolerant lines in tomato and other crops [ 41 , 42 ]. Our findings suggest that traditional single-gene marker-assisted selection approaches may be insufficient for complex salt tolerance improvement [ 43 ]. Instead, genomic selection approaches incorporating multiple systems-level factors would be more effective [ 44 ]. Base editing technologies might offer precise tools for making specific amino acid changes guided by our structural predictions [ 41 , 42 ]. Synthetic promoter engineering based on our comparative analysis of regulatory architecture represents another promising application [ 45 , 46 ]. This systems-level dysfunction model has profound implications for crop improvement beyond tomato. Cereals represent critical application targets, with rice and wheat benefiting from validation of our findings [ 47 ]. Recent CRISPR-based improvements in rice salt tolerance through editing of genes like OsRR22 provide concrete examples of translating systematic approaches [ 48 ]. Legume crops and vegetable crops, particularly Solanaceae family members, could similarly benefit from our systems-level approach [ 49 ] With projections that soil salinization will affect 50% of arable land by 2050, our research provides critical insights for developing climate-resilient crops [ 2 ]. The systems-level dysfunction model suggests that comprehensive systems-level engineering approaches will be necessary to restore salt tolerance in sensitive crops. While experimental validation remains essential, our work establishes a new paradigm for understanding complex stress tolerance traits that extends beyond salt tolerance to other abiotic stresses. Conclusion This study demonstrates that, although Solanum lycopersicum retains the main salt tolerance genes present in Arabidopsis thaliana , its salt sensitivity results from a combination of gene family expansions and losses, decreased regulatory motif complexity, reduced gene expression under salt stress, and structural divergence in key proteins. These multi-level constraints act together to restrict tomato’s ability to mount a coordinated response to salinity, highlighting that stress sensitivity emerges not from a single missing gene, but from cumulative, interconnected discrepancies in genetic, regulatory, and structural features. Our findings point toward the need for integrated breeding and biotechnology efforts, targeting regulatory enhancement, restoration of lost gene functions, and protein optimization, for the development of salt-tolerant tomato cultivars and set a framework for dissecting complex trait evolution in other crops facing environmental stresses. Declarations Ethics approval and consent to participate Not applicable Consent for publication Not applicable Availability of data and materials Data generated or analyzed during this study are included in this published article and its supplementary information files. archRaw data used during this study are available from the corresponding author on reasonable request. Competing interests The authors declare no competing interests. Funding This work was supported by special research grant (Grant ID – SRG-231002) from the Ministry of Science and Technology, Bangladesh. References Hasanuzzaman M, Bhuyan MHMB, Nahar K, Hossain MS, Al Mahmud J, Hossen MS, et al. Potassium: A vital regulator of plant responses and tolerance to abiotic stresses. Agronomy. 2018;8. https://doi.org/10.3390/agronomy8030031. Munns R, Tester M. Mechanisms of salinity tolerance. Annual Review of Plant Biology. 2008;59:651–81. https://doi.org/10.1146/annurev.arplant.59.032607.092911. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {\"props\":{\"pageProps\":{\"initialData\":{\"identity\":\"rs-7277116\",\"acceptedTermsAndConditions\":true,\"allowDirectSubmit\":true,\"archivedVersions\":[],\"articleType\":\"Research Article\",\"associatedPublications\":[],\"authors\":[{\"id\":503767898,\"identity\":\"f71a330f-5f25-4f11-8857-21356628e25c\",\"order_by\":0,\"name\":\"Tushar Ahmed 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\\u003c/strong\\u003e\\u003cem\\u003e\\u003cstrong\\u003eS. lycopersicum\\u003c/strong\\u003e\\u003c/em\\u003e\\u003cstrong\\u003e. \\u003c/strong\\u003eAn UpSet plot visualizing the shared and species-specific gene clusters between Arabidopsis thaliana and Solanum lycopersicum, revealing the extent of gene conservation and lineage-specific evolution in salt tolerance machinery.\\u003c/p\\u003e\",\"description\":\"\",\"filename\":\"1.png\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-7277116/v1/cb515d2a0c0db09ea078132c.png\"},{\"id\":89814668,\"identity\":\"a820c4e9-7ed7-4cfc-9bf3-b12e33b250f8\",\"added_by\":\"auto\",\"created_at\":\"2025-08-25 10:24:46\",\"extension\":\"png\",\"order_by\":2,\"title\":\"Figure 2\",\"display\":\"\",\"copyAsset\":false,\"role\":\"figure\",\"size\":193782,\"visible\":true,\"origin\":\"\",\"legend\":\"\\u003cp\\u003e\\u003cstrong\\u003eCollinearity between \\u003c/strong\\u003e\\u003cem\\u003e\\u003cstrong\\u003eA. thaliana\\u003c/strong\\u003e\\u003c/em\\u003e\\u003cstrong\\u003e and \\u003c/strong\\u003e\\u003cem\\u003e\\u003cstrong\\u003eS. lycopersicum\\u003c/strong\\u003e\\u003c/em\\u003e\\u003cstrong\\u003e Genomes.\\u003c/strong\\u003e Syntenic relationships illustrate extensive genomic rearrangement since the divergence of the two species.\\u003c/p\\u003e\",\"description\":\"\",\"filename\":\"2.png\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-7277116/v1/40fdfbc7ffa77d712944ab08.png\"},{\"id\":89814667,\"identity\":\"710448f0-0689-4935-943e-067bf21e2f6e\",\"added_by\":\"auto\",\"created_at\":\"2025-08-25 10:24:46\",\"extension\":\"png\",\"order_by\":3,\"title\":\"Figure 3\",\"display\":\"\",\"copyAsset\":false,\"role\":\"figure\",\"size\":44805,\"visible\":true,\"origin\":\"\",\"legend\":\"\\u003cp\\u003e\\u003cstrong\\u003eMaximum-likelihood phylogenetic trees of expanded and contracted salt tolerance gene families in \\u003c/strong\\u003e\\u003cem\\u003e\\u003cstrong\\u003eSolanum lycopersicum\\u003c/strong\\u003e\\u003c/em\\u003e\\u003cstrong\\u003e and \\u003c/strong\\u003e\\u003cem\\u003e\\u003cstrong\\u003eArabidopsis thaliana\\u003c/strong\\u003e\\u003c/em\\u003e\\u003cstrong\\u003e. \\u003c/strong\\u003eA. SOS3 family, showing bifurcation into two tomato-specific sub-clades and conservation with \\u003cem\\u003eArabidopsis\\u003c/em\\u003eparalogs. B. NHX family, indicating the retention of NHX1 orthologs in tomato and absence of NHX2 orthologs. C. SOS2 family, highlighting a recent duplication in tomato. Prefixes: AT (\\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e), SL (\\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e).\\u003c/p\\u003e\",\"description\":\"\",\"filename\":\"3.png\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-7277116/v1/8ab597e48fe6bb4b1f58456f.png\"},{\"id\":89815246,\"identity\":\"31f257fe-fa0f-4620-96da-450edd164eda\",\"added_by\":\"auto\",\"created_at\":\"2025-08-25 10:32:46\",\"extension\":\"png\",\"order_by\":4,\"title\":\"Figure 4\",\"display\":\"\",\"copyAsset\":false,\"role\":\"figure\",\"size\":66092,\"visible\":true,\"origin\":\"\",\"legend\":\"\\u003cp\\u003eSchematic illustration of key architectural differences in core and secondary salt tolerance related proteins. Tomato HKT1 shows divergence in both domain and transmembrane (TM) count compared to \\u003cem\\u003eArabidopsis\\u003c/em\\u003e. One of the two tomato HAK5 paralogs has a reduced number of TM regions. Four key protein families (NHX2, CHX17, WRKY8, MYB74) are entirely absent in tomato.\\u003c/p\\u003e\",\"description\":\"\",\"filename\":\"4.png\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-7277116/v1/459c2788a850168efe120aa2.png\"},{\"id\":89816900,\"identity\":\"d8896a95-7621-4283-85b9-5043bd305936\",\"added_by\":\"auto\",\"created_at\":\"2025-08-25 10:40:46\",\"extension\":\"png\",\"order_by\":5,\"title\":\"Figure 5\",\"display\":\"\",\"copyAsset\":false,\"role\":\"figure\",\"size\":20446,\"visible\":true,\"origin\":\"\",\"legend\":\"\\u003cp\\u003e\\u003cstrong\\u003eKa/Ks analysis of salt tolerance orthologs in tomato.\\u003c/strong\\u003e The bar chart depicts Ka/Ks values across gene families. The red dashed line indicates Ka/Ks = 1.0 threshold for positive selection. Only the NHX1 and SOS3 groups surpass this threshold, suggesting adaptive evolution of paralogs.\\u003c/p\\u003e\",\"description\":\"\",\"filename\":\"5.png\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-7277116/v1/43b4bc8e627ee623c3feb9f0.png\"},{\"id\":89814674,\"identity\":\"1c1f9770-caec-4a72-b2dd-a31801bdedf5\",\"added_by\":\"auto\",\"created_at\":\"2025-08-25 10:24:47\",\"extension\":\"png\",\"order_by\":6,\"title\":\"Figure 6\",\"display\":\"\",\"copyAsset\":false,\"role\":\"figure\",\"size\":56468,\"visible\":true,\"origin\":\"\",\"legend\":\"\\u003cp\\u003e\\u003cstrong\\u003eComparative density of stress-responsive cis-elements in \\u003c/strong\\u003e\\u003cem\\u003e\\u003cstrong\\u003eArabidopsis thaliana\\u003c/strong\\u003e\\u003c/em\\u003e\\u003cstrong\\u003e and \\u003c/strong\\u003e\\u003cem\\u003e\\u003cstrong\\u003eSolanum lycopersicum\\u003c/strong\\u003e\\u003c/em\\u003e\\u003cstrong\\u003e promoters. \\u003c/strong\\u003eGrouped bar chart visualizes the average count of ABRE (bZIP), DRE (AP2/ERF), MYB, and WRKY motifs per promoter. \\u003cem\\u003eArabidopsis\\u003c/em\\u003e genes consistently show higher motif abundance across all categories, suggesting stronger inducibility under salt stress.\\u003c/p\\u003e\",\"description\":\"\",\"filename\":\"6.png\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-7277116/v1/86c3a0b8d42205863e465c63.png\"},{\"id\":89814679,\"identity\":\"09f0ca2a-3844-44e2-b2fe-f8c74df13616\",\"added_by\":\"auto\",\"created_at\":\"2025-08-25 10:24:47\",\"extension\":\"png\",\"order_by\":7,\"title\":\"Figure 7\",\"display\":\"\",\"copyAsset\":false,\"role\":\"figure\",\"size\":24582,\"visible\":true,\"origin\":\"\",\"legend\":\"\\u003cp\\u003e\\u003cstrong\\u003eComparative Transcriptional Response to Salt Stress.\\u003c/strong\\u003e Bar chart displaying the Log2 Fold Change for key salt-tolerance genes in \\u003cem\\u003eArabidopsis\\u003c/em\\u003e and their tomato orthologs, highlighting the robust induction in \\u003cem\\u003eArabidopsis\\u003c/em\\u003e versus the blunted response in tomato.\\u003c/p\\u003e\",\"description\":\"\",\"filename\":\"7.png\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-7277116/v1/ee72cd985217f01dc85bf90d.png\"},{\"id\":89814688,\"identity\":\"8b092536-cb55-4649-a7c0-0ea4ee243234\",\"added_by\":\"auto\",\"created_at\":\"2025-08-25 10:24:47\",\"extension\":\"png\",\"order_by\":8,\"title\":\"Figure 8\",\"display\":\"\",\"copyAsset\":false,\"role\":\"figure\",\"size\":263425,\"visible\":true,\"origin\":\"\",\"legend\":\"\\u003cp\\u003e\\u003cstrong\\u003eSuperimposed 3D structures of salt-tolerance proteins from \\u003c/strong\\u003e\\u003cem\\u003e\\u003cstrong\\u003eA. thaliana\\u003c/strong\\u003e\\u003c/em\\u003e\\u003cstrong\\u003e (blue) and \\u003c/strong\\u003e\\u003cem\\u003e\\u003cstrong\\u003eS. lycopersicum\\u003c/strong\\u003e\\u003c/em\\u003e\\u003cstrong\\u003e (orange).\\u003c/strong\\u003e Each panel shows RMSD, TM-score, and sequence identity. While AVP1, NHX1, and SOS3 retain structural integrity, HKT1, SOS1, and SOS2 reveal substantial conformational divergence.\\u003c/p\\u003e\",\"description\":\"\",\"filename\":\"8.png\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-7277116/v1/36a9c115cf9d69941c65fa2c.png\"},{\"id\":95223933,\"identity\":\"34b20ad8-a5ee-4316-bedc-edd0215903e7\",\"added_by\":\"auto\",\"created_at\":\"2025-11-05 16:23:05\",\"extension\":\"pdf\",\"order_by\":0,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"manuscript-pdf\",\"size\":2510360,\"visible\":true,\"origin\":\"\",\"legend\":\"\",\"description\":\"\",\"filename\":\"manuscript.pdf\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-7277116/v1/7b5bf617-42c5-4e6d-9e8d-166e40976310.pdf\"},{\"id\":89814671,\"identity\":\"9447812e-cdc1-4dc2-9dbd-8ae9dfb8cc50\",\"added_by\":\"auto\",\"created_at\":\"2025-08-25 10:24:46\",\"extension\":\"xlsx\",\"order_by\":0,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"supplement\",\"size\":2145019,\"visible\":true,\"origin\":\"\",\"legend\":\"\",\"description\":\"\",\"filename\":\"SupplementaryFile1.xlsx\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-7277116/v1/fbfa0ceb0e9a5a77a54eccc2.xlsx\"}],\"financialInterests\":\"No competing interests reported.\",\"formattedTitle\":\"Comparative Multi-Omics Analysis Reveals Systems-Level Molecular Dysfunctions Underlying Salt Sensitivity in Solanum lycopersicum\",\"fulltext\":[{\"header\":\"Background\",\"content\":\"\\u003cp\\u003eSoil salinity represents one of the most formidable abiotic stress factors threatening agricultural productivity worldwide, affecting over 20% of cultivated land and causing substantial crop yield losses [\\u003cspan additionalcitationids=\\\"CR2\\\" citationid=\\\"CR1\\\" class=\\\"CitationRef\\\"\\u003e1\\u003c/span\\u003e\\u0026ndash;\\u003cspan citationid=\\\"CR3\\\" class=\\\"CitationRef\\\"\\u003e3\\u003c/span\\u003e]. The accumulation of excessive salts, particularly sodium (Na⁺) and chloride (Cl⁻) ions, disrupts cellular ion homeostasis, induces osmotic stress, and triggers oxidative damage, ultimately limiting plant growth and development [\\u003cspan citationid=\\\"CR4\\\" class=\\\"CitationRef\\\"\\u003e4\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR5\\\" class=\\\"CitationRef\\\"\\u003e5\\u003c/span\\u003e]. Salinization is estimated to impact 50% of all arable land by 2050. This environmental challenge poses an existential threat to global food security, particularly in the context of a growing world population and climate change intensification [\\u003cspan additionalcitationids=\\\"CR7\\\" citationid=\\\"CR6\\\" class=\\\"CitationRef\\\"\\u003e6\\u003c/span\\u003e\\u0026ndash;\\u003cspan citationid=\\\"CR8\\\" class=\\\"CitationRef\\\"\\u003e8\\u003c/span\\u003e].\\u003c/p\\u003e\\u003cp\\u003eEvolutionarily, plants have evolved sophisticated and diverse mechanisms to cope with salinity stress, primarily for maintaining optimal cytosolic Na⁺/K⁺ ratios through coordinated physiological and molecular responses [\\u003cspan citationid=\\\"CR4\\\" class=\\\"CitationRef\\\"\\u003e4\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR5\\\" class=\\\"CitationRef\\\"\\u003e5\\u003c/span\\u003e]. These adaptive strategies include multiple interconnected processes, including the exclusion of Na⁺ from root tissues, compartmentalization of toxic ions into vacuoles, synthesis of compatible osmolytes, and activation of antioxidant defense systems [\\u003cspan citationid=\\\"CR1\\\" class=\\\"CitationRef\\\"\\u003e1\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR4\\\" class=\\\"CitationRef\\\"\\u003e4\\u003c/span\\u003e]. The molecular foundation of plant salt tolerance has been extensively characterized through decades of research, revealing complex regulatory networks that compose these multifaceted responses to saline environments [\\u003cspan citationid=\\\"CR9\\\" class=\\\"CitationRef\\\"\\u003e9\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR10\\\" class=\\\"CitationRef\\\"\\u003e10\\u003c/span\\u003e].\\u003c/p\\u003e\\u003cp\\u003e\\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e, a model dicotyledonous plant, has emerged as the paradigmatic system for understanding plant salt tolerance mechanisms [\\u003cspan citationid=\\\"CR11\\\" class=\\\"CitationRef\\\"\\u003e11\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR12\\\" class=\\\"CitationRef\\\"\\u003e12\\u003c/span\\u003e]. Despite being classified as a glycophyte with moderate salt sensitivity, \\u003cem\\u003eArabidopsis\\u003c/em\\u003e possesses a comprehensive genetic toolkit for salt stress response, arranged around the well-characterized Salt Overly Sensitive (SOS) signaling pathway [\\u003cspan citationid=\\\"CR9\\\" class=\\\"CitationRef\\\"\\u003e9\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR11\\\" class=\\\"CitationRef\\\"\\u003e11\\u003c/span\\u003e]. This regulatory network, including the plasma membrane Na⁺/H⁺ antiporter SOS1, the serine/threonine kinase SOS2, and the calcium-binding protein SOS3, controls critical ion transport processes that prevent toxic Na⁺ accumulation in photosynthetic tissues [\\u003cspan citationid=\\\"CR4\\\" class=\\\"CitationRef\\\"\\u003e4\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR9\\\" class=\\\"CitationRef\\\"\\u003e9\\u003c/span\\u003e]. Additional key components include the high-affinity K⁺ transporter HKT1, which retrieves Na⁺ from the xylem, and the vacuolar Na⁺/H⁺ exchanger NHX1, which facilitates Na⁺ sequestration [\\u003cspan citationid=\\\"CR4\\\" class=\\\"CitationRef\\\"\\u003e4\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR9\\\" class=\\\"CitationRef\\\"\\u003e9\\u003c/span\\u003e]. The extensive characterization of these molecular mechanisms in \\u003cem\\u003eArabidopsis\\u003c/em\\u003e has provided fundamental insights into the genetic basis of plant salt tolerance and established a comprehensive framework for understanding glycophyte responses to salinity stress [\\u003cspan citationid=\\\"CR10\\\" class=\\\"CitationRef\\\"\\u003e10\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR13\\\" class=\\\"CitationRef\\\"\\u003e13\\u003c/span\\u003e].\\u003c/p\\u003e\\u003cp\\u003eIn contrast to the relative salt tolerance exhibited by \\u003cem\\u003eArabidopsis\\u003c/em\\u003e, many economically vital crop species demonstrate significantly higher sensitivity to saline conditions, resulting in substantial agricultural losses and food security concerns [\\u003cspan citationid=\\\"CR14\\\" class=\\\"CitationRef\\\"\\u003e14\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR15\\\" class=\\\"CitationRef\\\"\\u003e15\\u003c/span\\u003e]. \\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e (tomato), one of the world's most important horticultural crops, exemplifies this agricultural challenge as a salt-sensitive species that tolerates only moderate salinity levels (EC\\u0026thinsp;~\\u0026thinsp;2.5 dS m⁻\\u0026sup1;) before experiencing severe yield reductions [\\u003cspan citationid=\\\"CR14\\\" class=\\\"CitationRef\\\"\\u003e14\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR15\\\" class=\\\"CitationRef\\\"\\u003e15\\u003c/span\\u003e]. Tomato's salt sensitivity is persistent across all developmental stages, from germination and seedling establishment to reproductive maturity, with root systems being particularly vulnerable to elevated salt concentrations [\\u003cspan citationid=\\\"CR14\\\" class=\\\"CitationRef\\\"\\u003e14\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR16\\\" class=\\\"CitationRef\\\"\\u003e16\\u003c/span\\u003e]. This increased sensitivity is particularly concerning, given projections that tomato yields may decrease by 50% by 2050 due to salt stress alone, highlighting the urgent need to understand the molecular basis of crop salt sensitivity [\\u003cspan citationid=\\\"CR17\\\" class=\\\"CitationRef\\\"\\u003e17\\u003c/span\\u003e].\\u003c/p\\u003e\\u003cp\\u003eThe differences in salt tolerance among model plants like \\u003cem\\u003eArabidopsis\\u003c/em\\u003e and economically important crops such as tomato presents a compelling scientific paradox. They possess orthologs of key salt tolerance genes, including components of the SOS pathway, HKT transporters, and NHX exchangers, yet exhibit different physiological responses to salinity stress [\\u003cspan citationid=\\\"CR10\\\" class=\\\"CitationRef\\\"\\u003e10\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR14\\\" class=\\\"CitationRef\\\"\\u003e14\\u003c/span\\u003e] which indicates salt tolerance differences may arise from subtle variations in gene copy number, protein sequences, regulatory control mechanisms, or system-level integration of stress response pathways rather than the complete absence of tolerance machinery [\\u003cspan citationid=\\\"CR10\\\" class=\\\"CitationRef\\\"\\u003e10\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR13\\\" class=\\\"CitationRef\\\"\\u003e13\\u003c/span\\u003e]. Comparative genomic and transcriptomic analyses between salt-tolerant and salt-sensitive species have revealed that halophytes often constitutively express stress-response genes that are only induced under salt stress in glycophytes, indicating fundamental differences in gene regulation rather than gene presence [\\u003cspan citationid=\\\"CR10\\\" class=\\\"CitationRef\\\"\\u003e10\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR13\\\" class=\\\"CitationRef\\\"\\u003e13\\u003c/span\\u003e].\\u003c/p\\u003e\\u003cp\\u003eThe evolutionary and functional divergence of orthologous salt tolerance genes across plant species represents a critical knowledge gap that limits our understanding of crop salt sensitivity and limits efforts to develop salt-tolerant varieties [\\u003cspan citationid=\\\"CR18\\\" class=\\\"CitationRef\\\"\\u003e18\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR19\\\" class=\\\"CitationRef\\\"\\u003e19\\u003c/span\\u003e]. Recent advances in comparative genomics, transcriptomics, and systems biology approaches have provided powerful tools to dissect these complex relationships and identify the molecular determinants of species-specific salt tolerance [\\u003cspan citationid=\\\"CR20\\\" class=\\\"CitationRef\\\"\\u003e20\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR21\\\" class=\\\"CitationRef\\\"\\u003e21\\u003c/span\\u003e]. However, comprehensive comparative studies that integrate genomic architecture, protein structure-function relationships, evolutionary selection pressures, and gene expression dynamics between model tolerant species and sensitive crops remain limited.\\u003c/p\\u003e\\u003cp\\u003eUnderstanding the specific genetic and molecular mechanisms underlying the differential salt tolerance between \\u003cem\\u003eArabidopsis\\u003c/em\\u003e and tomato is therefore essential for developing rational strategies to enhance crop salt tolerance through breeding, biotechnology, or agronomic interventions. Such knowledge could inform targeted approaches to improve salt tolerance in tomato and other sensitive crops, potentially through gene editing, transgenic approaches, or marker-assisted breeding programs that leverage favorable alleles or regulatory elements from tolerant species [\\u003cspan citationid=\\\"CR18\\\" class=\\\"CitationRef\\\"\\u003e18\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR22\\\" class=\\\"CitationRef\\\"\\u003e22\\u003c/span\\u003e]. Furthermore, elucidating the evolutionary forces that have shaped salt tolerance mechanisms could provide insights into the adaptive potential of crop species and guide conservation and utilization of genetic resources for future agricultural sustainability [\\u003cspan citationid=\\\"CR21\\\" class=\\\"CitationRef\\\"\\u003e21\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR23\\\" class=\\\"CitationRef\\\"\\u003e23\\u003c/span\\u003e].\\u003c/p\\u003e\\u003cp\\u003eTherefore, the present study addresses this critical knowledge gap by conducting a comprehensive multi-layered \\u003cem\\u003ein silico\\u003c/em\\u003e investigation to elucidate the divergent salt tolerance mechanisms between \\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e and \\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e. Through integrative analyses including comparative genomics, protein structural modeling, evolutionary selection analysis, regulatory element analysis and transcriptomic profiling, this research aims to identify the molecular determinants of species-specific salt tolerance and provide systematic insights into crop salt sensitivity. The findings from this work will contribute to our fundamental understanding of plant salt tolerance evolution and provide a foundation for developing enhanced salt tolerance in economically important crop species.\\u003c/p\\u003e\"},{\"header\":\"Materials and Methods\",\"content\":\"\\u003cp\\u003e\\u003cb\\u003eData Acquisition and Curation\\u003c/b\\u003e\\u003c/p\\u003e\\u003cp\\u003eReference genomes, proteomes, and coding sequences for \\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e (TAIR10) and \\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e (SL3.0) were obtained from NCBI RefSeq [\\u003cspan citationid=\\\"CR24\\\" class=\\\"CitationRef\\\"\\u003e24\\u003c/span\\u003e]. Salt-tolerance genes in \\u003cem\\u003eA. thaliana\\u003c/em\\u003e were curated via literature review and categorized into two groups Core and Secondary. Core seven proteins with primary roles in Na⁺ transport and signaling and six Secondary protein representing upstream regulators and transport families.\\u003c/p\\u003e\\u003cp\\u003e\\u003cb\\u003eSynteny and Collinearity Analysis\\u003c/b\\u003e\\u003c/p\\u003e\\u003cp\\u003eLarge-scale chromosomal conservation was analyzed using MCScanX [\\u003cspan citationid=\\\"CR25\\\" class=\\\"CitationRef\\\"\\u003e25\\u003c/span\\u003e]. An all-vs-all BLASTp search (E-value\\u0026thinsp;\\u0026lt;\\u0026thinsp;1e\\u003csup\\u003e\\u0026minus;\\u0026thinsp;10\\u003c/sup\\u003e) was performed between the two proteomes. The BLAST results, along with simplified GFF files containing gene coordinate information, were used as input for MCScanX to identify collinear blocks between the two genomes.\\u003c/p\\u003e\\u003cp\\u003e\\u003cb\\u003eOrthologous Gene Identification\\u003c/b\\u003e\\u003c/p\\u003e\\u003cp\\u003eTo identify the corresponding tomato orthologs for the curated \\u003cem\\u003eArabidopsis\\u003c/em\\u003e genes, the complete proteomes of both species were analyzed using OrthoVenn3 web server using the Orthofinder algorithm [\\u003cspan citationid=\\\"CR26\\\" class=\\\"CitationRef\\\"\\u003e26\\u003c/span\\u003e]. The software performs an all-vs-all protein sequence comparison to cluster genes into orthologous families. The resulting Orthologous groups were parsed to create a map connecting the curated \\u003cem\\u003eArabidopsis\\u003c/em\\u003e proteins to their \\u003cem\\u003eSolanum\\u003c/em\\u003e counterparts.\\u003c/p\\u003e\\u003cp\\u003e\\u003cb\\u003ePhylogenetic Analysis\\u003c/b\\u003e\\u003c/p\\u003e\\u003cp\\u003eFor each Core gene family, protein sequences of all members from both species were extracted based on the OrthoVenn3 results. Multiple sequence alignments were generated using MAFFT (v7.490) [\\u003cspan citationid=\\\"CR27\\\" class=\\\"CitationRef\\\"\\u003e27\\u003c/span\\u003e] with default parameters. The resulting alignments were trimmed using TrimAl (v1.4) [\\u003cspan citationid=\\\"CR28\\\" class=\\\"CitationRef\\\"\\u003e28\\u003c/span\\u003e] to remove poorly aligned regions. Maximum-likelihood phylogenetic trees were then constructed using IQ-TREE (v2.2.0) [\\u003cspan citationid=\\\"CR29\\\" class=\\\"CitationRef\\\"\\u003e29\\u003c/span\\u003e] with the best-fit substitution model automatically determined by ModelFinder [\\u003cspan citationid=\\\"CR30\\\" class=\\\"CitationRef\\\"\\u003e30\\u003c/span\\u003e] and branch support assessed with 1,000 ultrafast bootstrap.\\u003c/p\\u003e\\u003cp\\u003e\\u003cb\\u003eProtein Domain Analysis\\u003c/b\\u003e\\u003c/p\\u003e\\u003cp\\u003eProtein domain architecture was analyzed using the InterProScan web server [\\u003cspan citationid=\\\"CR31\\\" class=\\\"CitationRef\\\"\\u003e31\\u003c/span\\u003e]. The resulting domain annotations were compared between orthologous groups to identify any gain, loss, or truncation of functional domains in the tomato lineage.\\u003c/p\\u003e\\u003cp\\u003e\\u003cb\\u003eSelection Pressure (Ka/Ks) Analysis\\u003c/b\\u003e\\u003c/p\\u003e\\u003cp\\u003eThe ratio of nonsynonymous to synonymous substitution rates (Ka/Ks) was calculated to determine the selection pressure on tomato genes. Protein orthologs were aligned using MAFFT and corresponding CDS alignments were generated with pal2nal.pl, and Ka/Ks ratios were computed using KaKs_Calculator [\\u003cspan citationid=\\\"CR32\\\" class=\\\"CitationRef\\\"\\u003e32\\u003c/span\\u003e].\\u003c/p\\u003e\\u003cp\\u003e\\u003cb\\u003ePromoter and Cis-Regulatory Element Analysis\\u003c/b\\u003e\\u003c/p\\u003e\\u003cp\\u003eIsolated the 2000 bp region upstream of each annotated start codon using the BEDTools suite to investigate regulatory architecture [\\u003cspan citationid=\\\"CR33\\\" class=\\\"CitationRef\\\"\\u003e33\\u003c/span\\u003e], guided by genome GFF3 annotation files. PlantPAN 4.0 [\\u003cspan citationid=\\\"CR34\\\" class=\\\"CitationRef\\\"\\u003e34\\u003c/span\\u003e] was used to scan these promoter sequences for known plant transcription factor binding sites. Later, four major cis-element families (ABRE [bZIP], DRE/CRT [AP2/ERF], MYB, WRKY W-box) were systematically analyzed for each orthologous gene pair.\\u003c/p\\u003e\\u003cp\\u003e\\u003cb\\u003eDifferential Gene Expression Analysis\\u003c/b\\u003e\\u003c/p\\u003e\\u003cp\\u003ePublicly available RNA-Seq datasets for salt stress were selected and analyzed with GEO2R of the NCBI Gene Expression Omnibus (GEO) [\\u003cspan citationid=\\\"CR35\\\" class=\\\"CitationRef\\\"\\u003e35\\u003c/span\\u003e]. The datasets used were GSE193762 for \\u003cem\\u003eA. thaliana\\u003c/em\\u003e and GSE106149 for \\u003cem\\u003eS. lycopersicum\\u003c/em\\u003e. The provided Log2 Fold Change (LogFC) values were used for the comparison.\\u003c/p\\u003e\\u003cp\\u003e\\u003cb\\u003eProtein Structure Prediction and Comparison\\u003c/b\\u003e\\u003c/p\\u003e\\u003cp\\u003eThree-dimensional protein structures of selected proteins were predicted using AlphaFold3 [\\u003cspan citationid=\\\"CR36\\\" class=\\\"CitationRef\\\"\\u003e36\\u003c/span\\u003e]. Structural alignments and similarity metrics (RMSD, TM-score) were calculated with TM-align [\\u003cspan citationid=\\\"CR37\\\" class=\\\"CitationRef\\\"\\u003e37\\u003c/span\\u003e].\\u003c/p\\u003e\"},{\"header\":\"Results\",\"content\":\"\\u003cp\\u003e\\u003cb\\u003eComparative Genomic Landscape\\u003c/b\\u003e\\u003c/p\\u003e\\u003cp\\u003eThe genomes of \\u003cem\\u003eA. thaliana\\u003c/em\\u003e and \\u003cem\\u003eS. lycopersicum\\u003c/em\\u003e exhibit significant differences in scale and complexity. The tomato genome, at approximately 950 Mb, is roughly seven times larger than the compact 135 Mb \\u003cem\\u003eArabidopsis\\u003c/em\\u003e genome. This expansion is reflected in the chromosome number, with \\u003cem\\u003eSolanum\\u003c/em\\u003e having 12 pairs compared to the 5 chromosomes of \\u003cem\\u003eArabidopsis\\u003c/em\\u003e. Despite this size difference, the number of protein-coding genes is comparable, with tomato encoding approximately 31,760 genes and \\u003cem\\u003eArabidopsis\\u003c/em\\u003e encoding around 27,000. An initial analysis of orthologous protein clusters revealed a substantial core of 11,582 shared protein families, alongside 1,605 clusters unique to \\u003cem\\u003eArabidopsis\\u003c/em\\u003e and 1,521 unique to tomato (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig1\\\" class=\\\"InternalRef\\\"\\u003e1\\u003c/span\\u003e). Synteny analysis further revealed extensive chromosomal rearrangement since the divergence of species, indicating that the genomic context of conserved genes has been significantly altered (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig2\\\" class=\\\"InternalRef\\\"\\u003e2\\u003c/span\\u003e).\\u003c/p\\u003e\\u003cp\\u003e\\u003c/p\\u003e\\u003cp\\u003e\\u003c/p\\u003e\\u003cp\\u003e\\u003cb\\u003eOrthologous Remodeling of Salt Stress Signaling Components in\\u003c/b\\u003e \\u003cb\\u003eSolanum lycopersicum\\u003c/b\\u003e\\u003c/p\\u003e\\u003cp\\u003eTo investigate the evolutionary conservation of the salt tolerance machinery between \\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e and \\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e, we performed targeted orthologous mapping of 13 curated \\u003cem\\u003eArabidopsis\\u003c/em\\u003e proteins associated with salt stress responses. The resulting comparative framework clarifies a complex evolutionary landscape marked by conserved core transporters, lineage-specific gene expansions, and selective gene loss, indicative of substantial reconfiguration of the tomato salt tolerance network (Table\\u0026nbsp;\\u003cspan refid=\\\"Tab1\\\" class=\\\"InternalRef\\\"\\u003e1\\u003c/span\\u003e).\\u003c/p\\u003e\\u003cp\\u003eOf the seven Core proteins identified in \\u003cem\\u003eArabidopsis\\u003c/em\\u003e, six retained orthologs in tomato, including plasma membrane Na⁺/H⁺ antiporter SOS1 (NP_001234698.2), high-affinity K⁺/Na⁺ transporter HKT1 (NP_001289833.1), vacuolar H⁺-pyrophosphatase AVP1 (NP_001307479.1), serine/threonine kinase SOS2 (NP_001234210.1, XP_069147947.1), and vacuolar exchanger NHX1 (NP_001233885.2, XP_010324159.1, XP_025884695.1). Notably, the Ca\\u0026sup2;⁺ sensor SOS3, serine kinase SOS2 and vacuolar exchanger NHX1 exhibited orthologous expansion in tomato. In contrast, NHX2 was absent in the tomato genome, suggesting a gene loss event or functional divergence compensated by NHX1 paralogs.\\u003c/p\\u003e\\u003cp\\u003e\\u003cdiv class=\\\"gridtable\\\"\\u003e\\u003ctable float=\\\"Yes\\\" id=\\\"Tab1\\\" border=\\\"1\\\"\\u003e\\u003ccaption language=\\\"En\\\"\\u003e\\u003cdiv class=\\\"CaptionNumber\\\"\\u003eTable 1\\u003c/div\\u003e\\u003cdiv class=\\\"CaptionContent\\\"\\u003e\\u003cp\\u003e\\u003cb\\u003eOrthologous mapping of salt tolerance genes.\\u003c/b\\u003e The analysis reveals selective gene loss in tomato, particularly for transcriptional regulators WRKY8, MYB74, and the vacuolar exchanger NHX2.\\u003c/p\\u003e\\u003c/div\\u003e\\u003c/caption\\u003e\\u003ccolgroup cols=\\\"5\\\"\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c1\\\" colnum=\\\"1\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c2\\\" colnum=\\\"2\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c3\\\" colnum=\\\"3\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c4\\\" colnum=\\\"4\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c5\\\" colnum=\\\"5\\\"\\u003e\\u003c/div\\u003e\\u003cthead\\u003e\\u003ctr\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eGroup\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eGene Name\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eArabidopsis\\u003c/em\\u003e ID\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eProtein Function\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eTomato Ortholog ID\\u003c/p\\u003e\\u003c/th\\u003e\\u003c/tr\\u003e\\u003c/thead\\u003e\\u003ctbody\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eCore\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eSOS1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_178307.2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eMembrane Na+/H\\u0026thinsp;+\\u0026thinsp;Antiporter\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eNP_001234698.2\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eCore\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eSOS2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_198391.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eSerine/Threonine Kinase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eNP_001234210.1, XP_069147947.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eCore\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eSOS3\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_001190377.1, NP_001331302.1, NP_001331303.1, NP_001331304.1, NP_197815.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eCalcium-Binding Protein (Sensor)\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eNP_001234705.1, XP_025885582.1, XP_025885583.1, XP_025885584.1, XP_069150952.1, XP_069150953.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eCore\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eHKT1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_567354.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eHigh-Affinity K+/Na\\u0026thinsp;+\\u0026thinsp;Transporter\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eNP_001289833.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eCore\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eNHX1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_198067.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eVacuolar Na+/H\\u0026thinsp;+\\u0026thinsp;Exchanger\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eNP_001233885.2, XP_010324159.1, XP_025884695.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eCore\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eNHX2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_187154.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eVacuolar Na+/H\\u0026thinsp;+\\u0026thinsp;Exchanger\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003e\\u003cb\\u003eNo Ortholog Found\\u003c/b\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eCore\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eAVP1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_173021.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eVacuolar H+-Pyrophosphatase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eNP_001307479.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eSecondary\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eWRKY8\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_199447.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eWRKY Transcription Factor\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003e\\u003cb\\u003eNo Ortholog Found\\u003c/b\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eSecondary\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eMYB74\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_192419.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eMYB Transcription Factor\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003e\\u003cb\\u003eNo Ortholog Found\\u003c/b\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eSecondary\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eCTR1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_195993.1, NP_850760.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eSerine/Threonine Kinase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eNP_001234454.1, XP_025888482.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eSecondary\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eGSO1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_193747.2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eLeucine-Rich Repeat Kinase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eXP_004239381.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eSecondary\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eHAK5\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_567404.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eHigh-Affinity K\\u0026thinsp;+\\u0026thinsp;Transporter\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eNP_001234372.2, XP_069147902.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eSecondary\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eCHX17\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_194101.1, NP_001328705.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eCation/H\\u0026thinsp;+\\u0026thinsp;Exchanger\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003e\\u003cb\\u003eNo Ortholog Found\\u003c/b\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003c/tbody\\u003e\\u003c/colgroup\\u003e\\u003c/table\\u003e\\u003c/div\\u003e\\u003c/p\\u003e\\u003cp\\u003eAmong the six secondary components, evolutionary outcomes were more variable. While CTR1 and HAK5 demonstrated moderate expansion, WRKY8, MYB74, and CHX17 does not have orthologs in tomato, pointing to potential lineage-specific transcriptional rewiring. GSO1 was conserved as a single-copy ortholog, indicating preservation of peptide-mediated signaling in root architecture.\\u003c/p\\u003e\\u003cp\\u003e\\u003cb\\u003ePhylogenetic Analysis Reveals Divergent Evolution of Key Salt Tolerance Gene Families in Tomato\\u003c/b\\u003e\\u003c/p\\u003e\\u003cp\\u003eTo further investigate the lineage-specific expansions and losses observed in our ortholog mapping, we constructed maximum-likelihood phylogenetic trees for three core salt tolerance gene families, SOS3 (calcium sensor), NHX (vacuolar Na⁺/H⁺ exchangers), and SOS2 (serine/threonine kinase). These trees reveal distinct evolutionary trajectories in \\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e compared to \\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e and provide structural insights into the remodeling of signaling pathways connected to salt stress.\\u003c/p\\u003e\\u003cp\\u003eThe phylogenetic reconstruction of the SOS3 family (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig3\\\" class=\\\"InternalRef\\\"\\u003e3\\u003c/span\\u003eA) discloses a pronounced expansion in tomato, consistent with the six co-orthologs identified earlier. The tree topology shows a divergence into two strongly supported clades. One clade group all five \\u003cem\\u003eArabidopsis\\u003c/em\\u003e SOS3 paralogs. The second clade comprises the tomato orthologs and no \\u003cem\\u003eArabidopsis\\u003c/em\\u003e members. The extended branch length (0.13301) separating these clades suggests an ancient duplication event exclusive to the tomato lineage. This divergence indicates the emergence of SOS3 families in \\u003cem\\u003eS. lycopersicum\\u003c/em\\u003e, which may confer distinct calcium-sensing roles or regulatory specificities under salinity stress.\\u003c/p\\u003e\\u003cp\\u003e\\u003c/p\\u003e\\u003cp\\u003eThe NHX phylogeny (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig3\\\" class=\\\"InternalRef\\\"\\u003e3\\u003c/span\\u003eB) provides clear divergence events in tomato. The tree separates into two clades with strong bootstrap support. The first clade contains \\u003cem\\u003eArabidopsis\\u003c/em\\u003e NHX1 (NP_198067.1) alongside the NHX2 protein from \\u003cem\\u003eArabidopsis\\u003c/em\\u003e (NP_187154.1). The second clade includes all three tomato orthologs, with no \\u003cem\\u003eArabidopsis\\u003c/em\\u003e representatives. The absence of tomato proteins in the NHX2 clade, coupled with a long branch between NHX1 and NHX2 clusters, indicates that tomato lost the NHX2 sub-family following an ancient duplication event. This loss may reduce vacuolar buffering redundancy and alter the ionic sequestration dynamics compared to \\u003cem\\u003eArabidopsis\\u003c/em\\u003e. On the other hand, the SOS2 tree (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig3\\\" class=\\\"InternalRef\\\"\\u003e3\\u003c/span\\u003eC) exhibits a simpler evolutionary pattern. The \\u003cem\\u003eArabidopsis\\u003c/em\\u003e SOS2 kinase (NP_198391.1) appears on an isolated branch, whereas the two tomato co-orthologs cluster tightly in a sister clade. The short internal branch length (0.01745) between these tomato sequences suggests a relatively recent duplication. Given their proximity and lack of divergence, the tomato SOS2 paralogs likely retain redundant or overlapping functional roles in the phosphorylation cascade of the salt stress response.\\u003c/p\\u003e\\u003cp\\u003e\\u003cb\\u003eCore Domain Architectures Are Broadly Conserved with Specific Divergence in Regulatory Paralogs\\u003c/b\\u003e\\u003c/p\\u003e\\u003cp\\u003eTo understand the molecular foundations behind the contrasting salt tolerance observed in the resilient \\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e and the sensitive \\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e, a comprehensive comparative analysis of their protein architectures associated with salt stress response was then conducted. The results reveal that although the core biochemical framework is broadly conserved between the two species, distinct structural deviations, particularly in membrane topology and intrinsic disorder of key regulatory proteins, combined with the complete absence of certain gene families in tomato, likely contribute to its pronounced sensitivity to salinity (Tables\\u0026nbsp;\\u003cspan refid=\\\"Tab2\\\" class=\\\"InternalRef\\\"\\u003e2\\u003c/span\\u003e \\u0026amp; \\u003cspan refid=\\\"Tab3\\\" class=\\\"InternalRef\\\"\\u003e3\\u003c/span\\u003e, Supplementary file 1).\\u003c/p\\u003e\\u003cp\\u003eAcross essential gene families, domain architectures were largely preserved. Proteins from both species retained canonical motifs such as Na⁺/H⁺ exchangers, H⁺-pyrophosphatases, cation transporters, and EF-hand calcium-binding domains (Table\\u0026nbsp;\\u003cspan refid=\\\"Tab2\\\" class=\\\"InternalRef\\\"\\u003e2\\u003c/span\\u003e). Transmembrane regions showed high similarity, suggesting that membrane insertion and transport functions are largely intact.\\u003c/p\\u003e\\u003cp\\u003eHowever, subtle structural distinctions may hold functional significance. For instance, tomato SOS1 exhibited a higher proportion of disordered regions (11.47%) relative to \\u003cem\\u003eArabidopsis\\u003c/em\\u003e (6.02%), potentially influencing its regulatory plasticity. \\u003cem\\u003eArabidopsis\\u003c/em\\u003e SOS2 harbored an additional transmembrane domain and a cytoplasmic localization signal absent in tomato homologs, which may alter its intracellular signaling dynamics. The SOS3 family presents another layer of divergence. Although tomato paralogs retain dual EF-hand motifs, the presence of six variants compared to five in \\u003cem\\u003eArabidopsis\\u003c/em\\u003e points to possible functional diversification or subfunctionalization. Similarly, tomato HKT1 features an extra transporter domain and more transmembrane regions than its \\u003cem\\u003eArabidopsis\\u003c/em\\u003e counterpart, suggesting at differences in ion selectivity or regulation under saline conditions.\\u003c/p\\u003e\\u003cp\\u003eAbove all, a major deviation was the complete absence of NHX2 in tomato (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig4\\\" class=\\\"InternalRef\\\"\\u003e4\\u003c/span\\u003e). While \\u003cem\\u003eArabidopsis\\u003c/em\\u003e NHX2 showed high structural similarity to NHX1, including 13 TM regions and a conserved exchanger domain, no orthologous protein was identified in tomato (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig3\\\" class=\\\"InternalRef\\\"\\u003e3\\u003c/span\\u003e, Table \\u003cspan refid=\\\"Tab2\\\" class=\\\"InternalRef\\\"\\u003e2\\u003c/span\\u003e). NHX2 is known to contribute significantly to vacuolar Na⁺ compartmentalization under salt stress, and its absence may reduce ion buffering capacity in tomato.\\u003c/p\\u003e\\u003cp\\u003e\\u003cdiv class=\\\"gridtable\\\"\\u003e\\u003ctable float=\\\"Yes\\\" id=\\\"Tab2\\\" border=\\\"1\\\"\\u003e\\u003ccaption language=\\\"En\\\"\\u003e\\u003cdiv class=\\\"CaptionNumber\\\"\\u003eTable 2\\u003c/div\\u003e\\u003cdiv class=\\\"CaptionContent\\\"\\u003e\\u003cp\\u003eComparative architectural analysis of Core proteins\\u003c/p\\u003e\\u003c/div\\u003e\\u003c/caption\\u003e\\u003ccolgroup cols=\\\"10\\\"\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c1\\\" colnum=\\\"1\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c2\\\" colnum=\\\"2\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c3\\\" colnum=\\\"3\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c4\\\" colnum=\\\"4\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c5\\\" colnum=\\\"5\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c6\\\" colnum=\\\"6\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c7\\\" colnum=\\\"7\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c8\\\" colnum=\\\"8\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c9\\\" colnum=\\\"9\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c10\\\" colnum=\\\"10\\\"\\u003e\\u003c/div\\u003e\\u003cthead\\u003e\\u003ctr\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eGene\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eSpecies\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eAccession\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eClass\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eDomains/ Motifs\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003e#Dom\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003eTM\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003eIDR (%)\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003eCytD\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003eExtD\\u003c/p\\u003e\\u003c/th\\u003e\\u003c/tr\\u003e\\u003c/thead\\u003e\\u003ctbody\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\" morerows=\\\"1\\\" rowspan=\\\"2\\\"\\u003e\\u003cp\\u003eAVP1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_173021.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eVacuolar H+-pyrophosphatase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eH\\u0026thinsp;+\\u0026thinsp;pyrophosphatase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e13\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e7\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e7\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_001307479.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eVacuolar H+-pyrophosphatase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eH\\u0026thinsp;+\\u0026thinsp;pyrophosphatase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e13\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e7\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e7\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\" morerows=\\\"1\\\" rowspan=\\\"2\\\"\\u003e\\u003cp\\u003eHKT1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_567354.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003ePotassium/sodium transporter\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eCation transporter\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e8\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e5\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e4\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_001289833.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003ePotassium/sodium transporter\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eCation transporter\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e10\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e6\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e5\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\" morerows=\\\"3\\\" rowspan=\\\"4\\\"\\u003e\\u003cp\\u003eNHX1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_198067.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eSodium/H\\u0026thinsp;+\\u0026thinsp;exchanger\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eNa+/H\\u0026thinsp;+\\u0026thinsp;exchanger\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e13\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e7\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e7\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_001233885.2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eSodium/H\\u0026thinsp;+\\u0026thinsp;exchanger\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eNa+/H\\u0026thinsp;+\\u0026thinsp;exchanger\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e12\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e2, 8.77%\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e6\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e7\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\" morerows=\\\"1\\\" rowspan=\\\"2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eXP_010324159.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eSodium/H\\u0026thinsp;+\\u0026thinsp;exchanger\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eNa+/H\\u0026thinsp;+\\u0026thinsp;exchanger\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e12\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e2, 8.77%\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e6\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e7\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eXP_025884695.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eSodium/H\\u0026thinsp;+\\u0026thinsp;exchanger\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eNa+/H\\u0026thinsp;+\\u0026thinsp;exchanger\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e12\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e2, 8.77%\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e6\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e7\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\" morerows=\\\"1\\\" rowspan=\\\"2\\\"\\u003e\\u003cp\\u003eNHX2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_187154.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eSodium/H\\u0026thinsp;+\\u0026thinsp;exchanger\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eNa+/H\\u0026thinsp;+\\u0026thinsp;exchanger\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e13\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e7\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e7\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colspan=\\\"8\\\" nameend=\\\"c10\\\" namest=\\\"c3\\\"\\u003e\\u003cp\\u003eAbsent in \\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\" morerows=\\\"1\\\" rowspan=\\\"2\\\"\\u003e\\u003cp\\u003eSOS1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_178307.2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eSodium/H\\u0026thinsp;+\\u0026thinsp;antiporter\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eNa+/H\\u0026thinsp;+\\u0026thinsp;exchanger\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e13\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e4, 6.02%\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e7\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e7\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_001234698.2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eSodium/H\\u0026thinsp;+\\u0026thinsp;antiporter\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eNa+/H\\u0026thinsp;+\\u0026thinsp;exchanger\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e13\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e3, 11.47%\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e7\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e7\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\" morerows=\\\"2\\\" rowspan=\\\"3\\\"\\u003e\\u003cp\\u003eSOS2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_198391.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eCalcium-dependent protein kinase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eNAF domain, Protein kinase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\" morerows=\\\"1\\\" rowspan=\\\"2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_001234210.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eCalcium-dependent protein kinase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eNAF domain, Protein kinase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eXP_069147947.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eCalcium-dependent protein kinase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eNAF domain, Protein kinase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\" morerows=\\\"6\\\" rowspan=\\\"7\\\"\\u003e\\u003cp\\u003eSOS3\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_197815.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eCalcineurin B-like protein\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eEF-hand domain\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\" morerows=\\\"5\\\" rowspan=\\\"6\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_001234705.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eCalcineurin B-like protein\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eEF-hand domain\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eXP_025885582.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eCalcineurin B-like protein\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eEF-hand domain\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eXP_025885583.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eCalcineurin B-like protein\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eEF-hand domain\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eXP_025885584.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eCalcineurin B-like protein\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eEF-hand domain\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eXP_069150952.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eCalcineurin B-like protein\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eEF-hand domain\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eXP_069150953.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eCalcineurin B-like protein\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eEF-hand domain\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003c/tbody\\u003e\\u003c/colgroup\\u003e\\u003c/table\\u003e\\u003c/div\\u003e\\u003c/p\\u003e\\u003cp\\u003e\\u003cem\\u003e#Dom \\u0026ndash; Number of domains/motifs; TM \\u0026ndash; Transmembrane regions; IDR (%) \\u0026ndash; No of Intrinsically disordered regions and % coverage; CytD \\u0026ndash; Cytoplasmic domains; ExtD \\u0026ndash; Extracellular domains.\\u003c/em\\u003e\\u003c/p\\u003e\\u003cp\\u003eWhile the core machinery remains largely intact, notable architectural differences among regulatory and transport proteins appear to further distinguish the salt response capabilities of tomato. For example, the CTR1 protein in \\u003cem\\u003eArabidopsis\\u003c/em\\u003e exhibits substantially higher disorder (15.23%) than its tomato counterparts (5\\u0026ndash;6%), possibly reflecting greater flexibility in assembling or modulating signaling complexes. Both species maintain well-conserved GSO1 orthologs, with complete LRR and kinase domains and matching topological features, suggesting preserved function. In contrast, tomato HAK5 variants display fewer transmembrane regions and greater variability across intracellular and extracellular segments, features that may compromise their transport efficiency.\\u003c/p\\u003e\\u003cp\\u003e\\u003cdiv class=\\\"gridtable\\\"\\u003e\\u003ctable float=\\\"Yes\\\" id=\\\"Tab3\\\" border=\\\"1\\\"\\u003e\\u003ccaption language=\\\"En\\\"\\u003e\\u003cdiv class=\\\"CaptionNumber\\\"\\u003eTable 3\\u003c/div\\u003e\\u003cdiv class=\\\"CaptionContent\\\"\\u003e\\u003cp\\u003eComparative architectural analysis of Secondary proteins.\\u003c/p\\u003e\\u003c/div\\u003e\\u003c/caption\\u003e\\u003ccolgroup cols=\\\"10\\\"\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c1\\\" colnum=\\\"1\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c2\\\" colnum=\\\"2\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c3\\\" colnum=\\\"3\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c4\\\" colnum=\\\"4\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c5\\\" colnum=\\\"5\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c6\\\" colnum=\\\"6\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c7\\\" colnum=\\\"7\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c8\\\" colnum=\\\"8\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c9\\\" colnum=\\\"9\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c10\\\" colnum=\\\"10\\\"\\u003e\\u003c/div\\u003e\\u003cthead\\u003e\\u003ctr\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eGene\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eSpecies\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eAccession\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eClass\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eDomains/ Motifs\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003e#Dom\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003eTM\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003eIDR (%)\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003eCytD\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003eExtD\\u003c/p\\u003e\\u003c/th\\u003e\\u003c/tr\\u003e\\u003c/thead\\u003e\\u003ctbody\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\" morerows=\\\"2\\\" rowspan=\\\"3\\\"\\u003e\\u003cp\\u003eCTR1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_195993.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eSerine/threonine protein kinase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eEDR1/CTR1 peptidase-like, Protein kinase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e4,\\u003c/p\\u003e\\u003cp\\u003e15.23%\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_001234454.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eSerine/threonine protein kinase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eEDR1/CTR1 peptidase-like, Protein kinase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e2,\\u003c/p\\u003e\\u003cp\\u003e5.26%\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eXP_025888482.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eSerine/threonine protein kinase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eEDR1/CTR1 peptidase-like, Protein kinase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e2,\\u003c/p\\u003e\\u003cp\\u003e5.98%\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\" morerows=\\\"1\\\" rowspan=\\\"2\\\"\\u003e\\u003cp\\u003eGSO1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_193747.2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eLRR receptor-like kinase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eLeucine-rich repeat (LRR), Protein kinase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e13\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eXP_004239381.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eLRR receptor-like kinase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eLeucine-rich repeat (LRR), Protein kinase\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e13\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\" morerows=\\\"2\\\" rowspan=\\\"3\\\"\\u003e\\u003cp\\u003eHAK5\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_567404.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eHigh-affinity potassium transporter\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eK\\u0026thinsp;+\\u0026thinsp;transporter domains\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e12\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e4,\\u003c/p\\u003e\\u003cp\\u003e9.68%\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e7\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e6\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_001234372.2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eHigh-affinity potassium transporter\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eK\\u0026thinsp;+\\u0026thinsp;transporter domains\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e12\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e2,\\u003c/p\\u003e\\u003cp\\u003e8.65%\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e7\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e6\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eXP_069147902.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eHigh-affinity potassium transporter\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eK\\u0026thinsp;+\\u0026thinsp;transporter domains\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e10\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e2,\\u003c/p\\u003e\\u003cp\\u003e9.97%\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e6\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e5\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\" morerows=\\\"1\\\" rowspan=\\\"2\\\"\\u003e\\u003cp\\u003eMYB74\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_192419.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eMYB transcription factor\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eMYB DNA-binding\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colspan=\\\"8\\\" nameend=\\\"c10\\\" namest=\\\"c3\\\"\\u003e\\u003cp\\u003eAbsent in \\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\" morerows=\\\"1\\\" rowspan=\\\"2\\\"\\u003e\\u003cp\\u003eWRKY8\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_199447.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eWRKY transcription factor\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003eWRKY DNA-binding\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e3,\\u003c/p\\u003e\\u003cp\\u003e29.75%\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colspan=\\\"8\\\" nameend=\\\"c10\\\" namest=\\\"c3\\\"\\u003e\\u003cp\\u003eAbsent in \\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\" morerows=\\\"1\\\" rowspan=\\\"2\\\"\\u003e\\u003cp\\u003eCHX17\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNP_194101.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eCation/H\\u0026thinsp;+\\u0026thinsp;antiporter\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003ePlant cation/H\\u0026thinsp;+\\u0026thinsp;antiporter\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e3\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e\\u003cp\\u003e12\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e6\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e7\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colspan=\\\"8\\\" nameend=\\\"c10\\\" namest=\\\"c3\\\"\\u003e\\u003cp\\u003eAbsent in \\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003c/tbody\\u003e\\u003c/colgroup\\u003e\\u003c/table\\u003e\\u003c/div\\u003e\\u003c/p\\u003e\\u003cp\\u003e\\u003cem\\u003e#Dom \\u0026ndash; Number of domains/motifs; TM \\u0026ndash; Transmembrane regions; IDR (%) \\u0026ndash; No of Intrinsically disordered regions and % coverage; CytD \\u0026ndash; Cytoplasmic domains; ExtD \\u0026ndash; Extracellular domains.\\u003c/em\\u003e\\u003c/p\\u003e\\u003cp\\u003eMost noticeably, the absence of entire gene families in tomato presents a undeniable explanation for its weakened tolerance to salt stress (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig4\\\" class=\\\"InternalRef\\\"\\u003e4\\u003c/span\\u003e). Tomato lacks orthologs for key transcription factors such as WRKY8 and MYB74, as well as the cation exchanger CHX17 (Table\\u0026nbsp;\\u003cspan refid=\\\"Tab3\\\" class=\\\"InternalRef\\\"\\u003e3\\u003c/span\\u003e). The loss of WRKY8 is especially consequential since its \\u003cem\\u003eArabidopsis\\u003c/em\\u003e homolog contains a substantial intrinsically disordered region (20.75%), indicating a role as a central regulatory hub. Without these transcriptional activators, tomatoes may be failing to initiate critical downstream protective responses that are active in \\u003cem\\u003eArabidopsis\\u003c/em\\u003e under saline conditions.\\u003c/p\\u003e\\u003cp\\u003e\\u003c/p\\u003e\\u003cp\\u003e\\u003cb\\u003ePositive Selection Drives Functional Innovation in Expanded Tomato Gene Families\\u003c/b\\u003e\\u003c/p\\u003e\\u003cp\\u003eTo quantitatively assess the evolutionary forces shaping salt tolerance in tomato, we calculated the non-synonymous to synonymous substitution rate (Ka/Ks) for each orthologous group. The comparative analysis revealed a clear contradiction in selective pressure. While single copy orthologs exhibit strong purifying selection consistent with functional conservation, expanded gene families in tomato demonstrate Ka/Ks ratios exceeding 1.0, indicating adaptive evolution through positive selection (Table\\u0026nbsp;\\u003cspan refid=\\\"Tab4\\\" class=\\\"InternalRef\\\"\\u003e4\\u003c/span\\u003e, Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig5\\\" class=\\\"InternalRef\\\"\\u003e5\\u003c/span\\u003e).\\u003c/p\\u003e\\u003cp\\u003e\\u003cdiv class=\\\"gridtable\\\"\\u003e\\u003ctable float=\\\"Yes\\\" id=\\\"Tab4\\\" border=\\\"1\\\"\\u003e\\u003ccaption language=\\\"En\\\"\\u003e\\u003cdiv class=\\\"CaptionNumber\\\"\\u003eTable 4\\u003c/div\\u003e\\u003cdiv class=\\\"CaptionContent\\\"\\u003e\\u003cp\\u003e\\u003cb\\u003eEvolutionary selection analysis of orthologous gene pairs.\\u003c/b\\u003e Ka/Ks ratios for salt tolerance gene families indicating the mode of selection pressure. Positive selection (Ka/Ks\\u0026thinsp;\\u0026gt;\\u0026thinsp;1.0) is observed in expanded families NHX1 and SOS3, while purifying selection characterizes conserved single-copy genes, suggesting different evolutionary constraints on gene families.\\u003c/p\\u003e\\u003c/div\\u003e\\u003c/caption\\u003e\\u003ccolgroup cols=\\\"4\\\"\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c1\\\" colnum=\\\"1\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c2\\\" colnum=\\\"2\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c3\\\" colnum=\\\"3\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c4\\\" colnum=\\\"4\\\"\\u003e\\u003c/div\\u003e\\u003cthead\\u003e\\u003ctr\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eGroup\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eGene Family\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eAvg. Ka/Ks Value\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eInferred Mode of Selection\\u003c/p\\u003e\\u003c/th\\u003e\\u003c/tr\\u003e\\u003c/thead\\u003e\\u003ctbody\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eCore\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eNHX1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e1.6735\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003ePositive Selection\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eCore\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eSOS3\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e1.0924\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003ePositive Selection\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eCore\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eSOS2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e0.8538\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eNear-Neutral Evolution\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eCore\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eHKT1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e0.4793\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003ePurifying Selection\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eCore\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eSOS1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e0.3671\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003ePurifying Selection\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eCore\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eAVP1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e0.2764\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003ePurifying Selection\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eCore\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eNHX2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eN/A\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e\\u003cb\\u003eGene Loss\\u003c/b\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eSecondary\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eCTR1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e0.1283\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eStrong Purifying Selection\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eSecondary\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eHAK5\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e0.6450\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003ePurifying Selection\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eSecondary\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eGSO1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e0.5538\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003ePurifying Selection\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eSecondary\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eWRKY8\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eN/A\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e\\u003cb\\u003eGene Loss\\u003c/b\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eSecondary\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eCHX17\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eN/A\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e\\u003cb\\u003eGene Loss\\u003c/b\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eSecondary\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eMYB74\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eN/A\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e\\u003cb\\u003eGene Loss\\u003c/b\\u003e\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003c/tbody\\u003e\\u003c/colgroup\\u003e\\u003c/table\\u003e\\u003c/div\\u003e\\u003c/p\\u003e\\u003cp\\u003eSalt tolerance genes with conserved copy number between \\u003cem\\u003eArabidopsis\\u003c/em\\u003e and tomato, including SOS1, HKT1, AVP1, CTR1, and GSO1, exhibited Ka/Ks ratios significantly below 1.0. These values indicate ongoing purifying selection against deleterious mutations, consistent with critical physiological roles and functional stability. The lowest Ka/Ks value was observed in CTR1 (0.1283), suggesting intense selective constraint on this ethylene pathway regulator. Similarly, core ion transporters like SOS1 (0.3671) and HKT1 (0.4793) showed strong conservation, reinforcing their indispensable roles in Na⁺ exclusion and K⁺ homeostasis. In contrast, the two tomato gene families that underwent marked expansion, NHX1 and SOS3, exhibited Ka/Ks ratios of 1.6735 and 1.0924, respectively. These values surpass the neutral threshold (Ka/Ks\\u0026thinsp;\\u0026gt;\\u0026thinsp;1.0), supporting the inference of positive selection driving diversification. Elevated substitution rates suggest that amino acid changes in these gene copies are being favored, reflecting neofunctionalization or enhanced regulatory flexibility to cope with complex salt stress conditions.\\u003c/p\\u003e\\u003cp\\u003eThis finding is particularly prominent in the NHX1 vacuolar transporter group, where paralog expansion coincides with signatures of adaptive evolution. Likewise, the SOS3 calcium sensor family includes paralogs which are under positive selection, indicating concurrent evolutionary innovation.\\u003c/p\\u003e\\u003cp\\u003e\\u003c/p\\u003e\\u003cp\\u003eMoreover, four orthologous groups, NHX2, WRKY8, CHX17, and MYB74, showed complete absence in tomato, consistent with gene loss events. The lack of selective retention suggests that these genes were not under strong purifying selection in the tomato lineage, allowing functional redundancy or dispensability to drive genome streamlining.\\u003c/p\\u003e\\u003cp\\u003eTogether, these data suggest a compensatory evolutionary mechanism in tomato. The loss of transcriptional regulators and redundant transporters may have created selective pressure that favored the expansion and rapid divergence of key effector proteins. Moreover, the higher Ka/Ks values in NHX1 and SOS3 orthologs indicate a mode of adaptive response, where gene family expansion facilitates flexible and robust salt stress responses.\\u003c/p\\u003e\\u003cp\\u003e\\u003cb\\u003eDivergent Promoter Architecture in Tomato Orthologs\\u003c/b\\u003e\\u003c/p\\u003e\\u003cp\\u003eThen we analyzed their promoter regions for the presence of key stress-responsive cis-regulatory elements, to investigate the regulatory potential of the curated genes. The analysis revealed a plain and consistent pattern, the promoters of \\u003cem\\u003eArabidopsis\\u003c/em\\u003e salt-tolerance genes are significantly enriched with binding sites for bZIP (ABRE), AP2/ERF (DRE), MYB, and WRKY transcription factors compared to their tomato orthologs (Table\\u0026nbsp;\\u003cspan refid=\\\"Tab5\\\" class=\\\"InternalRef\\\"\\u003e5\\u003c/span\\u003e, Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig6\\\" class=\\\"InternalRef\\\"\\u003e6\\u003c/span\\u003e, Supplementary file 1).\\u003c/p\\u003e\\u003cp\\u003e\\u003cdiv class=\\\"gridtable\\\"\\u003e\\u003ctable float=\\\"Yes\\\" id=\\\"Tab5\\\" border=\\\"1\\\"\\u003e\\u003ccaption language=\\\"En\\\"\\u003e\\u003cdiv class=\\\"CaptionNumber\\\"\\u003eTable 5\\u003c/div\\u003e\\u003cdiv class=\\\"CaptionContent\\\"\\u003e\\u003cp\\u003e\\u003cb\\u003ePromoter Cis-regulatory element analysis.\\u003c/b\\u003e Quantitative comparison of stress-responsive transcription factor binding sites in promoter regions of orthologous genes. 3 to 6 fold reduction in motif density in tomato compared to \\u003cem\\u003eArabidopsis\\u003c/em\\u003e, indicates compromised transcriptional responsiveness to salt stress.\\u003c/p\\u003e\\u003c/div\\u003e\\u003c/caption\\u003e\\u003ccolgroup cols=\\\"13\\\"\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c1\\\" colnum=\\\"1\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c2\\\" colnum=\\\"2\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c3\\\" colnum=\\\"3\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c4\\\" colnum=\\\"4\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c5\\\" colnum=\\\"5\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c6\\\" colnum=\\\"6\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c7\\\" colnum=\\\"7\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c8\\\" colnum=\\\"8\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c9\\\" colnum=\\\"9\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c10\\\" colnum=\\\"10\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c11\\\" colnum=\\\"11\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c12\\\" colnum=\\\"12\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c13\\\" colnum=\\\"13\\\"\\u003e\\u003c/div\\u003e\\u003cthead\\u003e\\u003ctr\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c1\\\" morerows=\\\"1\\\" rowspan=\\\"2\\\"\\u003e\\u003cp\\u003eGene Family\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colspan=\\\"6\\\" 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namest=\\\"c7\\\"\\u003e\\u003cp\\u003eOrtholog(s) ID\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003ebZIP\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003eAP2/ERF\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c11\\\"\\u003e\\u003cp\\u003eMYB\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c12\\\"\\u003e\\u003cp\\u003eWRKY\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colspan=\\\"1\\\" nameend=\\\"c13\\\" namest=\\\"c13\\\"\\u003e\\u0026nbsp;\\u003c/th\\u003e\\u003c/tr\\u003e\\u003c/thead\\u003e\\u003ctbody\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eSOS1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eNP_178307.2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e11\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e9\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003e15\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e7\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colspan=\\\"2\\\" nameend=\\\"c8\\\" namest=\\\"c7\\\"\\u003e\\u003cp\\u003eNP_001234698.2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e3\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c11\\\"\\u003e\\u003cp\\u003e4\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c12\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colspan=\\\"1\\\" 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namest=\\\"c13\\\"\\u003e\\u0026nbsp;\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eHKT1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eNP_567354.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e14\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e16\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003e18\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e9\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colspan=\\\"2\\\" nameend=\\\"c8\\\" namest=\\\"c7\\\"\\u003e\\u003cp\\u003eNP_001289833.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e3\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e4\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c11\\\"\\u003e\\u003cp\\u003e5\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c12\\\"\\u003e\\u003cp\\u003e2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colspan=\\\"1\\\" nameend=\\\"c13\\\" namest=\\\"c13\\\"\\u003e\\u0026nbsp;\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eNHX1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eNP_198067.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e9\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e12\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003e11\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e6\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colspan=\\\"2\\\" nameend=\\\"c8\\\" namest=\\\"c7\\\"\\u003e\\u003cp\\u003eNP_001233885.2, XP_010324159.1, XP_025884695.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e4, 3, 3\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e5, 6, 5\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c11\\\"\\u003e\\u003cp\\u003e6, 4, 5\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c12\\\"\\u003e\\u003cp\\u003e2, 1, 1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colspan=\\\"1\\\" nameend=\\\"c13\\\" namest=\\\"c13\\\"\\u003e\\u0026nbsp;\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eAVP1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd 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align=\\\"left\\\" colname=\\\"c12\\\"\\u003e\\u003cp\\u003e0\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colspan=\\\"1\\\" nameend=\\\"c13\\\" namest=\\\"c13\\\"\\u003e\\u0026nbsp;\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eCTR1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eNP_195993.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e10\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e13\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003e12\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e8\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colspan=\\\"2\\\" nameend=\\\"c8\\\" 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colname=\\\"c3\\\"\\u003e\\u003cp\\u003e12\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e15\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003e14\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e7\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colspan=\\\"2\\\" nameend=\\\"c8\\\" namest=\\\"c7\\\"\\u003e\\u003cp\\u003eXP_004239381.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e4\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e5\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c11\\\"\\u003e\\u003cp\\u003e6\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c12\\\"\\u003e\\u003cp\\u003e1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colspan=\\\"1\\\" nameend=\\\"c13\\\" namest=\\\"c13\\\"\\u003e\\u0026nbsp;\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eHAK5\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003eNP_567404.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e11\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e14\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c5\\\"\\u003e\\u003cp\\u003e13\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c6\\\"\\u003e\\u003cp\\u003e10\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colspan=\\\"2\\\" nameend=\\\"c8\\\" namest=\\\"c7\\\"\\u003e\\u003cp\\u003eNP_001234372.2, XP_069147902.1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c9\\\"\\u003e\\u003cp\\u003e3, 2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c10\\\"\\u003e\\u003cp\\u003e4, 3\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c11\\\"\\u003e\\u003cp\\u003e5, 4\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c12\\\"\\u003e\\u003cp\\u003e2, 1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colspan=\\\"1\\\" nameend=\\\"c13\\\" namest=\\\"c13\\\"\\u003e\\u0026nbsp;\\u003c/td\\u003e\\u003c/tr\\u003e\\u003c/tbody\\u003e\\u003c/colgroup\\u003e\\u003c/table\\u003e\\u003c/div\\u003e\\u003c/p\\u003e\\u003cp\\u003e\\u003cem\\u003eCounts for tomato orthologs are listed in the same order as their IDs.\\u003c/em\\u003e\\u003c/p\\u003e\\u003cp\\u003eThe results reveal a consistent and substantial reduction in cis-element density within tomato promoters compared to their \\u003cem\\u003eArabidopsis\\u003c/em\\u003e counterparts (Table\\u0026nbsp;\\u003cspan refid=\\\"Tab5\\\" class=\\\"InternalRef\\\"\\u003e5\\u003c/span\\u003e). Genes such as SOS1 and HKT1, which maintain strict one-to-one orthologous relationships and highly conserved protein domains, display blunt differences in regulatory potential. The promoter of AtHKT1 contained 14 ABRE and 16 DRE motifs, whereas its tomato ortholog possessed only 3 and 4, respectively. Similarly, the promoter of AtSOS1 harbored 42 total stress-responsive elements, compared to just 10 in its tomato counterpart.\\u003c/p\\u003e\\u003cp\\u003eThis trend persists across expanded tomato families, including SOS3 and NHX1. Despite their duplication, the average number of cis-regulatory motifs per tomato promoter remains notably lower than that of the single \\u003cem\\u003eArabidopsis\\u003c/em\\u003e homolog. For example, while AtSOS3 includes 6 ABREs and 11 DREs, the tomato paralogs range from 1 to 4 ABREs and 2 to 6 DREs, suggesting functional divergence in transcriptional regulation rather than compensation through promoter complexity.\\u003c/p\\u003e\\u003cp\\u003ePromoters of secondary regulators also show parallel reductions, with CTR1, GSO1, and HAK5 orthologs exhibiting diminished motif presence across all categories. This global decline in regulatory element abundance suggests that transcriptional activation under salt stress may be substantially weaker or delayed in tomato, regardless of ortholog conservation at the coding level.\\u003c/p\\u003e\\u003cp\\u003e\\u003c/p\\u003e\\u003cp\\u003eThese findings highlight a critical mechanistic constraint that tomato\\u0026rsquo;s salt sensitivity may result not only from gene loss or domain divergence, but also from depleted regulatory elements that weaken inducible gene expression.\\u003c/p\\u003e\\u003cp\\u003e\\u003cb\\u003eTranscriptomic Evidence of a Blunted Salt Stress Response in\\u003c/b\\u003e \\u003cb\\u003eS. lycopersicum\\u003c/b\\u003e\\u003c/p\\u003e\\u003cp\\u003eSalt-responsive gene expression profiles using publicly available RNA-Seq datasets were then analyzed to evaluate the transcriptional consequences of the observed genomic and regulatory divergence. Comparative analysis across the curated gene families revealed a pronounced differential response where \\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e consistently upregulated key stress-associated genes, whereas orthologous genes in \\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e displayed limited induction or were not expressed under the tested salt stress conditions (Table\\u0026nbsp;\\u003cspan refid=\\\"Tab6\\\" class=\\\"InternalRef\\\"\\u003e6\\u003c/span\\u003e; Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig7\\\" class=\\\"InternalRef\\\"\\u003e7\\u003c/span\\u003e).\\u003c/p\\u003e\\u003cp\\u003e\\u003cdiv class=\\\"gridtable\\\"\\u003e\\u003ctable float=\\\"Yes\\\" id=\\\"Tab6\\\" border=\\\"1\\\"\\u003e\\u003ccaption language=\\\"En\\\"\\u003e\\u003cdiv class=\\\"CaptionNumber\\\"\\u003eTable 6\\u003c/div\\u003e\\u003cdiv class=\\\"CaptionContent\\\"\\u003e\\u003cp\\u003e\\u003cb\\u003eComparative Log2 Fold Change (LogFC) of gene expression under salt stress based on corrected data.\\u003c/b\\u003e The analysis reveals opposite regulatory responses for key genes like HAK5 and SOS3, highlighting species-specific transcriptional dysfunction in tomato.\\u003c/p\\u003e\\u003c/div\\u003e\\u003c/caption\\u003e\\u003ccolgroup cols=\\\"4\\\"\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c1\\\" colnum=\\\"1\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c2\\\" colnum=\\\"2\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c3\\\" colnum=\\\"3\\\"\\u003e\\u003c/div\\u003e\\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c4\\\" colnum=\\\"4\\\"\\u003e\\u003c/div\\u003e\\u003cthead\\u003e\\u003ctr\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eGene Family\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eA. thaliana\\u003c/em\\u003e Avg. LogFC\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e\\u003cem\\u003eS. lycopersicum\\u003c/em\\u003e Avg. LogFC\\u003c/p\\u003e\\u003c/th\\u003e\\u003cth align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003eFold Change Difference\\u003c/p\\u003e\\u003c/th\\u003e\\u003c/tr\\u003e\\u003c/thead\\u003e\\u003ctbody\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eHAK5\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e3.42\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e-0.36\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e3.78\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eCHX17\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e2.32\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNot Expressed\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e-\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eSOS3\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e2.26\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e-0.27\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e2.53\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eSOS2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e1.05\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e-0.06\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e1.11\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eHKT1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e0.98\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e0.05\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e0.93\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eNHX2\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e0.43\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e0.04\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e0.39\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eSOS1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e0.04\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e0.15\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e-0.11\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eNHX1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e0.08\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNot Expressed\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e-\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eCTR1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e-0.53\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003e0.23\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e-0.76\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eGSO1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e-0.60\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNot Expressed\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e-\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eAVP1\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e-0.14\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNot Expressed\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e-\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eWRKY8\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e-0.09\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNot Expressed\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e-\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003ctr\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e\\u003cp\\u003eMYB74\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e\\u003cp\\u003e-0.08\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e\\u003cp\\u003eNot Expressed\\u003c/p\\u003e\\u003c/td\\u003e\\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e\\u003cp\\u003e-\\u003c/p\\u003e\\u003c/td\\u003e\\u003c/tr\\u003e\\u003c/tbody\\u003e\\u003c/colgroup\\u003e\\u003c/table\\u003e\\u003c/div\\u003e\\u003c/p\\u003e\\u003cp\\u003eA higher gene expression difference was observed for upstream regulators of the SOS pathway. SOS3, a calcium sensor critical for salt signaling, was strongly induced in \\u003cem\\u003eA. thaliana\\u003c/em\\u003e (+\\u0026thinsp;2.26), but downregulated in tomato (\\u0026ndash;0.27). Its downstream kinase SOS2 followed a similar trend, with high induction in \\u003cem\\u003eArabidopsis\\u003c/em\\u003e (+\\u0026thinsp;1.05) and negligible activation in tomato (\\u0026ndash;0.06) (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig7\\\" class=\\\"InternalRef\\\"\\u003e7\\u003c/span\\u003e). The Na⁺ transporter HKT1 was also markedly upregulated in \\u003cem\\u003eA. thaliana\\u003c/em\\u003e (+\\u0026thinsp;0.98), while remaining largely unresponsive in tomato (+\\u0026thinsp;0.05). Moreover, HAK5, a high-affinity K⁺ transporter central to ionic homeostasis, showed robust induction in \\u003cem\\u003eArabidopsis\\u003c/em\\u003e (+\\u0026thinsp;3.42) but was repressed in tomato (\\u0026ndash;0.36). Conversely, SOS1 exhibited low expression in both species.\\u003c/p\\u003e\\u003cp\\u003e\\u003c/p\\u003e\\u003cp\\u003eFurthermore, tomato orthologs of key regulatory and transport genes, including CHX17, NHX1, GSO1, AVP1, WRKY8, and MYB74, were found not expressed, which indicates transcriptional silencing or expression below detection thresholds (Table\\u0026nbsp;\\u003cspan refid=\\\"Tab6\\\" class=\\\"InternalRef\\\"\\u003e6\\u003c/span\\u003e).\\u003c/p\\u003e\\u003cp\\u003e\\u003cb\\u003eStructural Deviation in Key Salt Transporter Conformations\\u003c/b\\u003e\\u003c/p\\u003e\\u003cp\\u003eFinally, to assess whether sequence-level variation in salt-responsive genes translates into structural divergence, we modeled and compared the structures of core salt-tolerance proteins between \\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e and their orthologs in \\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e. These orthologous pairs from \\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e and \\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e reveal a spectrum of conservation and deviation in three-dimensional architecture, providing insight into functional evolution across lineages (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig8\\\" class=\\\"InternalRef\\\"\\u003e8\\u003c/span\\u003e).\\u003c/p\\u003e\\u003cp\\u003eStructurally, AVP1 exhibits near-perfect conservation (90% identity, RMSD\\u0026thinsp;=\\u0026thinsp;1.53 \\u0026Aring;, TM-score\\u0026thinsp;=\\u0026thinsp;0.98), reflecting strong purifying selection likely driven by its essential role in proton transport and vacuolar function. This high-fidelity alignment suggests that AVP1\\u0026rsquo;s attributes, including domain folding and membrane integration, are evolutionarily stable between species. NHX1 (75% identity, RMSD\\u0026thinsp;=\\u0026thinsp;2.52 \\u0026Aring;, TM-score\\u0026thinsp;=\\u0026thinsp;0.92) and SOS3 (73% identity, RMSD\\u0026thinsp;=\\u0026thinsp;2.00 \\u0026Aring;, TM-score\\u0026thinsp;=\\u0026thinsp;0.83) also demonstrate retained core architecture, although with moderate loop-level deviations. These minor topological shifts, particularly in SOS3's calcium-binding EF-hand motifs, may confer species-specific tuning of ion sensing and regulatory feedback under saline stress.\\u003c/p\\u003e\\u003cp\\u003eConversely, tomato orthologs of HKT1, SOS1, and SOS2 exhibit substantial structural remodeling. HKT1 shows the lowest sequence identity among the set (49%) yet retains a relatively high TM-score (0.88), indicating fold preservation despite notable RMSD (2.59 \\u0026Aring;). Structural displacement in helices and loop regions, critical for ion selectivity and passage, suggests impaired channel function in tomato, potentially explaining compromised salt uptake efficiency.\\u003c/p\\u003e\\u003cp\\u003e\\u003c/p\\u003e\\u003cp\\u003eSOS1 (61% identity, RMSD\\u0026thinsp;=\\u0026thinsp;4.19 \\u0026Aring;, TM-score\\u0026thinsp;=\\u0026thinsp;0.77) demonstrates the most noticeable conformational divergence, with widespread distortion across interfacial helices and domain junctions. These deviations may undermine its Na⁺ extrusion capability, aligning with previously reported salt sensitivity in tomato. Similarly, SOS2 (62% identity, RMSD\\u0026thinsp;=\\u0026thinsp;4.12 \\u0026Aring;, TM-score\\u0026thinsp;=\\u0026thinsp;0.80) shows slight displacement and loop remodeling that could weaken phosphorylation dynamics and signal relay efficiency under stress conditions.\\u003c/p\\u003e\"},{\"header\":\"Discussion\",\"content\":\"\\u003cp\\u003eOur comprehensive multi-layered analysis reveals that salt sensitivity of tomato plants results from coordinated systems-level dysfunction rather than the simple absence of individual salt tolerance genes. This paradigm challenges the traditional view that salt tolerance differences between species arise primarily from gene presence or absence [\\u003cspan citationid=\\\"CR38\\\" class=\\\"CitationRef\\\"\\u003e38\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR39\\\" class=\\\"CitationRef\\\"\\u003e39\\u003c/span\\u003e]. The identification of four completely lost gene families (NHX2, WRKY8, MYB74, CHX17) combined with structural and regulatory deterioration of conserved components establishes a novel framework for understanding crop salt sensitivity at the molecular level.\\u003c/p\\u003e\\u003cp\\u003eThe loss of NHX2 in tomato represents a critical gap in vacuolar ion sequestration capacity. In \\u003cem\\u003eArabidopsis\\u003c/em\\u003e, NHX2 functions synergistically with NHX1 to maintain ionic homeostasis under salt stress [\\u003cspan citationid=\\\"CR2\\\" class=\\\"CitationRef\\\"\\u003e2\\u003c/span\\u003e]. The absence of this buffering redundancy in tomatoes likely compromises the plant's ability to manage cytosolic Na⁺ concentrations effectively. The complete absence of transcriptional regulators WRKY8 and MYB74 in tomato suggests fundamental rewiring of salt stress gene expression networks. The dramatic reduction in WRKY motif density in tomato promoters provides molecular evidence for this transcriptional network breakdown ([\\u003cspan citationid=\\\"CR40\\\" class=\\\"CitationRef\\\"\\u003e40\\u003c/span\\u003e].\\u003c/p\\u003e\\u003cp\\u003eOur protein structural analysis reveals a paradoxical relationship between positive selection and functional deterioration in expanded tomato gene families. The NHX1 and SOS3 families, both showing Ka/Ks ratios\\u0026thinsp;\\u0026gt;\\u0026thinsp;1.0 indicative of positive selection, simultaneously exhibit structural features associated with reduced functionality. The increased disorder content in tomato SOS1 and loss of transmembrane domains in SOS2 suggest that adaptive evolution in tomato has proceeded along a route that compromises salt tolerance rather than enhancing it. This phenomenon may reflect relaxed selection pressure on salt tolerance during tomato domestication, where breeding focused on fruit quality and yield rather than stress tolerance [\\u003cspan citationid=\\\"CR40\\\" class=\\\"CitationRef\\\"\\u003e40\\u003c/span\\u003e].\\u003c/p\\u003e\\u003cp\\u003eThe 3 to 6 fold reduction in stress-responsive cis-element density in tomato promoters represents a systems-level collapse of transcriptional responsiveness to salt stress. This regulatory element depletion affects all major stress-responsive transcription factor binding sites [\\u003cspan citationid=\\\"CR38\\\" class=\\\"CitationRef\\\"\\u003e38\\u003c/span\\u003e]. The HAK5 potassium transporter exemplifies this regulatory dysfunction, showing robust salt-induced expression in \\u003cem\\u003eArabidopsis\\u003c/em\\u003e but repression in tomato. HAK5 is crucial for maintaining cytosolic K⁺/Na⁺ ratios under salt stress, and its inappropriate downregulation in tomato likely contributes significantly to salt sensitivity [\\u003cspan citationid=\\\"CR38\\\" class=\\\"CitationRef\\\"\\u003e38\\u003c/span\\u003e].\\u003c/p\\u003e\\u003cp\\u003eOur computational predictions provide a foundation for experimental validation through transgenic complementation studies and CRISPR/Cas9-mediated precision editing. Priority targets include NHX2 complementation, reducing disordered regions in tomato SOS1, and engineering promoters to increase cis-element density. Recent advances in CRISPR-based editing have successfully generated multi-stress tolerant lines in tomato and other crops [\\u003cspan citationid=\\\"CR41\\\" class=\\\"CitationRef\\\"\\u003e41\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR42\\\" class=\\\"CitationRef\\\"\\u003e42\\u003c/span\\u003e].\\u003c/p\\u003e\\u003cp\\u003eOur findings suggest that traditional single-gene marker-assisted selection approaches may be insufficient for complex salt tolerance improvement [\\u003cspan citationid=\\\"CR43\\\" class=\\\"CitationRef\\\"\\u003e43\\u003c/span\\u003e]. Instead, genomic selection approaches incorporating multiple systems-level factors would be more effective [\\u003cspan citationid=\\\"CR44\\\" class=\\\"CitationRef\\\"\\u003e44\\u003c/span\\u003e]. Base editing technologies might offer precise tools for making specific amino acid changes guided by our structural predictions [\\u003cspan citationid=\\\"CR41\\\" class=\\\"CitationRef\\\"\\u003e41\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR42\\\" class=\\\"CitationRef\\\"\\u003e42\\u003c/span\\u003e]. Synthetic promoter engineering based on our comparative analysis of regulatory architecture represents another promising application [\\u003cspan citationid=\\\"CR45\\\" class=\\\"CitationRef\\\"\\u003e45\\u003c/span\\u003e, \\u003cspan citationid=\\\"CR46\\\" class=\\\"CitationRef\\\"\\u003e46\\u003c/span\\u003e].\\u003c/p\\u003e\\u003cp\\u003eThis systems-level dysfunction model has profound implications for crop improvement beyond tomato. Cereals represent critical application targets, with rice and wheat benefiting from validation of our findings [\\u003cspan citationid=\\\"CR47\\\" class=\\\"CitationRef\\\"\\u003e47\\u003c/span\\u003e]. Recent CRISPR-based improvements in rice salt tolerance through editing of genes like OsRR22 provide concrete examples of translating systematic approaches [\\u003cspan citationid=\\\"CR48\\\" class=\\\"CitationRef\\\"\\u003e48\\u003c/span\\u003e]. Legume crops and vegetable crops, particularly Solanaceae family members, could similarly benefit from our systems-level approach [\\u003cspan citationid=\\\"CR49\\\" class=\\\"CitationRef\\\"\\u003e49\\u003c/span\\u003e]\\u003c/p\\u003e\\u003cp\\u003eWith projections that soil salinization will affect 50% of arable land by 2050, our research provides critical insights for developing climate-resilient crops [\\u003cspan citationid=\\\"CR2\\\" class=\\\"CitationRef\\\"\\u003e2\\u003c/span\\u003e]. The systems-level dysfunction model suggests that comprehensive systems-level engineering approaches will be necessary to restore salt tolerance in sensitive crops. While experimental validation remains essential, our work establishes a new paradigm for understanding complex stress tolerance traits that extends beyond salt tolerance to other abiotic stresses.\\u003c/p\\u003e\"},{\"header\":\"Conclusion\",\"content\":\"\\u003cp\\u003eThis study demonstrates that, although \\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e retains the main salt tolerance genes present in \\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003e, its salt sensitivity results from a combination of gene family expansions and losses, decreased regulatory motif complexity, reduced gene expression under salt stress, and structural divergence in key proteins. These multi-level constraints act together to restrict tomato\\u0026rsquo;s ability to mount a coordinated response to salinity, highlighting that stress sensitivity emerges not from a single missing gene, but from cumulative, interconnected discrepancies in genetic, regulatory, and structural features. Our findings point toward the need for integrated breeding and biotechnology efforts, targeting regulatory enhancement, restoration of lost gene functions, and protein optimization, for the development of salt-tolerant tomato cultivars and set a framework for dissecting complex trait evolution in other crops facing environmental stresses.\\u003c/p\\u003e\"},{\"header\":\"Declarations\",\"content\":\"\\u003cp\\u003e\\u003cstrong\\u003eEthics approval and consent to participate\\u003c/strong\\u003e\\u003c/p\\u003e\\n\\u003cp\\u003eNot applicable\\u003c/p\\u003e\\n\\u003cp\\u003e\\u003cstrong\\u003eConsent for publication\\u003c/strong\\u003e\\u003c/p\\u003e\\n\\u003cp\\u003eNot applicable\\u003c/p\\u003e\\n\\u003cp\\u003e\\u003cstrong\\u003eAvailability of data and materials\\u003c/strong\\u003e\\u003c/p\\u003e\\n\\u003cp\\u003eData generated or analyzed during this study are included in this published article and its supplementary information files. archRaw data used during this study are available from the corresponding author on reasonable request.\\u003c/p\\u003e\\n\\u003cp\\u003e\\u003cstrong\\u003eCompeting interests\\u003c/strong\\u003e\\u003c/p\\u003e\\n\\u003cp\\u003eThe authors declare no competing interests.\\u003c/p\\u003e\\n\\u003cp\\u003e\\u003cstrong\\u003eFunding\\u003c/strong\\u003e\\u003c/p\\u003e\\n\\u003cp\\u003eThis work was supported by special research grant (Grant ID – SRG-231002) from the Ministry of Science and Technology, Bangladesh.\\u003c/p\\u003e\"},{\"header\":\"References\",\"content\":\"\\u003col\\u003e\\n \\u003cli\\u003eHasanuzzaman M, Bhuyan MHMB, Nahar K, Hossain MS, Al Mahmud J, Hossen MS, et al. 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BMC Plant Biol. 2013;13. https://doi.org/10.1186/1471-2229-13-32.\\u003c/li\\u003e\\n \\u003cli\\u003eLi S, Li J, He Y, Xu M, Zhang J, Du W, et al. Precise gene replacement in rice by RNA transcript-templated homologous recombination. Nat Biotechnol. 2019;37:445\\u0026ndash;50. https://doi.org/10.1038/s41587-019-0065-7.\\u003c/li\\u003e\\n \\u003cli\\u003eDo PT, Nguyen CX, Bui HT, Tran LTN, Stacey G, Gillman JD, et al. Demonstration of highly efficient dual gRNA CRISPR/Cas9 editing of the homeologous GmFAD2-1A and GmFAD2-1B genes to yield a high oleic, low linoleic and \\u0026alpha;-linolenic acid phenotype in soybean. BMC Plant Biol. 2019;19. https://doi.org/10.1186/s12870-019-1906-8.\\u003c/li\\u003e\\n\\u003c/ol\\u003e\"}],\"fulltextSource\":\"\",\"fullText\":\"\",\"funders\":[],\"hasAdminPriorityOnWorkflow\":false,\"hasManuscriptDocX\":true,\"hasOptedInToPreprint\":true,\"hasPassedJournalQc\":\"\",\"hasAnyPriority\":false,\"hideJournal\":true,\"highlight\":\"\",\"institution\":\"\",\"isAcceptedByJournal\":false,\"isAuthorSuppliedPdf\":false,\"isDeskRejected\":\"\",\"isHiddenFromSearch\":false,\"isInQc\":false,\"isInWorkflow\":false,\"isPdf\":false,\"isPdfUpToDate\":true,\"isWithdrawnOrRetracted\":false,\"journal\":{\"display\":true,\"email\":\"info@researchsquare.com\",\"identity\":\"researchsquare\",\"isNatureJournal\":false,\"hasQc\":true,\"allowDirectSubmit\":true,\"externalIdentity\":\"\",\"sideBox\":\"\",\"snPcode\":\"\",\"submissionUrl\":\"/submission\",\"title\":\"Research Square\",\"twitterHandle\":\"researchsquare\",\"acdcEnabled\":true,\"dfaEnabled\":false,\"editorialSystem\":\"\",\"reportingPortfolio\":\"\",\"inReviewEnabled\":false,\"inReviewRevisionsEnabled\":true},\"keywords\":\"Salt Tolerance, Comparative Genomics, Crop Improvement, Transcriptional Regulation, SOS Pathway, Evolutionary Selection\",\"lastPublishedDoi\":\"10.21203/rs.3.rs-7277116/v1\",\"lastPublishedDoiUrl\":\"https://doi.org/10.21203/rs.3.rs-7277116/v1\",\"license\":{\"name\":\"CC BY 4.0\",\"url\":\"https://creativecommons.org/licenses/by/4.0/\"},\"manuscriptAbstract\":\"\\u003cp\\u003e\\u003cstrong\\u003eBackground\\u003c/strong\\u003e\\u003c/p\\u003e\\n\\u003cp\\u003eSoil salinity threatens over 20% of global cultivated land and is projected to affect 50% of arable areas by 2050, posing critical challenges to food security. While \\u003cem\\u003eArabidopsis thaliana\\u003c/em\\u003eexhibits moderate salt tolerance through well-characterized mechanisms including the SOS signaling pathway, economically vital crops like \\u003cem\\u003eSolanum lycopersicum\\u003c/em\\u003e (tomato) demonstrate extreme salt sensitivity despite possessing orthologs of key salt tolerance genes. Understanding the molecular determinants underlying this species-specific salt tolerance disparity is essential for developing rational crop improvement strategies.\\u003c/p\\u003e\\n\\u003cp\\u003e\\u003cstrong\\u003eResults\\u003c/strong\\u003e\\u003c/p\\u003e\\n\\u003cp\\u003eThrough comprehensive multi-layered\\u003cem\\u003e silico\\u003c/em\\u003e analysis of 14 curated salt tolerance genes, we revealed complex evolutionary patterns underlying salt sensitivity of tomato. Four critical genes (NHX2, WRKY8, MYB74, CHX17) were completely lost in tomato, while five others underwent expansion but with compromised functionality. Noticeably, key regulatory genes exhibited opposite transcriptional responses under salt stress. HAK5 showed robust induction in \\u003cem\\u003eArabidopsis\\u003c/em\\u003e (+3.42 LogFC) but repression in tomato (-0.36 LogFC), while SOS3 demonstrated strong activation in \\u003cem\\u003eArabidopsis\\u003c/em\\u003e (+2.26 LogFC) versus downregulation in tomato (-0.27 LogFC). Promoter analysis revealed 3 to 6 fold depletion of stress-responsive cis-elements in tomato genes, with WRKY motifs showing the greatest disparity. Structural modeling identified significant conformational divergence in critical proteins, including increased disorder in tomato SOS1 and loss of transmembrane domain in SOS2. Evolutionary analysis revealed positive selection in expanded gene families, indicating adaptive evolution that paradoxically correlates with reduced salt tolerance.\\u003c/p\\u003e\\n\\u003cp\\u003e\\u003cstrong\\u003eConclusions\\u003c/strong\\u003e\\u003c/p\\u003e\\n\\u003cp\\u003eTomato's salt sensitivity results from systems-level dysfunction involving coordinated gene loss, structural protein divergence, transcriptional network remodeling, and regulatory element depletion rather than simple absence of salt tolerance machinery. These findings necessitate a paradigm shift from gene complementation approaches toward comprehensive systems-level engineering strategies for enhancing crop salt tolerance, providing a mechanistic framework for developing salt-tolerant crops essential for future food security.\\u003c/p\\u003e\",\"manuscriptTitle\":\"Comparative Multi-Omics Analysis Reveals Systems-Level Molecular Dysfunctions Underlying Salt Sensitivity in Solanum lycopersicum\",\"msid\":\"\",\"msnumber\":\"\",\"nonDraftVersions\":[{\"code\":1,\"date\":\"2025-08-25 10:24:42\",\"doi\":\"10.21203/rs.3.rs-7277116/v1\",\"editorialEvents\":[{\"type\":\"communityComments\",\"content\":0}],\"status\":\"published\",\"journal\":{\"display\":true,\"email\":\"info@researchsquare.com\",\"identity\":\"researchsquare\",\"isNatureJournal\":false,\"hasQc\":true,\"allowDirectSubmit\":true,\"externalIdentity\":\"\",\"sideBox\":\"\",\"snPcode\":\"\",\"submissionUrl\":\"/submission\",\"title\":\"Research Square\",\"twitterHandle\":\"researchsquare\",\"acdcEnabled\":true,\"dfaEnabled\":false,\"editorialSystem\":\"\",\"reportingPortfolio\":\"\",\"inReviewEnabled\":false,\"inReviewRevisionsEnabled\":true}}],\"origin\":\"\",\"ownerIdentity\":\"9723a4ca-7a83-4997-ace3-7a7003314081\",\"owner\":[],\"postedDate\":\"August 25th, 2025\",\"published\":true,\"recentEditorialEvents\":[],\"rejectedJournal\":[],\"revision\":\"\",\"amendment\":\"\",\"status\":\"posted\",\"subjectAreas\":[],\"tags\":[],\"updatedAt\":\"2025-11-04T09:09:45+00:00\",\"versionOfRecord\":[],\"versionCreatedAt\":\"2025-08-25 10:24:42\",\"video\":\"\",\"vorDoi\":\"\",\"vorDoiUrl\":\"\",\"workflowStages\":[]},\"version\":\"v1\",\"identity\":\"rs-7277116\",\"journalConfig\":\"researchsquare\"},\"__N_SSP\":true},\"page\":\"/article/[identity]/[[...version]]\",\"query\":{\"redirect\":\"/article/rs-7277116\",\"identity\":\"rs-7277116\",\"version\":[\"v1\"]},\"buildId\":\"8U1c8b4HqxoKbykW_rLl7\",\"isFallback\":false,\"isExperimentalCompile\":false,\"dynamicIds\":[84888],\"gssp\":true,\"scriptLoader\":[]}","source_license":"CC-BY-4.0","license_restricted":false}