Comparative analysis of complete chloroplast genome of the Peruvian landrace of Capsicum chinense, arnaucho chili pepper, and related species of the Capsiceae tribe

Comparative analysis of complete chloroplast genome of the Peruvian landrace of Capsicum chinense, arnaucho chili pepper, and related species of the Capsiceae tribe | 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 analysis of complete chloroplast genome of the Peruvian landrace of Capsicum chinense, arnaucho chili pepper, and related species of the Capsiceae tribe Gianmarco Castillo, Kevin R. Quiroz-Hidalgo, Diego H. Takei-Idiaquez, and 5 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5657151/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 Although many complete chloroplast (cp) genomes of different types of peppers have already been published, there has been no comprehensive study that summarizes all the characteristics of the Peruvian landrace “arnaucho” chili pepper (ACP) comparing it with other types of genomes in its Capsiceae tribe. In this study, a comprehensive analysis was conducted using data from cp genomes obtained from NCBI GenBank. These 14 genomes were annotated using Geseq, followed by genomic comparisons, chloroplast structure analysis, phylogeny, and repetitive sequence analysis, employing a variety of bioinformatics tools. The findings revealed length variations among the cp genomes, ranging from 156,583 bp in C. lycianthoides to 157,390 bp in C. pubescens , with a GC content of 37% across all genomes. The comparative genome analysis revealed that the greatest variation among the 14 genomes occurred in the non-coding regions. Arnaucho chili pepper exhibited greater divergence in coding regions with C. lycianthoides , specifically in the genes accD , rpl20 , rps12 , clpP , ycf2 , ndhF , ndhA , ycf1 , and rpl2 . The results of the phylogeny and pairwise distance analysis in this study support that the arnaucho chili pepper clusters with C. galapagoense , with an average distance value of 0.00002733. Additionally, the repetitive sequence analysis determined that ACP maintains a number of repetitive sequences similar to other Capsicum species but possesses a lower number of SSRs (33). Finally, it was determined that the junction regions of ACP have a total length of 156,931 bp, similar to C. galapagoense with 156,959 bp. The four boundary regions exhibited consistent gene patterns, except for the JSB region, where the ycf1 gene in ACP was located only in the IRb region, whereas it was absent in other Capsicum species. This research provides additional effective evidence for characterizing the entire cp genome and classifying species and genera within the Capsiceae tribe. In-silico Germplasm Chili pepper Bioinformatics Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Introduction The genus Capsicum is the most important in the Solanaceae family. This genus comprises a total of 30 species, including sweet varieties like bell peppers and spicy ones like chili peppers. Both varieties come in various colors, such as red, yellow, green, orange, and, in some cases, purple. They also display heart-shaped or bell-like forms (Antonio et al. 2018 & Dong et al. 2013). It is estimated that Capsicum appeared in human history around 7500 B.C. and began to be cultivated between 5200 and 3400 B.C. The use of these fruits was not only for their flavor but also for ethnobotanical purposes, such as medicinal preparations, treatment of wounds, stomach aches, fever, as an anti-infective agent, and for treating hypertension when chewed (Florencia el al. 2022). This genus includes domesticated and wild species. Fossil studies of Capsicum spp. starch found seven sites dating back 6,000 years, ranging from the Bahamas to southern Peru (Perry et al. 2007). Currently, the production, use, and domestication of Capsicum have spread worldwide. Since the 1650s, when it was introduced by the Spanish, it has continued to the present day, leading to selective breeding associated with different environmental conditions (Hernandez et al. 2022 & Aguilar-Melendez et al 2009). These fruits are an important ingredient in the daily diet of millions of people, used in various dishes as they are a great source of vitamin C and antioxidants. Additionally, Peru is a country that harbors the greatest biological diversity of these fruits in South America, with a potential source of genes with traits of interest for germplasm conservation (Minguez-Mosquera, 1992; Meckelmann, 2013 & Ibiza et al, 2012 ). Peru has various varieties, such as “mochero” chili pepper, “panca” chili pepper, “dulce” chili pepper, and “arnaucho” or “supano” chili pepper (Lopez et al. 2020). The arnaucho chili pepper (ACP) is a cultivar native to the Supe Valley in the province of Barranca, about 200 km north of Lima. This fruit is sold in markets in the provinces of Barranca, Huaura, and the district of Huacho. It is identified by its purple color and triangular or globular shape (Arbizu et al. 2022 ). Next-generation sequencing (NGS) studies have accelerated the generation of high-throughput data and genomic information, including the identification of DNA markers such as single nucleotide polymorphisms, among others. Moreover, the reduction in genome sequencing costs allows for the discovery of thousands of markers in a single step. Thanks to this technology, it is gaining widespread acceptance in the field of crop breeding (Ray, 2014 ). With this technology, several studies have been conducted on the sequencing of Capsicum , such as the study by Sebastian et al. (2024), which demonstrates that the most domesticated species of C. annuum exhibited a higher degree of divergence, very similar to their divergent genotypes, compared to their counterparts. Another study of the chloroplast genome of C. chinense revealed that the species was more closely related to C. annuum var. glabriusculum (Paar, et al. 2016). Additionally, the study of C. eximium , native to southern Bolivia, identified 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Of all these genes, 21 are duplicated in the inverted region, and in the phylogenetic analysis, it was grouped within the Capsicum clade. (Sebastian, et al. 2019). On the other hand, studies of the draft genome of C. chinense using Illumina HiSeq 2500 sequencing technology identified 71.96% of the repetitive DNA in the assembled genome, with a lower number of SSRs in the genome compared to other Capsicum species, reporting the first draft genome of the ACP (Estrada, et al. 2024 ). Bioinformatics tools today are useful for understanding the functional and structural analysis of genomes, transcriptomes, proteomes, and more. Due to the use of these tools, we have been able to gain a deeper understanding of biomedical and plant sciences. They have become essential for predictive analysis in the era of big data, having a significant impact on research (Mansoor, et al. 2024 ). The advent of high-throughput sequencing tools, cutting-edge biotechnological techniques, and bioinformatics analyses has led to greater ease in characterizing plant traits (Roychowdhury, et al. 2023 ). There is a large volume of accumulated data, both in NCBI and EMBL, and therefore, the management and extraction of this data have become of great interest. This information is manageable for conducting further studies, utilizing algorithms based on mathematical and statistical models to handle these biological data (Li, et al. 2013 ). Bioinformatics and in silico analysis allowed us to understand the processes occurring at the cellular level, as it facilitates the identification of genes. This enables the enhancement of precision agriculture, optimizing natural resources, improving the efficiency of the production process, and reducing costs (Angel Gaviria, 2023). Studies conducted by Arbizu et al. ( 2022 ) presented the first complete chloroplast genome (cp) of this local cultivar of Peruvian chili pepper (arnaucho) using high-throughput sequencing technology, providing us with a phylogenetic result of this species with its closest relative, C. galapagoense . In this work, we continue the studies on the ACP, revealing its structure, divergence, and evolution, using bioinformatics tools to gain a deeper understanding of the chloroplast genome of this species, which is endemic to Peru and belongs to the province of Barranca. Materials and methods Sequence annotation and comparison of chloroplast genomes A total of twelve complete chloroplast genome sequences were retrieved from the Capsiceae plant tribe via the Organelle Genome Resources of NCBI (accessed on September 29, 2024), with the following GenBank accession numbers: MZ379791.1 ( C. chinense ), NC_018552.1 ( C. annuum ), KX913219.1 ( C. tovarii ), KR078312.1 ( C. frutescens ), NC_033524.1 ( C. galapagoense ), KX013217.1 ( C. chinense ), KU041709.1 ( C. chinense ), MH559321.1 ( C. chinense ), NC_030543.1 ( C. chinense ), KX913220.1 ( C. eximium ), MH559320.1 ( C. baccatum ), NC_039694.1 ( C. pubescens ), NC_026551.1 ( C. lycianthoides ), and NC_033525.1 ( C. chapecoense ). The Geseq program (https://chlorobox.mpimp-golm.mpg.de/geseq.html Frazer, 2004) was used to annotate and locate the genes of all cp genomes from the Capsiceae tribe, with default options selected (CDS, tRNA, rRNA, IR, and the interspaced rps12 gene) (Tillich et al., 2017). Additionally, tRNA-scan v2.0 (Chan and Lowe, 2019), available on the same server, was used as a secondary tRNA annotator. The GC content calculator provided by JaimeMcGowan (2024) was also employed via its web service (available online: https://jamiemcgowan.ie/bioinf/gc_content.html) to analyze the GC content in the 12 cp genomes (Table 1). Furthermore, we used the annotated cp genome of C. chinense (MZ379791.1) as the reference genome to compare with the other cp genomes of the Capsiceae plant tribe. The VISTA program (https://genome.lbl.gov/vista/index.shtml, accessed on September 29, 2024) was employed in Shuffle-LAGAN mode (Brudno et al., 2003) to analyze the sequence similarity within the Capsiceae tribe. Finally, we visualized the cp genome architecture of the ACP using program OGDRAW v1.3.1 (Greiner, 2019). A prior analysis of the genetic content was conducted to identify the functions of its chloroplast genome (Table 2) Codon usage of protein-coding sequences of C. chinense For this analysis, the 86 protein-coding genes of C. chinense (MZ379791) were used. The number of codons (Nc) and the relative synonymous codon usage (RSCU) were calculated using the MEGA11 program (Tamura, 2021) and the RSCU calculator available via JaimeMcGowan's web service (available online: https://jamiemcgowan.ie/bioinf/rscu.html, McGowan, 2024). Subsequently, codon usage and the relative synonymous codon usage (RSCU) values were manually analyzed by comparing the results from both programs. The Nc provides an intuitively meaningful measure of codon preference within a gene (Wright, 1990). Additionally, an RSCU value greater than 1.00 indicates a lack of bias, while a value less than 1.00 is considered indicative of bias, as described by the research of Sharp and Li (1987). The result was visualized using R v4.4.1 (R Core Team, 2024) with the ggplot2 and tidyr packages. Phylogenomic analysis and pairwise distances To reveal the evolutionary relationship of the Capsiceae tribe with a total of fifteen annotated complete cp genomes, a sequence alignment of the 14 species was performed. The genomes of the Capsiceae tribe include two additional species from the Solanaceae family. In this case, we used Solanum lycopersicum NC_007898 and Physalis peruviana MH019242 as outgroup. The sequences were retrieved from the GenBank NCBI database (https://www.ncbi.nlm.nih.gov/genbank/) and aligned using the MAFFT v7 web server (Katoh and Stanley, 2013; https://mafft.cbrc.jp/alignment/server/index.html) with default options. The alignment was then manually refined using Aliview v1.28 (Larsson, 2014). After the genomes were previously aligned and refined, a nucleotide substitution analysis was performed. In this case, the best-fitting model was TVM+I+G, determined using the Akaike information criterion (AIC) by the JModelTest v2.1.10 program (https://github.com/ddarriba/jmodeltest2). The phylogenetic reconstruction was performed using the Maximum Likelihood (ML) method using MEGA11 (Tamura, 2021) with 1000 Bootstrap repetitions, employing the Kimura 2 model and complete deletion. Additionally, the tree was visualized using the iTol v6 tool (https://itol.embl.de/, Letunic, 2024). Additionally, an alignment of only the Capsiceae tribe was performed to study the pairwise distances of the 14 cp genomes. We used MEGA11 with 1000 Bootstrap repetitions, a nucleotide substitution model, the p-distance method, and complete deletion of missing data. These results were visualized in a raincloud plot using R, employing the tidyr, ggplot2, and ggrain packages. Identification of repetitive sequences and SSR analysis In this analysis of repetitive sequences, we used various programs, including REPuter v2.7.4 (available online: https://bibiserv.cebitec.uni-bielefeld.de/reputer/, Kurtz et al., 2001), to identify repetitive sequences (including forward, reverse, and complementary repeat sequences). For the identification of these repetitive sequences, the following parameters were used: a minimum repeat size of 30 bp and a Hamming distance of 3 (with 90% or more sequence identity). Additionally, for palindromic sequences, the RepEX web server (available online: http://bioserver2.physics.iisc.ac.in/RepEx/query.html, Michael et al., 2019) was used with the following input parameters: repeat type set to "Palindrome" and a repeat length of more than 10. Additionally, for the detection of tandem repeats, the web tool (https://tandem.bu.edu/trf/home, Benson, 1999) was used with the default parameters in its advanced option. Finally, simple sequence repeats (SSR) or microsatellites in the genomes were examined using the MISA web tool (https://webblast.ipk-gatersleben.de/misa/, Bier et al., 2017) with SSR search parameters set for repeat lengths with a minimum threshold of 10, 5, 4, 3, 3, and 3 repeat units for mono-, di-, tri-, tetra-, penta-, and hexanucleotides, respectively. The results were visualized in bar charts, pie charts, balloon plots, and heatmaps using R v4.4.1 with the tidyr, ggplot2, ggpubr, pheatmap, and RColorBrewer packages. Analysis of shifts at the boundaries between the single-copy regions (LSC and SSC) and the inverted repeats (IRA and IRB) A comparison of the positions of the boundaries between the single-copy regions (LSC and SSC) and the inverted regions (IRA and IRB) was made across the 14 species of the Capsiceae tribe. These boundaries were named JLB (boundary between LSC-IRB), JSB (boundary between IRB-SSC), JSA (boundary between SSC-IRA), and JLA (boundary between IRA-LSC). For the positions of the boundaries, the distance between these and the nearest genes to these regions or located on their boundary was calculated using the online program (https://irscope.shinyapps.io/irapp/, Amiryousefi, 2018). Results Sequence annotation and comparison of chloroplast genomes Through a search in the NCBI database, complete cp genome sequences of 14 species from the Capsicum genus were obtained for subsequent comparative analysis and prior genome annotation. The Geseq program was used to obtain the structural features and genetic content of the cp genome of the ACP, as shown in Fig. 1 . The results obtained with the other cp genomes of the Capsicum genus showed a four-part structure, consisting of an LSC region, an SSC region, and two IRs. In the IR regions, each of which ranges from 25,624 bp ( C. lycianthoides ) to 25,910 bp ( C. baccatum ). The IRs were separated by an LSC region, which ranged from 87,688 bp ( C. pubescens ) to 86,813 bp ( C. lycianthoides ), and an SSC region, which ranged from 17,849 bp ( C. annuum ) to 18,522 bp (C. lycianthoides). The GC content in the 12 cp genomes of the Capsicum tribe was similar, with an average of 37%. Additionally, the size of the cp genomes in the 14 genomes of the Capsiceae tribe ranged from 156,583 bp in C. lycianthoides to 157,390 bp in C. pubescens (Table 1 ). The ACP had a genome size of 156,931 bp, and the average genome size for the Capsiceae tribe was a total of 156,741 bp. The genome size of the Capsicum tribe, specifically of Arnaucho chili pepper, is similar to the first genome studied in this tribe, as well as the cp genomes used in this study, approximately 156 kb, except for C. baccatum and C. pubescens , which both had 157 kb (Raveendar et al., 2024). Table 1 Comparación de datos de secuencias de los genomas completos de cloroplastos de la tribu Capsiceae Genbank Number Scientific name Genome size bp LSC región (bp) IRs región (bp) SSC región (bp) Total genes CDS GC% rRNA tRNA NC_018552 C. annuun 156,781 87,366 25,783 17,849 132 87 37,37 8 37 KX913219 C. tovarii 156,816 87,379 25,792 17,853 132 87 37,72 8 37 KR078312 C. frutescens 156,817 87,380 25,792 17,853 131 87 37,72 8 37 MZ379791 C. chinense 156,931 87,325 25,847 17,912 133 86 37,71 8 37 NC_033524 C. galapagoense 156,959 87,347 25,847 17,918 132 87 37,71 8 37 KX913217 C. chinense 156,936 87,330 25,847 17,912 132 87 37,72 8 37 KU041709 C. chinense 156,807 87,290 25,803 17,911 113 79 37,70 4 30 MH559321 C. chinense 156,858 87,288 25,855 17,860 132 86 37,43 4 30 NC_030543 C. chinense 156,807 87,290 25,803 17,911 113 79 37,73 4 30 KX913220 C. eximium 156,947 87,341 25,847 17,912 132 87 37,72 8 37 MH559320 C. baccatum 157,144 87,351 25,910 17,973 113 79 37,66 4 39 NC_039694 C. pubescens 157,390 87,688 25,887 17,928 131 86 37,69 8 37 NC_026551 C. lycianthoides 156,583 86,813 25,624 18,522 127 83 37,76 8 36 NC_033525 C. chacoense 156,959 87,379 25,859 17,898 132 87 37,68 8 37 The cp genome of the ACP pepper was annotated to predict a total of 133 genes, including 86 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes. Among the annotated genes, a total of 11 large ribosomal proteins ( rpl ), 14 small ribosomal proteins ( rps ), 8 different rRNA genes, 4 DNA-dependent RNA polymerases ( rpo ), 38 different tRNA genes ( trn ), 5 genes encoding the photosystem I protein complex ( psa ), 14 genes encoding the photosystem II protein complex ( psb ), 6 genes encoding the cytochrome b6/f complex ( pet ), 12 genes encoding NADH dehydrogenase proteins ( ndh ), 6 genes encoding ATP synthase proteins ( atp ), the ATP-dependent Clp protease proteolytic subunit ( clpP ), the large subunit of ribulose-1,5-bisphosphate carboxylase ( rbcL ), maturase K ( matK ), genes encoding cytochrome C biogenesis proteins ( ccsA ), the beta subunit of acetyl-CoA carboxylase ( accD ), the membrane envelope protein ( cemA ), 4 ycf1 genes ( ycf ), the gene encoding translation initiation factor 1 ( infA ), and a gene of unknown function ( pafI ) were found. In addition, the annotation results revealed that 24 of these genes contain introns ( ndhB , petB , petD , rpl2 , rps12 , trnA-UGC , trnG-UCC , trnI-GAU , trnL-UAA , atpF , clpP1 , ndhA , ndhB , rpl16 , rpl2 , rpoC1 , rps12 -fragment, rps12 , rps16 , trnA -UGC, trnI -GAU, trnK -UUU, trnV -UAC, pafI ), and four of them contain two introns ( pafI , clpP1 , and the two rps12 structures). The majority of the genes are expressed as a single copy, with the exception of 18 genes that were duplicated in the IR regions. Table 2 Genetic content and its functions of the chloroplast genome of C. chinense Arnaucho chili pepper. Category Group of genes Name of genes Large subunit of ribosomal proteins rpl2 a , rpl4, rpl16 a , rpl20, rpl22, rpl23, rpl32, rpl33 rpl36 Pequeño subconjunto de proteínas ribosómicas. rps2, rps3, rps4, rps7, rps8, rps11, rps12 a , rps14, rps15, rps16, rps18, rps19 ARN polimerasa dependiente de ADN rpoA, rpoB, rpoC a Sef-replication Ribosomal RNA genes rrn4.5, rrn5, rrn16, rrn23 trnC-GCA, trnG-GCC, trnG-UCC a , trnG-UCC, trnL-CAA, trnL-UAA, trnL-UAG, trnM-CAU, trnN-GUU Transfer RNA genes trnA-UGC, trnD-GUC, trnE-UUC, trnH-GUG, trnI-CAU, trnI-GAU, trnK-UUU, trnR-ACG, trnR-UCU trnS-GGA,trnT-GGU, trnV-GAC,trnL-CAA,, trnP-UGG , trnQ-UUG, trnR-ACG, trnS-GCU, trnS-UGA, trnT-UGU, trnV-GAC, trnV-UAC a , trnW-CCA, trnY-GUA, trnfM-CAU Photosystem I psaA, psaB, psaC, psaI, psaJ Photosystem II psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbT, psbZ Genes for photosynthesis RUBISCO rbcL Subunits of ATPsynthase atpA, atpB, atpE, atpF a , atpH, atpI Subunit of NADH-dehydrogenase ndhA a , ndhB a , ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK Cytochrome b/f complex petA, petB a , petD a , petG, petL, petN Protease clpP b Mutrase matK Other genes Envelope membrane protein cemA Translation initiation factor infA C-type cytochrome synthesis gene ccsA Subunit of Acetyl-CoA-carboxylase accD Genes of unknown function Conserved hypothetical chlroplast ycf1, ycf2 , pafI Comparative analysis of the cp genome sequences of the Capsiceae tribe Finally, the results from the mVista web server provided the information needed to assess the divergence among the 14 cp genome sequences in the Capsiceae tribe, using ACP as a reference. It was observed that the highest divergence was found in C. lycianthoides compared to our reference genome. These results provided information that the sequence variation was higher in the non-coding regions across all genomes, with lower variation observed in the coding regions of the genes. However, C. lycianthoides exhibited variation in more than one coding gene, including the genes accD , rpl20 , rps12 , clpP , ycf2 , ndhF , ndhA , ycf1 , and rpl2 . In addition, the four C. chinense species' cp genomes showed significant variation in the accD gene, along with C. eximium , C. pubescens and C. baccatum which also exhibited variation in the same gene. On the other hand, the species C. galapagoense showed significant variation in the rpl20 gene, along with C. annuum , C. baccatum , C. pubescens , C. lycianthoides and C. chacoense . These results justify further research to better determine and understand the clade of C. chinense , as it is unclear whether this fragment was altered in its cp genome due to a mutation caused by environmental factors (since the species are found in different habitats), or if it was simply a result of incomplete genome assembly. Codon usage analysis in the Arnaucho chili pepper For this codon analysis, the software Mega11 was used, and the number of times each codon is repeated and the relative synonymous codon usage (RSCU) were calculated from the protein-coding sequences (CDS). The most used codon in the C. chinense genome was AAA, which codes for lysine (2140), followed by UUU, which codes for phenylalanine (2118), and lastly AUU, which codes for isoleucine (1864). In the stop codons of C. chinense , the most used codons were UAA (1136) and UGA (982). Finally, the least present amino acid codons in the C. chinense genome were GGG, which codes for glycine (578), and ACC, which codes for threonine (576). Phylogenetic analysis and pairwise distance The results obtained from the ML phylogenetic analysis showed that different cultivars of C. chinense grouped with others of the same species, forming monophyletic groups. It can also be observed that there is a genetic relationship between our C. chinense and C. galapagoense , demonstrating that the ACP is a sister species to C. galapagoense , a result similar to the findings of Arbizu et al. ( 2022 ). Additionally, the results obtained at each node were very similar to the recent studies conducted by Sebastián et al. (2024), showing that the C. chinense clade is related to C. galapagoense . In the pairwise distance results of the 14 cp genomes using the p-distance algorithm, the ACP was compared as the reference with the other genomes of the Capsiceae tribe. As expected, the highest average distance was found between Arnaucho chili pepper and C. lycianthoides (0.00021523), while the lowest was between C. chinense and C. galapagoense (0.00002733). Additionally, the following cp genomes were observed: C. eximium with a distance of 0.00003181, and the other four C. chinense genomes with average distances of 0.00003422, 0.00003551, and two with 0.00003822. Thanks to these results, the distributions and densities between the distances within the Capsiceae tribe can be observed. Similarly, as seen in the phylogenetic results, the five C. chinense genomes, C. galapagoense , and C. eximium exhibit a similar distribution and probability density trend, in contrast to the other plastid genomes of their tribe. Analysis of repetitive sequences The analysis detected different types of repetitive sequences within the genome of the Arnaucho chili pepper, as well as across the entire tribe, consisting of 14 cp genome sequences. These simple sequence repeats (SSRs) are tandemly repeated DNA of 1 to 6 base pairs in length, commonly used as molecular markers to identify species, revealing gene rearrangements and losses during their evolution (Nashima et al. 2020 ; Mcdonald et al. 2011 ). The results obtained in the ACP genome predicted a total of 36 SSRs, consisting of 33 mononucleotides, 1 trinucleotide, and 2 pentanucleotides, revealing a significantly different pattern compared to all fourteen cp genomes of the Capsicum tribe, including the cp genomes of the four C. chinense and C. galapagoense , which belong to the same clade (Raveendar et al. 2015 ). In addition, Reputter, RepEX, and Tandem Repeats Finder characterized a total of 172 palindromic sequences, 41 forward sequences, 3 reverse sequences, 0 complementary sequences, and 55 tandem repeats, maintaining similarity with the other genomes in these repetitive sequences (Fig. 6 ). Additionally, the other repetitive sequences from the 14 chloroplast genomes were also characterized and subsequently compared in a balloon plot. These results can be seen in (Fig. 07 ) and (Table 03 ). Table 3 The different types of repetitive sequences and SSRs in the 14 chloroplast genomes of the Capsiceae tribe Scientific name Genbank Number Palindromos Forward Reverse Tandem SSR C. annun NC_018552 175 44 5 62 44 C. tovarii KX913219 175 39 1 62 50 C. frutescens KR078312 175 29 1 62 50 C. chinense MZ379791 172 41 3 55 36 C. galapogense NC_033524 172 39 2 59 50 C. chinense KX913217 172 39 3 57 50 C. chinense KU041709 163 32 3 57 49 C. eximium KX913220 172 45 3 59 50 C. baccanturn MH559320 174 49 0 64 50 C. pubescens NC_039694 173 49 0 66 52 C. lycianthoides NC_026551 181 31 1 50 54 C. chacoense NC_033525 178 41 1 60 55 C. chinense MH559321 172 33 1 57 50 C. chinense NC_030543 172 16 1 57 51 In the detection of simple sequence repeats (SSRs), a heatmap was created for the comparative analysis of SSR motif frequencies. There was a higher frequency of the thymine (T) motif in the Capsiceae tribe, ranging from 14 in C. annuum to 26 in C. lycianthoides , followed by the adenine (A) motif. It was noted that its frequency was identical across all genomes, except for C. annuum , which had a total of 11, and C. lycianthoides , which had 14. This result can also be observed with the TTA (trimer) motifs, where the cp genomes of C. baccatum and C. lycianthoides do not show these motifs, while the others all exhibited the same frequency of 1. Studies on SSR in plants indicate that trimers are the most frequent in most groups of higher plants, such as monocots and dicots. This is consistent with the results described for this tribe, confirming studies outlined by Victoria et al. ( 2011 ). In addition, the frequency of motifs such as AT, CT, TA, TTC, AAAC, AAAT, AATT, ATAA, CTAT, TTTG, TTATT, TTTTA, TATAG, TTCATT, TAAT, G, and TTTTAA in the identified SSRs was entirely different, where all exhibited varying frequencies, except for the ACP, as previously described in the analysis. In the predicted number of SSRs, Arnaucho chili pepper showed the lowest amount of SSRs according to MISAweb, compared to C. galapagoense and the other two C. chinense individuals, which exhibited similar quantities ranging from 51 to 49 SSRs (Fig. 7 ). Comparative analysis in the binding regions The chloroplast genomes of the Capsiceae tribe showed a magnitude of displacement between the unique copy regions and the inverted repeats, considering their position relative to the nearest genes (Fig. 7 ). These boundaries were named JLB (LSC-IRB), JSB (IRB-SSC), JSA (SSC-IRA), and JLA (IRA-LSC) (Caycho et al. 2023 ). The length of the IR in the Capsiceae tribe varies from 156,583 bp to 157,390 bp across the 14 plastid genomes. Our Arnaucho chili pepper possesses a length of 156,931 bp, similar to C. galapagoense with 156,959 bp and C. chinense (KU041709) with 156,936 bp, respectively. This indicates that the IR expansion was almost identical, with no significant expansion observed among these plastid genomes. It was very different with the other three C. chinense genomes, which have 156,858 bp (MH559321) and two with 156,807 bp (KU041709 and NC_030543), where there were apparently only two small contractions of 124 bp and 73 bp. These expansions and contractions of the IR boundary contribute to the size and variations of the plastid genomes (Zhang et al., 2023 ). Within the 14 plastid genomes of the Capsiceae tribe examined, the four distinct boundaries and their genes located near these boundaries were identified, showing consistent patterns, as well as some absences in the analyzed genomes (Fig. 08 ). Specifically, regarding the junction between LSC and IRb (JLB), where all plastid genomes showed the structure of the rps19 gene spanning from the LSC region to IRb, there was a difference in length ranging from 206 bp to 218 bp. Additionally, Arnaucho chili pepper and the other four C. chinense species, including C. galapagoense , exhibited the same position and size for the rps19 gene. The rpl22 and rpl2 genes are located in the LSC and IRB regions. Similarly, for the JSB boundary, where the union between the SSC and IRB regions occurs, two genes, ycf1 and ndhF , were positioned. The ndhF gene was located in the SSC regions, while it was observed that ycf1 crossed from the SSC region to the IRB region, except in Arnaucho chili pepper and C. lycianthoides . Additionally, it was absent in C. pubescens , C. baccatum , and C. chinense (MH559321). The ycf1 genes that spanned both the SSC and IRB regions had the same size of 1160 bp, while those located only in the IRB region had a size of 1127 bp in C. chinense and 1043 bp in C. lycianthoides . The ndhF gene (2222 bp) in the plastid of Arnaucho chili pepper showed a slight positional difference compared to C. galapagoense and the other four C. chinense genomes, and it was located adjacent to the JSB boundary. At the JSA boundary between SSC and IRA, the closest genes in the Capsiceae tribe showed that the ycf1 gene was intact at the JSA boundary and crossed from SSC to the IRA region. However, the length of this gene varied from 5693 bp in C. lycianthoides to 5735 bp in C. baccatum . Additionally, four C. chinense showed the same length for the gene ycf1 with a size of 5720 bp, except for C. chinense which had 5675 bp and C. galapagoense with 5726 bp. Finally, the analysis of the junction between the IRA and LSC regions (JLA) showed that the gene rpl2 was present in IRA, except in C. lycianthoides , which did not contain this gene. The genes trnH and psbA were located at the LSC boundary and were present in all the chloroplast genomes. Discussion The native Arnaucho pepper, also known as “supano”, “campiñero” or “arnaucho campiñero”, is an ecotype from the Supe Valley in the Barranca province, and is very important in the Peruvian gastronomy, especially in the Lima. This Capsicum chinense cultivar has been cultivated since in family gardens for self-consumption sin the 1960s. Starting in the 1980s, it began to be cultivated in small plots with marketing intentions, where its distribution was through seeds and seedlings, from farmer to farmer, via family members or neighbors, and it continues to be distributed this way to this day (Aliaga et al. 2020 ). Currently, the first chloroplast genome sequencing has been carried out, with the objectives of characterizing the species and understanding its phylogenetic evolution (Arbizu et al. 2022 ). In this study, we collected the chloroplast genomes of different Capsicum species from the Organelle Genome Resources database of NCBI. The collected genomes were then annotated using the Geseq tool, and the chloroplast genomes were compared using the Arnaucho chili pepper as the reference genome to further study its evolution, structure, and comparison of its cp genome. The cp genome of C. chinense Arnaucho chili pepper was 156,931 bp (156.9 Kb) in length, also exhibiting a classic quadripartite circular structure: a large single-copy region (LSC), a small single-copy region (SSC), and two inverted repeats (IRA and IRB). These regions were also present in the other Capsicum species. Additionally, we found that the cp genomes of the Capsiceae tribe varied slightly in size but maintained a GC content of 37%. This finding aligns with previous reports indicating that the chloroplast genome structure in most angiosperms is typically maternally inherited and remains largely unchanged (Birky, 1995 ). The lengths of the LSC region ranged from 86,813 bp ( C. lycianthoides ) to 87,688 bp ( C. pubescens ), while the SSC region ranged from 17,849 bp ( C. annum ) to 18,522 bp ( C. lycianthoides ), and the IR region ranged from 25,624 bp ( C. lycianthoides ) to 25,910 bp ( C. baccatum ). These results were similar to studies reported by Raveendar et al. (2024). The same has been found in other important Solanaceae crop species, such as S. lycopersicum , S. tuberosum , and P. peruviana (Zhao et al. 2019 ; Chen et al. 2021 ; Feng et al. 2020 ). The chloroplast genomic regions of Solanaceae maintain a similar size among closely related species, as in the case of the Arnaucho chili pepper, an important crop for human consumption. Additionally, in another exotic Solanaceae plant, N. physalodes , studies described by Chen & Zhang ( 2019 ) revealed that the total length of its chloroplast genome was 156,729 bp (157.7 kb), showing a similar length to Capsicum species. However, some Solanaceae species exhibit regions of varying lengths. For example, studies conducted on other Solanaceae species reported Datura stramonium with a size of 155,871 bp and the African boxwood shrub Lycium ferocissimum with 155,894 bp, showing a contraction of around 1,000 bp (Yang et al. 2014 & Li et al. 2019). However, these species exhibited similar boundary regions to the Capsiceae tribe, specifically in the IR region, which measured 25,601 bp in D. stramonium and 25,476 bp in L. ferocissimum , and in the LSC region, which measured 86,302 bp in D. stramonium and 86,536 bp in L. ferocissimum . This suggests that the reduction in chloroplast genomes of these species occurs in the SSC regions, possibly due to genetic variations present in this family (Su et al. 2020 ). Additionally, in the annotated chloroplast genome of C. chinense , 133 genes were identified, including a total of 86 CDS, 8 rRNA, 37 tRNA, and 2 pseudogenes. Compared to other Capsicum species, this variety has more genes in its chloroplast but fewer protein-coding sequences. Most of the genes are present as a single copy, except for 18 genes that are duplicated in the IR regions. These 18 duplicated genes in the IR region have also been found in other Solanaceae species that are not Capsicum (Asaf et al. 2016 ). In the genomic sequence comparison analysis conducted by mVISTA, it was revealed that C. lycianthoides exhibited the greatest divergence in relation to C. chinense Arnaucho chili pepper. The analysis showed that the greatest variation occurred in the non-coding regions compared to the coding regions present in all genomes of the Capsiceae tribe. Additionally, the variations observed in the coding regions were present in all the genomes, specifically in the genes accD , rpl20 , ycf1 , ycf2 , and ndhA . On the other hand, the alignment between the Arnaucho chili pepper and C. galapagoense showed only one significant variation, which occurred in the rpl20 gene. Meanwhile, the alignment between the ACP and the other four C. chinense individuals showed variations in the accD gene (Fig. 02 ). The analysis of codon usage is essential for understanding the complexities of genomic structure, dynamic evolution, and the selective pressure imposed on genes (Morton, 1998 ). We found that the most commonly used codon in the C. chinense genome was AAA, which codes for the amino acid lysine, followed by UUU, which codes for phenylalanine, and finally AUU, which codes for isoleucine. These patterns indicate a preference for codons that end in A or T/U. Previous studies have shown that higher RSCU values indicate similar results in extensive research on Solanaceae species, with a tendency to be rich in A/U or A/T in chloroplast genomes (Mehmetoğlu et al. 2023 and Wang et al. 2023 ). This means that there is already a selective pressure favoring the use of codons in chloroplast genomes, commonly detected at the third position of codons. Phylogenetic trees are used to understand the evolutionary relationships between species, and they can be based on genomic regions or the complete genome sequence. The angiosperm tree of life has been primarily determined through plastid genome analysis. These chloroplast genomes are highly conserved in both sequence and structure, making them highly valuable for taxonomic studies and plant classification (Amenu et al. 2022 ; Zuntini et al. 2024 ). Here, a phylogenetic tree reconstruction was performed using the complete genome sequence of the pepper along with 14 additional Capsicum genomes. The goal was to classify it within its corresponding tribe and determine its phylogenetic position. The tribe was divided into six groups (green, mustard, light blue, purple, red, and yellow), along with one additional group (pink) representing two Solanaceae genome sequences used to root the tree. The analysis revealed that the Arnaucho chili pepper and C. galapagoense clustered in the corresponding group alongside other C. chinense and C. eximium , showing a genetic relationship among these species. This previous result had already been reported in a study described by Arbizu et al. ( 2022 ). To determine the pairwise distance between chloroplast genomes, an analysis was conducted using Mega11. This analysis was performed using the p-distance method with complete removal of missing data. The results showed that the p-distance values ranged from 0.00002733 for the closest species, C. galapagoense , to 0.00021523 for the most distant species, C. lycianthoides , respectively. These p-distance studies have also been conducted in other families, such as the Styracaceae. Here, we present one of the first results of p-distance analysis in the Capsicum tribe (Song et al. 2022 ). Within each genome, a large number of repetitive sequences, also known as SSRs (Simple Sequence Repeats), are present. These repetitive sequences exhibit high sequence repeatability, high variability, and co-dominant heterozygous inheritance. These sequences are molecular genetic markers suitable for species identification, as well as for ecological and evolutionary studies (Yang et al. 2017; Li et al. 2014 ). Analyses of these SSR sequences offer a perspective as potential markers specific to each genus (Shirasawa et al. 2010 ). In general, the most abundant nucleotides in chloroplast genomes are A and T, or A/T repeats, which are prevalent in angiosperms, rather than G and C or G/C repeats (Kurt et al. 2023 ). In this SSR analysis of Arnaucho chili pepper, a total of 36 SSR markers were identified, comprising 33 mononucleotides, 1 trinucleotide, and 2 pentanucleotides. This revealed a lower pattern compared to the different types of Capsicum species present in this study. The repetitive sequence repetitions, including palindromic sequences, reverse sequences, forward sequences, and tandem repeats, showed values of 172, 41, 3, and 55, respectively. In the comparison of the number of repetitive sequences across the 14 cp genomes, it was observed that none of the genomes contained complementary sequences. There was a variation in the number of reverse sequences, ranging from 1 to 5 in relative magnitude, with the exception of C. baccatum and C. pubescens , which did not present these repetitive sequences (shown in red). For forward sequences, the relative magnitude of repetitive sequences ranged from 16 to 49. In the complementary sequences, a relative magnitude of repetitive sequences was observed between 50 and 66 (shown in light blue), and lastly, for tandem sequences, the relative magnitude was greater than 150, ranging from 163 to 181. In comparison to the SSR sequences, these repetitive sequences appeared similarly to the repetitive sequences found in the other genomes, corroborating that this particular chili variety has fewer SSR sequences in its genome compared to the other Capsicum species detailed in this research. The IR regions can indicate the size of cp genomes because they expand or contract, reflecting the distance between species to some extent (Zhao et al., 2023). These highly variable IR regions can provide molecular marker studies in cp genomes, which are important for research related to species identification, phylogeny, and population genetics (Xiao et al., 2024 ). Our analysis of the ACP genome revealed that it retains an IR region of 25,847 bp (25 kb), leading to a total genome length of 156,931 bp. It is important to highlight that the chloroplast genome length of this Peruvian landrace closely resembles that of C. galapagoense and C. chinense (GenBank KU041709), indicating similar IR expansion. However, its structure is distinctly different. In the Arnaucho chili pepper, the JSB boundary composed of IRb and SSC contains the ycf1 gene, which is located exclusively within the IRb structure. In contrast, C. galapagoense and C. chinense possess the ycf1 gene spanning both the IRb and SSC structures at the JSB boundary. The current taxonomy of this Peruvian landrace is questioned based on the present work, and also by Arbizu et al. ( 2022 ). The ycf1 gene in the ACP is 1127 bp long, similar in size to the 1043 bp ycf1 gene in C. lycianthoides , positioned solely at the junction. This gene's variation plays a key role in the structural variation of chloroplast genomes within the Capsiceae tribe. This result regarding the IR structure indicates that the ycf1 gene in most angiosperms is generally larger and more diverse. In some cases, the ycf1 gene may be absent, which could lead to a reduction in protein-coding capacity and variation in the IRb/SSC boundary structure. As noted by Ge et al. ( 2019 ), this variation can influence the overall stability and function of the chloroplast genome, potentially affecting the plant's metabolic processes and adaptation to different environments. The presence of ycf1 and its position within the IR regions plays a significant role in the genomic architecture and evolutionary dynamics of angiosperms. Conclusion Here, we report the in-silico analysis of the Arnaucho chili pepper along with 13 chloroplast genomes from the Capsiceae tribe, including both hot and sweet peppers, obtained from the NCBI database. We compared the 14 chloroplast genome sequences. In this comparative analysis, highly variable sites were identified, specifically non-coding regions, as well as coding regions of genes that could serve as potential markers for species identification. In this case, rpl20 , accD , ycf1 , ycf2 , and ndhA were highlighted. It was also observed that this Arnaucho chili pepper exhibited patterns of codons A (adenine) and U (uracil), similar to the other types of peppers present. It was discovered in its phylogenetic reconstruction and p-distance analysis that this Capsicum species is closely related in evolutionary terms to C. galapagoense . All the genomes of the Capsiceae tribe were highly conserved, except in the IRB region at the JSB boundary. This complete cp genome of Arnaucho pepper showed different genetic characteristics regarding its SSR sequence identification compared to the other genomes. It was found to possess 36 SSR sequences, which is fewer than the other pepper genomes used in the present study. Additionally, in the other repetitive sequences, it was completely different, displaying similarities to the other types of chloroplast genomes of peppers studied. These studies may be useful for future research on the diversity or genetic improvement of this Peruvian chili pepper landrace. Declarations Acknowledgments We would like to thank the Vicerrectorado de Investigación of UNTRM. Author contributions GC: Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – original draft. KRQ-H: Data curation, Formal analysis, Investigation, Software, Validation, Visualization, Writing – original draft. DHT-I: Data curation, Formal analysis, Investigation, Software, Validation, Visualization, Writing – original draft. JEB-G: Data curation, Formal analysis, Investigation, Software, Validation, Visualization, Writing – original draft. YAC-R: Data curation, Formal analysis, Investigation, Software, Validation, Visualization, Writing – original draft. SC-L: Conceptualization, Formal analysis, Investigation, Methodology, Project administration, Supervision, Validation, Visualization, Writing – review & editing. CIA: Conceptualization, Data curation, Investigation, Resources, Supervision, Validation, Visualization, Writing – review & editing. PMR-G: Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – review & editing. Funding This research received not external funding. Conflict of interest The authors declare that they have no conflicts of interest in this research. Data Availability No datasets were generated during the current study. Conflicts of interest The authors declare no competing interests. References Aguilar-Meléndez A, Morrell PL, Roose ML, Kim SC. Genetic diversity and structure in semiwild and domesticated chiles ( Capsicum annuum ; Solanaceae) from Mexico. Am J Bot. 2009;96(6):1190–202 Aliaga, J., Portalatino, E., Obregon, K., Rodriguez, A. & Jimenez, J. (2020). Presencia del "aji nativo supano" (Capsicum chinense Jacq.) en el valle de Supe, Peru. Peruvian Agricultural Research. (1). 58-63. DOI: 10.51431/par.v1i2.584 Amenu, S.G., Wei, N., Wu, L. et al. Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution. BMC Plant Biol 22, 88 (2022). https://doi.org/10.1186/s12870-022-03480-5 Amiryousefi, A., Hyvönen, J., Poczai, P. IRscope: an online program to visualize the junction sites of chloroplast genomes, Bioinformatics, Volume 34, Issue 17, September 2018, Pages 3030–3031, https://doi.org/10.1093/bioinformatics/bty220 Ángel Gaviria, I.J. (2023). La bioinformática como herramienta para el conocimiento de microorganismos edáficos con potencial para la producción agrícola sostenible, recuperación y conservación de suelos [Tesis de maestría, Universidad Libre]. Antonio, A.S., Wiedermann, L.S.M. & Veiga, F.J. (2018). The genus Capsicum: a phytochemical review of bioactive secondary metabolites. RSC Advances. 25767-25784. DOI: 10.1039/c8ra02067a Arbizu, C. I., Saldaña, C. L., Ferro-Mauricio, R. D., Chávez-Galarza, J. C., Herrera, J., Contreras-Liza, S., … Maicelo, J. L. (2022). Characterization of the complete chloroplast genome of a Peruvian landrace of Capsicum chinense Jacq. (Solanaceae), arnaucho chili pepper. Mitochondrial DNA Part B , 7 (1), 156–158. https://doi.org/10.1080/23802359.2021.2014366 Asaf, S., Khan, A.L., Khan, A.R., Waqas, M., Kang, S., Khan, M., Lee, S. & Lee, I. (2016). Complete Chloroplast Genome of Nicotiana otophora and its Comparison with Related Species. Front Plant Sci. Sec. Evolutionary and Population Genetics. https://doi.org/10.3389/fpls.2016.00843 Beier S, Thiel T, Münch T, Scholz U, Mascher M (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics 33 2583–2585. dx.doi.org/10.1093/bioinformatics/btx198 Benson 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research. Vol 27. Pages 573-580. https://doi.org/10.1093/nar/27.2.573 Birky Jr, C.W. (1995). Uniparental inheritance of mitochndrial and chloroplast genes: mechanisms and evolution. PNAS. Vol 92. 11331-11338. https://doi.org/10.1073/pnas.92.25.11331 Brudno, M., Malde, S., Poliakov, A., Do, C.B., Couronne, O., Dubchak, I., and Batzoglou, S. Glocal Alignment: Finding Rearrangements During Alignment, 2003. Bioinformatics, 19S1: i54-i62. Caycho, E., La Torre, R. & Orjeda, G. Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (subfamily: Caesalpinioideae). BMC Plant Biol 23 , 570 (2023). https://doi.org/10.1186/s12870-023-04581-5 Chan, P.P., Lin, B.Y., Mak, A.J., and Lowe, T.M. (2021)tRNAscan-SE 2.0: Improved Detection and Functional Classification of Transfer RNA Genes. Nucl. Acids Res. 49 :9077–9096. Chen, Q., & Zhang, D. (2019). The complete chloroplast genome sequence of the medicinal plant Nicandra physalodes (Linn.) Gaertn. (Solanaceae). Mitochondrial DNA Part B, 4(2), 3053–3054. https://doi.org/10.1080/23802359.2019.1666674 Chen, S., Zhao, Y., Zhang, J. Y., Zhang, J. Y., Wang, Y. P., Mou, B., … Han, Y. Z. (2021). Characterization of the complete chloroplast genome of the Solanum tuberosum L. cv. Shepody (Solanaceae). Mitochondrial DNA Part B, 6(8), 2342–2344. https://doi.org/10.1080/23802359.2021.1934135 Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9(8), 772. Dong, X., Li, X., Ding, L., Cui, F., Tang, Z., Liu, Z., Stage Extraction of Capsaicinoids and Red Pigments from Fresh Red Pepper (Capsicum) Fruits with Ethanol as Solvent, LWT - Food Science and Technology (2014), doi: 10.1016/j.lwt.2014.04.051. Estrada, R., Tantalean, J.F.C., Saldaña, C.L. et al. Draft genome and SSR data mining of a Peruvian landrace of Capsicum chinense, the arnaucho chili pepper. Genet Resour Crop Evol (2024). https://doi.org/10.1007/s10722-024-01941-4 Feng, S., Zheng, K., Jiao, K., Cai, Y., Chen, C., Mao, Y., Wang, L., Zhan, X., Ying, Q. & Wang, H. (2020). Complete chloroplast genomes of four Physalis species (Solanaceae): lights into genome structure, comparative analysis, and phylogenetic relationships. BMC Plant Biol 20, 242. https://doi.org/10.1186/s12870-020-02429-w Florencio, V. & Valdir, Jr. (2022). Chapter 1: Origin and Evolution of Capsicum. Chemistry and Nutritional Effects of Capsicum . Page: 1-14. https://doi.org/10.1039/9781839160646-00001 Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9. Ge, Y., Dong, X., Wu, B., Wang, N., Chen, D., Chen, H., Zou, M., Xu, Tan, L. & Zhan, R. (2019). Evolutionary analysis of six chloroplast genomes from three Persea americana ecological races: Insights into sequence divergences and phylogenetic relationships. PLoS ONE 14(9): e0221827. https://doi.org/10.1371/journal.pone.0221827 Greiner S, Lehwark P and Bock R (2019) OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Research 47: W59-W64. https://doi.org/10.1093/nar/gkz238 Hernandez, A.A., Pineda, A.L., Rojas, J.C. & Diaz, H.P. (2022). In vitro regeneration of arnaucho (Capsicum chinense Jacq.) from apical buds. Manglar. (1). 71-75. DOI: http://dx.doi.org/10.17268/manglar.2021.009 Ibiza, V.P.; Blanca, J.; Cañizares, J.; Nuez, F. Taxonomy and genetic diversity of domesticated Capsicum species in the Andean region. Genet. Resour. Crop Evol. 2012, 59, 1077−1088. DOI 10.1007/s10722-011-9744-z Katoh, K., Standley, D. (2013). MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution. Vol4. Pág 772-780. doi: 10.1093/molbev/mst010 Kurtz, S. and Choudhuri, Jomuna V. and Ohlebusch, Enno and Schleiermacher, Chris and Stoye, Jens and Giegerich, Robert (2001) REPuter: The Manifold Applications of Repeat Analysis on a Genomic Scale, Nucleic Acids Res., Nucleic Acids Res., 29(22):4633-4642. Kurt, S., Kaymaz, Y., Ateş, D. et al. Complete chloroplast genome of Lens lamottei reveals intraspecies variation among with Lens culinaris. Sci Rep 13, 14959 (2023). https://doi.org/10.1038/s41598-023-41287-y Larsson, A. (2014). AliView: a fast and lightweight alignment viewer and editor for large data sets. Bioinformatics 30(22): 3276-3278.http://dx.doi.org/10.1093/bioinformatics/btu531 Letunic I and Bork P (2024) Nucleic Acids Res doi: 10.1093/nar/gkae268 Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool Li, M., Qi, X.M., Lam, H. (2013). Silicon Era of Carbon-Based Life: Application of Genomics and Bioinformatics in Crop Stress Research. Mol. Sci. 14. 11444-11483. https://doi.org/10.3390/ijms140611444 Li, X. et al. Plant DNA barcoding: From gene to genome. Biol. Rev. Camb. Philos. Soc. 90, 157–166 (2014). Li, Z., Zhang, X., Zhang, Q., & Yisilam, G. (2020). Complete chloroplast genome of Lycium ferocissimum (Solanaceae), a species native to South Africa. Mitochondrial DNA Part B, 5(1), 756–757. https://doi.org/10.1080/23802359.2020.1715301 Liu H, Liu X, Sun C, Li HL, Li ZX, Guo Y, Fu XQ, Liao QH, Zhang WL, Liu YQ. Chloroplast Genome Comparison and Phylogenetic Analysis of the Commercial Variety Actinidia chinensis 'Hongyang'. Genes (Basel). 2023 Nov 27;14(12):2136. doi: 10.3390/genes14122136. PMID: 38136958; PMCID: PMC10743354. López Medina, E., López Zabaleta, A., Gil Rivero, A. E., Mostacero, J., De La Cruz, A.J. y Villena, L. (2020) Morfometría de frutos y semillas del “ají mochero” Capsicum chinense Jacq. Ciencia & Tecnología Agropecuaria, 21(3), 1-11. https://doi.org/10.21930/rcta.vol21_num3_art:1598. Mansoor, S., Hamid, S., Thanh, T.T., Park, J. Suk, Y.C. (2024). Advance computational tools for multiomics data learning. Biotechnol Adv. Vol 77. https://doi.org/10.1016/j.biotechadv.2024.108447 McDonald MJ, Wang W-C, Huang H-D, Leu J-Y (2011) Clusters of Nucleotide Substitutions and Insertion/Deletion Mutations Are Associated with Repeat Sequences. PLoS Biol 9(6): e1000622. https://doi.org/10.1371/journal.pbio.1000622 Meckelmann, S., Riegel, D.W., Zonneveld, M.J., Rios, L., Pe;a, K., Ugas, R., Quinonez, L., Mueller-Seitz, E. & Petz, M. (2013). Compositional Characterization of Native Peruvian Chili Peppers (Capsicum spp.). Agric Food Chem. Vol 61. Pages: 2530-2537. DOI: 10.1021/jf304986q Mehmetoğlu, E., Kaymaz, Y., Ateş, D. et al. The complete chloroplast genome of Cicer reticulatum and comparative analysis against relative Cicer species. Sci Rep 13, 17871 (2023). https://doi.org/10.1038/s41598-023-44599-1 Michael, D., Gurusaran, M., Santhosh, R., Khaja, Md.H., Satheesh, S.N., Suhan, S., Sivaranjan, P., Jaiswal, A. & Sekar, K. (2019). RepEx: A web server to extract sequence repeats from protein and DNA sequences. Computational Biology and Chemistry. Vol: 78. Pages: 424-430. https://doi.org/10.1016/j.compbiolchem.2018.12.015 Minguez-Mosquera, M.I., Jaren-Galan, M. and Garrido-FErnandez, J. (1992). Color Quality in Paprika. J. Agric. Food Cherm. Vol:40. Pages 2384-2388. https://doi.org/10.1021/jf00024a012 Morton, B.R. (1998). Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages. J Mol Evol.;46(4):449–59. McGowan, J. (2024). RSCU calculator. Online Bioinformatics Tools. https://jamiemcgowan.ie/bioinf/rscu.html Nashima K, Hosaka F, Terakami S, et al. SSR markers developed using next-generation sequencing technology in pineapple, Ananas comosus (L.) Merr. Breed Sci. 2020;70(3):415–21. Park, H. S., Lee, J., Lee, S. C., Yang, T. J., & Yoon, J. B. (2016). The complete chloroplast genome sequence of Capsicum chinense Jacq. (Solanaceae). Mitochondrial DNA Part B , 1 (1), 164–165. https://doi.org/10.1080/23802359.2016.1144113 Perry L, Dickau R, Zarrillo S et al (1979) (2007) Fósiles de almidón y la domesticación y dispersión de chiles ( Capsicum spp. L.) en las Américas. Ciencia 315:986–988.https://doi.org/10.1126/science.1136914 Ray, S. & Saty, P. (2014). Next generation sequencing technologies for next generation plant breeding. Front Plant Sci. Vol 5. https://doi.org/10.3389/fpls.2014.00367 Raveendar, S., Jeon, Y., Lee, J., Lee, G., Lee, K.J., Cho, G., Ma, K., Lee, S. and Chung, J. (2015). The Compmplete Chloroplast Genome Sequence of Korean Landrace “Subicho” Pepper ( Capsicum annuum var. annuum ). Plant breeding and Biotechnology. Vol 3. 88-94https://doi.org/10.9787/PBB.2015.3.2.08888 Roychowdhury, R., Prakash, S.D., Gupta, A., Parihar, P., Chandrasekhar, K., Sarker, U., Kumar, A., Pandurang, D.R. & Sudhakar, C. (2023). Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant's Abiotic Stress Tolerance Responses. Genes. Vol 14. https://doi.org/10.3390/genes14061281 Sharp, P.M. & Li, W.H. (1987). The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research. Vol 3. Pages: 1281-1295. doi: 10.1093/nar/15.3.1281 Sebastin, R., Lee, K. J., Cho, G. T., Shin, M. J., Kim, S. H., Hyun, D. Y., & Lee, J. R. (2019). The complete chloroplast genome sequence of a Bolivian wild chili pepper, Capsicum eximium Hunz. (Solanaceae). Mitochondrial DNA Part B , 4 (1), 1634–1635. https://doi.org/10.1080/23802359.2019.1601533 Sebastin, R., Kim, J., Jo, IH. et al. Comparative chloroplast genome analyses of cultivated and wild Capsicum species shed light on evolution and phylogeny. BMC Plant Biol 24 , 797 (2024). https://doi.org/10.1186/s12870-024-05513-7 Shirasawa, K., Asamizu, E., Fukuoka, H., Ohyama, A., Sato, S., Nakamura, Y., Tabata, S., Sasamoto, S., Wada, T., Kishida, Y., Tsuruoka, H., Fujishiro, T., Yamada, M. & Isobe, S. (2010). An interspecific linkage map of SSR and intronic polymorphism markers in tomato. Theor Appl Genet. Vol 121. Pages 731-739. https://doi.org/10.1007/s00122-010-1344-3 Shiragaki K, Yokoi S, Tezuka T. 2020. Phylogenetic analysis and molecular diversity of capsicum based on rDNA-ITS region. Horticulturae. 6(4):87. Song, F., Zhao, W., Xu, J., Li, M. & Zhang, Y. (2022). Chloroplast Genome Evolution and Species Identification of Styrax (Styracaceae). BioMed Research International. https://doi.org/10.1155/2022/5364094 Su Q, Liu L, Zhao M, Zhang C, Zhang D, Li Y, et al. Los genomas completos del cloroplasto de diecisiete Aegilops tauschii : análisis comparativo del genoma e inferencia filogenética. PeerJ. 2020;8:e8678. Tamura, K., Stecher, G., and Kumar, S. (2021) MEGA11: Molecular Evolutionary Genetics Analysis version 11. Molecular Biology and Evolution 38:3022-3027 Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R and Greiner S (2017). GeSeq – versatile and accurate annotation of organelle genomes. Nucleic Acids Research 45: W6-W11. https://doi.org/10.1093/nar/gkx391 Tripodi P, Rabanus-Wallace MT, Barchi L, Kale S, Esposito S, Acquadro A, Schafleitner R, van Zonneveld M, Prohens J, Diez MJ. 2021. Global range expansion history of pepper (Capsicum spp.) revealed by over 10,000 genebank accessions. Proc Natl Acad Sci USA. 118(34):e2104315118. Victoria, F.C., Maia, L.C., Oliveira, A.C. (2011). In silico comparative analysis of SSR markers in plants. BMC Plat Biology. 11-15. https://doi.org/10.1186/1471-2229-11-15 Wang, X., Bai, S., Zhang, Z., Zheng, F., Song, L., Wen, L., Guo, M., Cheng, G., Yao, W., Gao, Y. & Li, J. (2023). Front Plant Sci. Sec. Plant Bioinformatics. Vol 13. https://doi.org/10.3389/fpls.2023.1179009 Write, F. (1990). The 'effective number of codons' used in a gene. Gene. Vol 87. Pages: 23-29. https://doi.org/10.1016/0378-1119(90)90491-9 Xiao, F., Zhao, Y., Wang, X. et al. Characterization of the chloroplast genome of Gleditsia species and comparative analysis. Sci Rep 14, 4262 (2024). https://doi.org/10.1038/s41598-024-54608-6 Yang, Y., Yuanye, D., Qing, L., Jinjian, L. & Xiwen, L. (2015). Complete Chloroplast Genome Sequence of Poisonous and Medicinal Plant Datura stramonium: Organizations and Implications for Genetic Engineering. PLOS ONE 10(2): e0118236. https://doi.org/10.1371/journal.pone.0118236 Yang, Z. & Ji, Y. Comparative and Phylogenetic Analyses of the Complete Chloroplast Genomes of Three Arcto-Tertiary Relicts: Camptotheca acuminata, Davidia involucrata, and Nyssa sinensis. Front. Plant. Sci. 8, 1536 (2017). Zhang, D., Tu, J., Ding, X., Guan, W., Gong, L., Qiu, X. & Huang, Z. (2023). Analysis of the chloroplast genome and phylogenetic evolution of Bidens pilosa. BMC Genomics.(113). https://doi.org/10.1186/s12864-023-09195-7 Zhao, C., Sun, K., Chen, S., Liang, C., Meng, J., Tang, Y., & Song, S. (2019). Characterization the complete chloroplast genome of the tomato (Solanum lycopersicum L.) from China. Mitochondrial DNA Part B, 4(1), 1374–1376. https://doi.org/10.1080/23802359.2019.1598300 Zuntini, A.R., Carruthers, T., Maurin, O. et al. Phylogenomics and the rise of the angiosperms. Nature 629, 843–850 (2024). https://doi.org/10.1038/s41586-024-07324-0 Additional Declarations No competing interests reported. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. 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-5657151","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":392418451,"identity":"f48f9d9d-14c3-4025-9c8f-0a7092c43bba","order_by":0,"name":"Gianmarco Castillo","email":"","orcid":"","institution":"Universidad Nacional José Faustino Sánchez Carrión (UNJFSC)","correspondingAuthor":false,"prefix":"","firstName":"Gianmarco","middleName":"","lastName":"Castillo","suffix":""},{"id":392418452,"identity":"aadde6f2-8baf-4dee-8be6-8b2b9e074dcd","order_by":1,"name":"Kevin R. Quiroz-Hidalgo","email":"","orcid":"","institution":"Universidad Nacional José Faustino Sánchez Carrión (UNJFSC)","correspondingAuthor":false,"prefix":"","firstName":"Kevin","middleName":"R.","lastName":"Quiroz-Hidalgo","suffix":""},{"id":392418453,"identity":"b1d25966-4d27-4b8c-bb71-cfac93f4355f","order_by":2,"name":"Diego H. Takei-Idiaquez","email":"","orcid":"","institution":"Universidad Nacional José Faustino Sánchez Carrión (UNJFSC)","correspondingAuthor":false,"prefix":"","firstName":"Diego","middleName":"H.","lastName":"Takei-Idiaquez","suffix":""},{"id":392418454,"identity":"2e2a542f-794b-4960-94d4-543f0417cb00","order_by":3,"name":"Julio E. Ballen-Gavidia","email":"","orcid":"","institution":"Universidad Nacional José Faustino Sánchez Carrión (UNJFSC)","correspondingAuthor":false,"prefix":"","firstName":"Julio","middleName":"E.","lastName":"Ballen-Gavidia","suffix":""},{"id":392418458,"identity":"8a5e8be4-bb5e-4b3c-affc-55821769c3e4","order_by":4,"name":"Yhovana A. Changanaqui-Rengifo","email":"","orcid":"","institution":"Universidad Nacional José Faustino Sánchez Carrión (UNJFSC)","correspondingAuthor":false,"prefix":"","firstName":"Yhovana","middleName":"A.","lastName":"Changanaqui-Rengifo","suffix":""},{"id":392418459,"identity":"f6e4e736-3a4d-4e39-8715-5e02aba71eb5","order_by":5,"name":"Sergio Contreras-Liza","email":"","orcid":"","institution":"Universidad Nacional José Faustino Sánchez Carrión (UNJFSC)","correspondingAuthor":false,"prefix":"","firstName":"Sergio","middleName":"","lastName":"Contreras-Liza","suffix":""},{"id":392418460,"identity":"235571a1-a9f0-4f69-8fd3-9320d5c27c6b","order_by":6,"name":"Carlos I. Arbizu","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABFElEQVRIiWNgGAWjYHACxgNgSoKxgYGhAibIhl8PkpYzDAw8JGgBWdhGhBb+9rMPDnz4wyBvPru5+TPvvMN59tKnExg+lB1mMGdvwKpF4ky6wcGZbQyGc+4cbDDm3Xa4mIcvdwPjjHOHGSx7DmDVYsCQxnCYt4GBcYZEYkMyUEtiDw/vBmbetsMMBjcSsGvhf8ZwmOcPgz1Iy2HeOVAtf0Fa7j/ArkUCaAsPG0MiUEtjM28DVAsj2Bbs3pe48YwB6BeJ5BkyB5sZ5xxLT+w5w7vhYM+5dB7LHuwO4+9PY3zw4Y+N7Qzp9scf3tRYJ7b38G588KPMWs6cHbv3YZahckFqeQzwacAOyNAyCkbBKBgFwxMAANm6XzNrREnaAAAAAElFTkSuQmCC","orcid":"","institution":"Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas (UNTRM)","correspondingAuthor":true,"prefix":"","firstName":"Carlos","middleName":"I.","lastName":"Arbizu","suffix":""},{"id":392418462,"identity":"cbeb2b42-8e6c-4f01-a041-e53a9f05e075","order_by":7,"name":"Pedro M. Rodriguez-Grados","email":"","orcid":"","institution":"Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas (UNTRM)","correspondingAuthor":false,"prefix":"","firstName":"Pedro","middleName":"M.","lastName":"Rodriguez-Grados","suffix":""}],"badges":[],"createdAt":"2024-12-17 00:53:10","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-5657151/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5657151/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":72075557,"identity":"3ee438ab-2376-4cd3-8223-3ac8549c711c","added_by":"auto","created_at":"2024-12-21 15:38:04","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":607179,"visible":true,"origin":"","legend":"\u003cp\u003eA circular map of the chloroplast genome of the Arnaucho chili pepper (ACP). The genes inside the circle are transcribed in a clockwise direction, while the genes outside the circle are transcribed in a counterclockwise direction. The dark gray area in the inner circle reflects the GC content of the cp genome, while the light gray area represents the AT content. In the center of the circle, the fruit of ACP is shown in the logarithmic growth phase. The genes belonging to different functional groups are shown as color-coded blocks\u003c/p\u003e","description":"","filename":"floatimage1.png","url":"https://assets-eu.researchsquare.com/files/rs-5657151/v1/a0f5e1be21c8a43b97313d0d.png"},{"id":72075558,"identity":"0a1cd78c-4de0-4f27-a0f6-5eb27fc860b4","added_by":"auto","created_at":"2024-12-21 15:38:04","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":501874,"visible":true,"origin":"","legend":"\u003cp\u003eGraphical representation of the genomic alignment of the chloroplasts of the Capsiceae tribe. This graph shows the identity of the genomes, using the Arnaucho chili pepper as the reference genome\u003c/p\u003e","description":"","filename":"floatimage2.png","url":"https://assets-eu.researchsquare.com/files/rs-5657151/v1/7930827a410b07dc67bf9082.png"},{"id":72075556,"identity":"7512f9b1-5a59-4355-8ac5-0c69f90f8a22","added_by":"auto","created_at":"2024-12-21 15:38:04","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":72295,"visible":true,"origin":"","legend":"\u003cp\u003eThe RSCU values of the STOP codons and the amino acids encoded by more than one codon in the 78 genes of the chloroplast genome of Arnaucho chili pepper\u003c/p\u003e","description":"","filename":"floatimage3.png","url":"https://assets-eu.researchsquare.com/files/rs-5657151/v1/2f62897f9762dd036e9ff7dd.png"},{"id":72075561,"identity":"3ceab128-263c-44ed-93ec-5af8f2a027da","added_by":"auto","created_at":"2024-12-21 15:38:04","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":139109,"visible":true,"origin":"","legend":"\u003cp\u003ePhylogenetic reconstruction of the 14 chloroplast genome sequences of the Capsiceae tribe, including two genomes from an outgroup of Solanaceae. Colors highlight the clade within the \u003cem\u003eCapsicum \u003c/em\u003ephylogeny.\u003c/p\u003e","description":"","filename":"floatimage4.png","url":"https://assets-eu.researchsquare.com/files/rs-5657151/v1/f027518baa96217492b205b5.png"},{"id":72076111,"identity":"37fec4f4-d2e3-4892-a1b1-005b61af2514","added_by":"auto","created_at":"2024-12-21 15:46:04","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":65058,"visible":true,"origin":"","legend":"\u003cp\u003eEstimates of Evolutionary Divergence of cp Genomes in the 14 Sequences of the Capsiceae Tribe\u003c/p\u003e\n\u003cp\u003eAnalysis of repetitive sequences\u003c/p\u003e","description":"","filename":"floatimage5.png","url":"https://assets-eu.researchsquare.com/files/rs-5657151/v1/2b08d5c7c12a423087eda648.png"},{"id":72075583,"identity":"33010529-4ca2-4f50-b034-bb814b52bd36","added_by":"auto","created_at":"2024-12-21 15:38:06","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":34073,"visible":true,"origin":"","legend":"\u003cp\u003eFrequency of simple sequence repeats (SSR) and repetitive regions in the Arnaucho chili pepper chloroplast genome. (A) The number of distinct types of SSRs. (B) The total number of SSR motifs. (C) Distribution of repetitive regions\u003c/p\u003e","description":"","filename":"floatimage6.png","url":"https://assets-eu.researchsquare.com/files/rs-5657151/v1/05a67a15278c465263f95944.png"},{"id":72075563,"identity":"b46e9555-7f42-4dc7-923a-83ff3ff27896","added_by":"auto","created_at":"2024-12-21 15:38:05","extension":"png","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":82555,"visible":true,"origin":"","legend":"\u003cp\u003eComparison in the number of sequences repeated in 14 chloroplast genomes of the tribe capsiceae. The complementary repetitive sequences are represented in blue with a value of 0. The reverse repetitive sequences are represented in red with values ranging from 1 to 5, and none were found in \u003cem\u003eC. baccatum\u003c/em\u003eand \u003cem\u003eC. pubescens\u003c/em\u003e. The forward repetitive sequences, colored in yellow, range from 16 to 49. The tandem repetitive sequences, colored in light blue, were present in amounts of \u0026gt;= 50. Finally, the palindromic sequences, appearing in all Capsicum species, had a value \u0026gt; 150\u003c/p\u003e","description":"","filename":"floatimage7.png","url":"https://assets-eu.researchsquare.com/files/rs-5657151/v1/db5f87310e04b1448531c71f.png"},{"id":72075573,"identity":"c03e222a-7298-48f0-a89a-4460a112dc49","added_by":"auto","created_at":"2024-12-21 15:38:05","extension":"png","order_by":8,"title":"Figure 8","display":"","copyAsset":false,"role":"figure","size":241047,"visible":true,"origin":"","legend":"\u003cp\u003eComparative analysis of simple sequence repeats (SSRs). (A) Heatmap of the SSR motif frequencies identified in the Capsiceae tribe. (B) Total number of SSRs predicted in the Capsiceae tribe\u003c/p\u003e","description":"","filename":"floatimage8.png","url":"https://assets-eu.researchsquare.com/files/rs-5657151/v1/f725998a8858f87d077cc632.png"},{"id":72075579,"identity":"3bea8447-6d5c-434d-b6fa-a16423400814","added_by":"auto","created_at":"2024-12-21 15:38:05","extension":"png","order_by":9,"title":"Figure 9","display":"","copyAsset":false,"role":"figure","size":1203672,"visible":true,"origin":"","legend":"\u003cp\u003eComparison of boundaries between single-copy regions (LSC and SSC) and inverted repeat regions (IRB and IRA) in the genome of the\u003cem\u003e \u003c/em\u003eArnaucho chili pepper and 13 plastid genome sequences from the Capsiceae tribe. The genomes are represented as bars divided into each region. The boxes above and below the bars are representations of the genes. The arrows indicate the distance in base pairs (bp) from the ends of the genes to the nearest boundaries. As seen, all the boundaries present the same structure, except for the JSB boundary, where the gene \u003cem\u003eycf1\u003c/em\u003e is present in both the IRb and SSC regions in some genomes, while in others, it is only present in the IRb region, and in some cases, it is completely absent\u003c/p\u003e","description":"","filename":"floatimage9.png","url":"https://assets-eu.researchsquare.com/files/rs-5657151/v1/a40462c6267e3aebf18756d2.png"},{"id":72436912,"identity":"15381afe-cc8a-44ba-9776-6a7610359187","added_by":"auto","created_at":"2024-12-27 06:03:12","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":4067963,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5657151/v1/5397ed73-f0f5-4026-b83a-b2278421bc31.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Comparative analysis of complete chloroplast genome of the Peruvian landrace of Capsicum chinense, arnaucho chili pepper, and related species of the Capsiceae tribe","fulltext":[{"header":"Introduction","content":"\u003cp\u003eThe genus \u003cem\u003eCapsicum\u003c/em\u003e is the most important in the Solanaceae family. This genus comprises a total of 30 species, including sweet varieties like bell peppers and spicy ones like chili peppers. Both varieties come in various colors, such as red, yellow, green, orange, and, in some cases, purple. They also display heart-shaped or bell-like forms (Antonio et al. \u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e2018\u003c/span\u003e \u0026amp; Dong et al. 2013). It is estimated that \u003cem\u003eCapsicum\u003c/em\u003e appeared in human history around 7500 B.C. and began to be cultivated between 5200 and 3400 B.C. The use of these fruits was not only for their flavor but also for ethnobotanical purposes, such as medicinal preparations, treatment of wounds, stomach aches, fever, as an anti-infective agent, and for treating hypertension when chewed (Florencia el al. 2022). This genus includes domesticated and wild species. Fossil studies of \u003cem\u003eCapsicum\u003c/em\u003e spp. starch found seven sites dating back 6,000 years, ranging from the Bahamas to southern Peru (Perry et al. 2007). Currently, the production, use, and domestication of \u003cem\u003eCapsicum\u003c/em\u003e have spread worldwide. Since the 1650s, when it was introduced by the Spanish, it has continued to the present day, leading to selective breeding associated with different environmental conditions (Hernandez et al. \u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e2022\u003c/span\u003e \u0026amp; Aguilar-Melendez et al 2009).\u003c/p\u003e \u003cp\u003eThese fruits are an important ingredient in the daily diet of millions of people, used in various dishes as they are a great source of vitamin C and antioxidants. Additionally, Peru is a country that harbors the greatest biological diversity of these fruits in South America, with a potential source of genes with traits of interest for germplasm conservation (Minguez-Mosquera, 1992; Meckelmann, 2013 \u0026amp; Ibiza et al, \u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e2012\u003c/span\u003e). Peru has various varieties, such as \u0026ldquo;mochero\u0026rdquo; chili pepper, \u0026ldquo;panca\u0026rdquo; chili pepper, \u0026ldquo;dulce\u0026rdquo; chili pepper, and \u0026ldquo;arnaucho\u0026rdquo; or \u0026ldquo;supano\u0026rdquo; chili pepper (Lopez et al. 2020). The arnaucho chili pepper (ACP) is a cultivar native to the Supe Valley in the province of Barranca, about 200 km north of Lima. This fruit is sold in markets in the provinces of Barranca, Huaura, and the district of Huacho. It is identified by its purple color and triangular or globular shape (Arbizu et al. \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2022\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eNext-generation sequencing (NGS) studies have accelerated the generation of high-throughput data and genomic information, including the identification of DNA markers such as single nucleotide polymorphisms, among others. Moreover, the reduction in genome sequencing costs allows for the discovery of thousands of markers in a single step. Thanks to this technology, it is gaining widespread acceptance in the field of crop breeding (Ray, \u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e2014\u003c/span\u003e). With this technology, several studies have been conducted on the sequencing of \u003cem\u003eCapsicum\u003c/em\u003e, such as the study by Sebastian et al. (2024), which demonstrates that the most domesticated species of \u003cem\u003eC. annuum\u003c/em\u003e exhibited a higher degree of divergence, very similar to their divergent genotypes, compared to their counterparts. Another study of the chloroplast genome of \u003cem\u003eC. chinense\u003c/em\u003e revealed that the species was more closely related to \u003cem\u003eC. annuum\u003c/em\u003e var. \u003cem\u003eglabriusculum\u003c/em\u003e (Paar, et al. 2016). Additionally, the study of \u003cem\u003eC. eximium\u003c/em\u003e, native to southern Bolivia, identified 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Of all these genes, 21 are duplicated in the inverted region, and in the phylogenetic analysis, it was grouped within the \u003cem\u003eCapsicum\u003c/em\u003e clade. (Sebastian, et al. 2019). On the other hand, studies of the draft genome of \u003cem\u003eC. chinense\u003c/em\u003e using Illumina HiSeq 2500 sequencing technology identified 71.96% of the repetitive DNA in the assembled genome, with a lower number of SSRs in the genome compared to other \u003cem\u003eCapsicum\u003c/em\u003e species, reporting the first draft genome of the ACP (Estrada, et al. \u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e2024\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eBioinformatics tools today are useful for understanding the functional and structural analysis of genomes, transcriptomes, proteomes, and more. Due to the use of these tools, we have been able to gain a deeper understanding of biomedical and plant sciences. They have become essential for predictive analysis in the era of big data, having a significant impact on research (Mansoor, et al. \u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e2024\u003c/span\u003e). The advent of high-throughput sequencing tools, cutting-edge biotechnological techniques, and bioinformatics analyses has led to greater ease in characterizing plant traits (Roychowdhury, et al. \u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e2023\u003c/span\u003e). There is a large volume of accumulated data, both in NCBI and EMBL, and therefore, the management and extraction of this data have become of great interest. This information is manageable for conducting further studies, utilizing algorithms based on mathematical and statistical models to handle these biological data (Li, et al. \u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e2013\u003c/span\u003e). Bioinformatics and in silico analysis allowed us to understand the processes occurring at the cellular level, as it facilitates the identification of genes. This enables the enhancement of precision agriculture, optimizing natural resources, improving the efficiency of the production process, and reducing costs (Angel Gaviria, 2023).\u003c/p\u003e \u003cp\u003eStudies conducted by Arbizu et al. (\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2022\u003c/span\u003e) presented the first complete chloroplast genome (cp) of this local cultivar of Peruvian chili pepper (arnaucho) using high-throughput sequencing technology, providing us with a phylogenetic result of this species with its closest relative, \u003cem\u003eC. galapagoense\u003c/em\u003e. In this work, we continue the studies on the ACP, revealing its structure, divergence, and evolution, using bioinformatics tools to gain a deeper understanding of the chloroplast genome of this species, which is endemic to Peru and belongs to the province of Barranca.\u003c/p\u003e"},{"header":"Materials and methods","content":"\u003cp\u003eSequence annotation and comparison of chloroplast genomes\u003c/p\u003e\n\u003cp\u003eA total of twelve complete chloroplast genome sequences were retrieved from the Capsiceae plant tribe via the Organelle Genome Resources of NCBI (accessed on September 29, 2024), with the following GenBank accession numbers: MZ379791.1 (\u003cem\u003eC. chinense\u003c/em\u003e), NC_018552.1 (\u003cem\u003eC. annuum\u003c/em\u003e), KX913219.1 (\u003cem\u003eC. tovarii\u003c/em\u003e), KR078312.1 (\u003cem\u003eC. frutescens\u003c/em\u003e), NC_033524.1 (\u003cem\u003eC. galapagoense\u003c/em\u003e), KX013217.1 (\u003cem\u003eC. chinense\u003c/em\u003e), KU041709.1 (\u003cem\u003eC. chinense\u003c/em\u003e), MH559321.1 (\u003cem\u003eC. chinense\u003c/em\u003e), NC_030543.1 (\u003cem\u003eC. chinense\u003c/em\u003e), KX913220.1 (\u003cem\u003eC. eximium\u003c/em\u003e), MH559320.1 (\u003cem\u003eC. baccatum\u003c/em\u003e), NC_039694.1 (\u003cem\u003eC. pubescens\u003c/em\u003e), NC_026551.1 (\u003cem\u003eC. lycianthoides\u003c/em\u003e), and NC_033525.1 (\u003cem\u003eC. chapecoense\u003c/em\u003e). The Geseq program (https://chlorobox.mpimp-golm.mpg.de/geseq.html Frazer, 2004) was used to annotate and locate the genes of all cp genomes from the Capsiceae tribe, with default options selected (CDS, tRNA, rRNA, IR, and the interspaced \u003cem\u003erps12\u003c/em\u003e gene) (Tillich et al., 2017). Additionally, tRNA-scan v2.0 (Chan and Lowe, 2019), available on the same server, was used as a secondary tRNA annotator. The GC content calculator provided by JaimeMcGowan (2024) was also employed via its web service (available online: https://jamiemcgowan.ie/bioinf/gc_content.html) to analyze the GC content in the 12 cp genomes (Table 1). Furthermore, we used the annotated cp genome of \u003cem\u003eC. chinense\u003c/em\u003e (MZ379791.1) as the reference genome to compare with the other cp genomes of the Capsiceae plant tribe. The VISTA program (https://genome.lbl.gov/vista/index.shtml, accessed on September 29, 2024) was employed in Shuffle-LAGAN mode (Brudno et al., 2003) to analyze the sequence similarity within the Capsiceae tribe. Finally, we visualized the cp genome architecture of the ACP using program OGDRAW v1.3.1 (Greiner, 2019). A prior analysis of the genetic content was conducted to identify the functions of its chloroplast genome (Table 2)\u003c/p\u003e\n\u003cp\u003eCodon usage of protein-coding sequences of \u003cem\u003eC. chinense\u0026nbsp;\u003c/em\u003e\u003c/p\u003e\n\u003cp\u003eFor this analysis, the 86 protein-coding genes of \u003cem\u003eC. chinense\u003c/em\u003e (MZ379791) were used. The number of codons (Nc) and the relative synonymous codon usage (RSCU) were calculated using the MEGA11 program (Tamura, 2021) and the RSCU calculator available via JaimeMcGowan\u0026apos;s web service (available online: https://jamiemcgowan.ie/bioinf/rscu.html, McGowan, 2024). Subsequently, codon usage and the relative synonymous codon usage (RSCU) values were manually analyzed by comparing the results from both programs. The Nc provides an intuitively meaningful measure of codon preference within a gene (Wright, 1990). Additionally, an RSCU value greater than 1.00 indicates a lack of bias, while a value less than 1.00 is considered indicative of bias, as described by the research of Sharp and Li (1987). The result was visualized using R v4.4.1 (R Core Team, 2024) with the ggplot2 and tidyr packages.\u003c/p\u003e\n\u003cp\u003ePhylogenomic analysis and pairwise distances\u003c/p\u003e\n\u003cp\u003eTo reveal the evolutionary relationship of the Capsiceae tribe with a total of fifteen annotated complete cp genomes, a sequence alignment of the 14 species was performed. The genomes of the Capsiceae tribe include two additional species from the Solanaceae family. In this case, we used \u003cem\u003eSolanum lycopersicum\u003c/em\u003e NC_007898 and \u003cem\u003ePhysalis peruviana\u003c/em\u003e MH019242 as outgroup. The sequences were retrieved from the GenBank NCBI database (https://www.ncbi.nlm.nih.gov/genbank/) and aligned using the MAFFT v7 web server (Katoh and Stanley, 2013; https://mafft.cbrc.jp/alignment/server/index.html) with default options. The alignment was then manually refined using Aliview v1.28 (Larsson, 2014). After the genomes were previously aligned and refined, a nucleotide substitution analysis was performed. In this case, the best-fitting model was TVM+I+G, determined using the Akaike information criterion (AIC) by the JModelTest v2.1.10 program (https://github.com/ddarriba/jmodeltest2). The phylogenetic reconstruction was performed using the Maximum Likelihood (ML) method using MEGA11 (Tamura, 2021) with 1000 Bootstrap repetitions, employing the Kimura 2 model and complete deletion. Additionally, the tree was visualized using the iTol v6 tool (https://itol.embl.de/, Letunic, 2024). Additionally, an alignment of only the Capsiceae tribe was performed to study the pairwise distances of the 14 cp genomes. We used MEGA11 with 1000 Bootstrap repetitions, a nucleotide substitution model, the p-distance method, and complete deletion of missing data. These results were visualized in a raincloud plot using R, employing the tidyr, ggplot2, and ggrain packages.\u003c/p\u003e\n\u003cp\u003eIdentification of repetitive sequences and SSR analysis\u003c/p\u003e\n\u003cp\u003eIn this analysis of repetitive sequences, we used various programs, including REPuter v2.7.4 (available online: https://bibiserv.cebitec.uni-bielefeld.de/reputer/, Kurtz et al., 2001), to identify repetitive sequences (including forward, reverse, and complementary repeat sequences). For the identification of these repetitive sequences, the following parameters were used: a minimum repeat size of 30 bp and a Hamming distance of 3 (with 90% or more sequence identity). Additionally, for palindromic sequences, the RepEX web server (available online: http://bioserver2.physics.iisc.ac.in/RepEx/query.html, Michael et al., 2019) was used with the following input parameters: repeat type set to \u0026quot;Palindrome\u0026quot; and a repeat length of more than 10. Additionally, for the detection of tandem repeats, the web tool (https://tandem.bu.edu/trf/home, Benson, 1999) was used with the default parameters in its advanced option. Finally, simple sequence repeats (SSR) or microsatellites in the genomes were examined using the MISA web tool (https://webblast.ipk-gatersleben.de/misa/, Bier et al., 2017) with SSR search parameters set for repeat lengths with a minimum threshold of 10, 5, 4, 3, 3, and 3 repeat units for mono-, di-, tri-, tetra-, penta-, and hexanucleotides, respectively. The results were visualized in bar charts, pie charts, balloon plots, and heatmaps using R v4.4.1 with the tidyr, ggplot2, ggpubr, pheatmap, and RColorBrewer packages.\u003c/p\u003e\n\u003cp\u003eAnalysis of shifts at the boundaries between the single-copy regions (LSC and SSC) and the inverted repeats (IRA and IRB)\u003c/p\u003e\n\u003cp\u003eA comparison of the positions of the boundaries between the single-copy regions (LSC and SSC) and the inverted regions (IRA and IRB) was made across the 14 species of the Capsiceae tribe. These boundaries were named JLB (boundary between LSC-IRB), JSB (boundary between IRB-SSC), JSA (boundary between SSC-IRA), and JLA (boundary between IRA-LSC). For the positions of the boundaries, the distance between these and the nearest genes to these regions or located on their boundary was calculated using the online program (https://irscope.shinyapps.io/irapp/, Amiryousefi, 2018).\u003c/p\u003e"},{"header":"Results","content":"\u003cp\u003eSequence annotation and comparison of chloroplast genomes\u003c/p\u003e \u003cp\u003eThrough a search in the NCBI database, complete cp genome sequences of 14 species from the \u003cem\u003eCapsicum\u003c/em\u003e genus were obtained for subsequent comparative analysis and prior genome annotation. The Geseq program was used to obtain the structural features and genetic content of the cp genome of the ACP, as shown in Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e. The results obtained with the other cp genomes of the \u003cem\u003eCapsicum\u003c/em\u003e genus showed a four-part structure, consisting of an LSC region, an SSC region, and two IRs. In the IR regions, each of which ranges from 25,624 bp (\u003cem\u003eC. lycianthoides\u003c/em\u003e) to 25,910 bp (\u003cem\u003eC. baccatum\u003c/em\u003e). The IRs were separated by an LSC region, which ranged from 87,688 bp (\u003cem\u003eC. pubescens\u003c/em\u003e) to 86,813 bp (\u003cem\u003eC. lycianthoides\u003c/em\u003e), and an SSC region, which ranged from 17,849 bp (\u003cem\u003eC. annuum\u003c/em\u003e) to 18,522 bp (C. lycianthoides). The GC content in the 12 cp genomes of the Capsicum tribe was similar, with an average of 37%. Additionally, the size of the cp genomes in the 14 genomes of the Capsiceae tribe ranged from 156,583 bp in \u003cem\u003eC. lycianthoides\u003c/em\u003e to 157,390 bp in \u003cem\u003eC. pubescens\u003c/em\u003e (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). The ACP had a genome size of 156,931 bp, and the average genome size for the Capsiceae tribe was a total of 156,741 bp. The genome size of the Capsicum tribe, specifically of Arnaucho chili pepper, is similar to the first genome studied in this tribe, as well as the cp genomes used in this study, approximately 156 kb, except for \u003cem\u003eC. baccatum\u003c/em\u003e and \u003cem\u003eC. pubescens\u003c/em\u003e, which both had 157 kb (Raveendar et al., 2024).\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\u003eComparaci\u0026oacute;n de datos de secuencias de los genomas completos de cloroplastos de la tribu Capsiceae\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"11\"\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=\"char\" char=\".\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c8\" colnum=\"8\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c9\" colnum=\"9\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c10\" colnum=\"10\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c11\" colnum=\"11\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eGenbank Number\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eScientific name\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGenome size bp\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eLSC regi\u0026oacute;n (bp)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eIRs regi\u0026oacute;n (bp)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003eSSC regi\u0026oacute;n (bp)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003eTotal genes\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c8\"\u003e \u003cp\u003eCDS\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c9\"\u003e \u003cp\u003eGC%\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c10\"\u003e \u003cp\u003erRNA\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c11\"\u003e \u003cp\u003etRNA\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNC_018552\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eC. annuun\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e156,781\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e87,366\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e25,783\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e17,849\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e132\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e87\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e37,37\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c10\"\u003e \u003cp\u003e8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c11\"\u003e \u003cp\u003e37\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eKX913219\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eC. \u003cem\u003etovarii\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e156,816\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e87,379\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e25,792\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e17,853\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e132\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e87\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e37,72\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c10\"\u003e \u003cp\u003e8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c11\"\u003e \u003cp\u003e37\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eKR078312\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eC. frutescens\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e156,817\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e87,380\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e25,792\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e17,853\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e131\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e87\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e37,72\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c10\"\u003e \u003cp\u003e8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c11\"\u003e \u003cp\u003e37\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMZ379791\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eC. chinense\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e156,931\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e87,325\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e25,847\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e17,912\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e133\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e86\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e37,71\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c10\"\u003e \u003cp\u003e8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c11\"\u003e \u003cp\u003e37\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNC_033524\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eC. galapagoense\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e156,959\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e87,347\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e25,847\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e17,918\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e132\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e87\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e37,71\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c10\"\u003e \u003cp\u003e8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c11\"\u003e \u003cp\u003e37\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eKX913217\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eC. chinense\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e156,936\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e87,330\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e25,847\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e17,912\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e132\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e87\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e37,72\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c10\"\u003e \u003cp\u003e8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c11\"\u003e \u003cp\u003e37\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eKU041709\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eC. chinense\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e156,807\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e87,290\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e25,803\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e17,911\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e113\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e79\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e37,70\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c10\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c11\"\u003e \u003cp\u003e30\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMH559321\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eC. chinense\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e156,858\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e87,288\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e\u003cem\u003e25,855\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e17,860\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e132\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e86\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e37,43\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c10\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c11\"\u003e \u003cp\u003e30\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNC_030543\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eC. chinense\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e156,807\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e87,290\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e\u003cem\u003e25,803\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e17,911\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e113\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e79\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e37,73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c10\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c11\"\u003e \u003cp\u003e30\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eKX913220\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eC. eximium\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e156,947\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e87,341\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e25,847\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e17,912\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e132\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e87\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e37,72\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c10\"\u003e \u003cp\u003e8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c11\"\u003e \u003cp\u003e37\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMH559320\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eC. baccatum\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e157,144\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e87,351\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e25,910\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e17,973\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e113\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e79\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e37,66\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c10\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c11\"\u003e \u003cp\u003e39\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNC_039694\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eC. pubescens\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e157,390\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e87,688\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e25,887\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e17,928\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e131\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e86\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e37,69\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c10\"\u003e \u003cp\u003e8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c11\"\u003e \u003cp\u003e37\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNC_026551\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eC. lycianthoides\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e156,583\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e86,813\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e25,624\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e18,522\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e127\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e83\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e37,76\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c10\"\u003e \u003cp\u003e8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c11\"\u003e \u003cp\u003e36\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNC_033525\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eC. chacoense\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e156,959\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e87,379\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e25,859\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e17,898\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e132\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e87\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c9\"\u003e \u003cp\u003e37,68\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c10\"\u003e \u003cp\u003e8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c11\"\u003e \u003cp\u003e37\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 \u003c/p\u003e \u003cp\u003eThe cp genome of the ACP pepper was annotated to predict a total of 133 genes, including 86 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes. Among the annotated genes, a total of 11 large ribosomal proteins (\u003cem\u003erpl\u003c/em\u003e), 14 small ribosomal proteins (\u003cem\u003erps\u003c/em\u003e), 8 different rRNA genes, 4 DNA-dependent RNA polymerases (\u003cem\u003erpo\u003c/em\u003e), 38 different tRNA genes (\u003cem\u003etrn\u003c/em\u003e), 5 genes encoding the photosystem I protein complex (\u003cem\u003epsa\u003c/em\u003e), 14 genes encoding the photosystem II protein complex (\u003cem\u003epsb\u003c/em\u003e), 6 genes encoding the cytochrome b6/f complex (\u003cem\u003epet\u003c/em\u003e), 12 genes encoding NADH dehydrogenase proteins (\u003cem\u003endh\u003c/em\u003e), 6 genes encoding ATP synthase proteins (\u003cem\u003eatp\u003c/em\u003e), the ATP-dependent Clp protease proteolytic subunit (\u003cem\u003eclpP\u003c/em\u003e), the large subunit of ribulose-1,5-bisphosphate carboxylase (\u003cem\u003erbcL\u003c/em\u003e), maturase K (\u003cem\u003ematK\u003c/em\u003e), genes encoding cytochrome C biogenesis proteins (\u003cem\u003eccsA\u003c/em\u003e), the beta subunit of acetyl-CoA carboxylase (\u003cem\u003eaccD\u003c/em\u003e), the membrane envelope protein (\u003cem\u003ecemA\u003c/em\u003e), 4 ycf1 genes (\u003cem\u003eycf\u003c/em\u003e), the gene encoding translation initiation factor 1 (\u003cem\u003einfA\u003c/em\u003e), and a gene of unknown function (\u003cem\u003epafI\u003c/em\u003e) were found. In addition, the annotation results revealed that 24 of these genes contain introns (\u003cem\u003endhB\u003c/em\u003e, \u003cem\u003epetB\u003c/em\u003e, \u003cem\u003epetD\u003c/em\u003e, \u003cem\u003erpl2\u003c/em\u003e, \u003cem\u003erps12\u003c/em\u003e, \u003cem\u003etrnA-UGC\u003c/em\u003e, \u003cem\u003etrnG-UCC\u003c/em\u003e, \u003cem\u003etrnI-GAU\u003c/em\u003e, \u003cem\u003etrnL-UAA\u003c/em\u003e, \u003cem\u003eatpF\u003c/em\u003e, \u003cem\u003eclpP1\u003c/em\u003e, \u003cem\u003endhA\u003c/em\u003e, \u003cem\u003endhB\u003c/em\u003e, \u003cem\u003erpl16\u003c/em\u003e, \u003cem\u003erpl2\u003c/em\u003e, \u003cem\u003erpoC1\u003c/em\u003e, \u003cem\u003erps12\u003c/em\u003e-fragment, \u003cem\u003erps12\u003c/em\u003e, \u003cem\u003erps16\u003c/em\u003e, \u003cem\u003etrnA\u003c/em\u003e-UGC, \u003cem\u003etrnI\u003c/em\u003e-GAU, \u003cem\u003etrnK\u003c/em\u003e-UUU, \u003cem\u003etrnV\u003c/em\u003e-UAC, \u003cem\u003epafI\u003c/em\u003e), and four of them contain two introns (\u003cem\u003epafI\u003c/em\u003e, \u003cem\u003eclpP1\u003c/em\u003e, and the two \u003cem\u003erps12\u003c/em\u003e structures). The majority of the genes are expressed as a single copy, with the exception of 18 genes that were duplicated in the IR regions.\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\u003eGenetic content and its functions of the chloroplast genome of \u003cem\u003eC. chinense\u003c/em\u003e Arnaucho chili pepper.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"3\"\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 \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCategory\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eGroup of genes\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eName of genes\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLarge subunit of ribosomal proteins\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003erpl2\u003c/em\u003e\u003csup\u003e\u003cem\u003ea\u003c/em\u003e\u003c/sup\u003e, \u003cem\u003erpl4, rpl16\u003c/em\u003e\u003csup\u003e\u003cem\u003ea\u003c/em\u003e\u003c/sup\u003e, \u003cem\u003erpl20, rpl22, rpl23, rpl32, rpl33 rpl36\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePeque\u0026ntilde;o subconjunto de prote\u0026iacute;nas ribos\u0026oacute;micas.\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003erps2, rps3, rps4, rps7, rps8, rps11, rps12\u003c/em\u003e\u003csup\u003e\u003cem\u003ea\u003c/em\u003e\u003c/sup\u003e, \u003cem\u003erps14, rps15, rps16, rps18, rps19\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eARN polimerasa dependiente de ADN\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003erpoA, rpoB, rpoC\u003c/em\u003e\u003csup\u003e\u003cem\u003ea\u003c/em\u003e\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSef-replication\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eRibosomal RNA genes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003errn4.5, rrn5, rrn16, rrn23\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003etrnC-GCA, trnG-GCC, trnG-UCC\u003c/em\u003e\u003csup\u003e\u003cem\u003ea\u003c/em\u003e\u003c/sup\u003e, \u003cem\u003etrnG-UCC, trnL-CAA, trnL-UAA, trnL-UAG, trnM-CAU, trnN-GUU\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eTransfer RNA genes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003etrnA-UGC, trnD-GUC, trnE-UUC, trnH-GUG, trnI-CAU, trnI-GAU, trnK-UUU, trnR-ACG, trnR-UCU\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003etrnS-GGA,trnT-GGU, trnV-GAC,trnL-CAA,, trnP-UGG\u003c/em\u003e,\u003c/p\u003e \u003cp\u003e\u003cem\u003etrnQ-UUG, trnR-ACG, trnS-GCU, trnS-UGA, trnT-UGU, trnV-GAC, trnV-UAC\u003c/em\u003e\u003csup\u003e\u003cem\u003ea\u003c/em\u003e\u003c/sup\u003e, \u003cem\u003etrnW-CCA, trnY-GUA, trnfM-CAU\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePhotosystem I\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003epsaA, psaB, psaC, psaI, psaJ\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePhotosystem II\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003epsbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbT, psbZ\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eGenes for photosynthesis\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eRUBISCO\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003erbcL\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eSubunits of ATPsynthase\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003eatpA, atpB, atpE, atpF\u003c/em\u003e\u003csup\u003e\u003cem\u003ea\u003c/em\u003e\u003c/sup\u003e, \u003cem\u003eatpH, atpI\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eSubunit of NADH-dehydrogenase\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003endhA\u003c/em\u003e\u003csup\u003e\u003cem\u003ea\u003c/em\u003e\u003c/sup\u003e, \u003cem\u003endhB\u003c/em\u003e\u003csup\u003e\u003cem\u003ea\u003c/em\u003e\u003c/sup\u003e,\u003cem\u003endhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCytochrome b/f complex\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003epetA, petB\u003c/em\u003e\u003csup\u003e\u003cem\u003ea\u003c/em\u003e\u003c/sup\u003e, \u003cem\u003epetD\u003c/em\u003e\u003csup\u003e\u003cem\u003ea\u003c/em\u003e\u003c/sup\u003e, \u003cem\u003epetG, petL, petN\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eProtease\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003eclpP\u003c/em\u003e\u003csup\u003e\u003cem\u003eb\u003c/em\u003e\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMutrase\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003ematK\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eOther genes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eEnvelope membrane protein\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003ecemA\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eTranslation initiation factor\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003einfA\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eC-type cytochrome synthesis gene\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003eccsA\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eSubunit of Acetyl-CoA-carboxylase\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003eaccD\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eGenes of unknown function\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eConserved hypothetical chlroplast\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003eycf1, ycf2\u003c/em\u003e,\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003epafI\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\u003eComparative analysis of the cp genome sequences of the \u003cem\u003eCapsiceae\u003c/em\u003e tribe\u003c/p\u003e \u003cp\u003eFinally, the results from the mVista web server provided the information needed to assess the divergence among the 14 cp genome sequences in the Capsiceae tribe, using ACP as a reference. It was observed that the highest divergence was found in \u003cem\u003eC. lycianthoides\u003c/em\u003e compared to our reference genome. These results provided information that the sequence variation was higher in the non-coding regions across all genomes, with lower variation observed in the coding regions of the genes. However, \u003cem\u003eC. lycianthoides\u003c/em\u003e exhibited variation in more than one coding gene, including the genes \u003cem\u003eaccD\u003c/em\u003e, \u003cem\u003erpl20\u003c/em\u003e, \u003cem\u003erps12\u003c/em\u003e, \u003cem\u003eclpP\u003c/em\u003e, \u003cem\u003eycf2\u003c/em\u003e, \u003cem\u003endhF\u003c/em\u003e, \u003cem\u003endhA\u003c/em\u003e, \u003cem\u003eycf1\u003c/em\u003e, and \u003cem\u003erpl2\u003c/em\u003e. In addition, the four \u003cem\u003eC. chinense\u003c/em\u003e species' cp genomes showed significant variation in the \u003cem\u003eaccD\u003c/em\u003e gene, along with \u003cem\u003eC. eximium\u003c/em\u003e, \u003cem\u003eC. pubescens\u003c/em\u003e and \u003cem\u003eC. baccatum\u003c/em\u003e which also exhibited variation in the same gene. On the other hand, the species \u003cem\u003eC. galapagoense\u003c/em\u003e showed significant variation in the \u003cem\u003erpl20\u003c/em\u003e gene, along with \u003cem\u003eC. annuum\u003c/em\u003e, \u003cem\u003eC. baccatum\u003c/em\u003e, \u003cem\u003eC. pubescens\u003c/em\u003e, \u003cem\u003eC. lycianthoides\u003c/em\u003e and \u003cem\u003eC. chacoense\u003c/em\u003e. These results justify further research to better determine and understand the clade of \u003cem\u003eC. chinense\u003c/em\u003e, as it is unclear whether this fragment was altered in its cp genome due to a mutation caused by environmental factors (since the species are found in different habitats), or if it was simply a result of incomplete genome assembly.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eCodon usage analysis in the Arnaucho chili pepper\u003c/p\u003e \u003cp\u003eFor this codon analysis, the software Mega11 was used, and the number of times each codon is repeated and the relative synonymous codon usage (RSCU) were calculated from the protein-coding sequences (CDS). The most used codon in the \u003cem\u003eC. chinense\u003c/em\u003e genome was AAA, which codes for lysine (2140), followed by UUU, which codes for phenylalanine (2118), and lastly AUU, which codes for isoleucine (1864). In the stop codons of \u003cem\u003eC. chinense\u003c/em\u003e, the most used codons were UAA (1136) and UGA (982). Finally, the least present amino acid codons in the \u003cem\u003eC. chinense\u003c/em\u003e genome were GGG, which codes for glycine (578), and ACC, which codes for threonine (576).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003ePhylogenetic analysis and pairwise distance\u003c/p\u003e \u003cp\u003eThe results obtained from the ML phylogenetic analysis showed that different cultivars of \u003cem\u003eC. chinense\u003c/em\u003e grouped with others of the same species, forming monophyletic groups. It can also be observed that there is a genetic relationship between our \u003cem\u003eC. chinense\u003c/em\u003e and \u003cem\u003eC. galapagoense\u003c/em\u003e, demonstrating that the ACP is a sister species to \u003cem\u003eC. galapagoense\u003c/em\u003e, a result similar to the findings of Arbizu et al. (\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). Additionally, the results obtained at each node were very similar to the recent studies conducted by Sebasti\u0026aacute;n et al. (2024), showing that the \u003cem\u003eC. chinense\u003c/em\u003e clade is related to \u003cem\u003eC. galapagoense\u003c/em\u003e.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eIn the pairwise distance results of the 14 cp genomes using the p-distance algorithm, the ACP was compared as the reference with the other genomes of the Capsiceae tribe. As expected, the highest average distance was found between Arnaucho chili pepper and \u003cem\u003eC. lycianthoides\u003c/em\u003e (0.00021523), while the lowest was between \u003cem\u003eC. chinense\u003c/em\u003e and \u003cem\u003eC. galapagoense\u003c/em\u003e (0.00002733). Additionally, the following cp genomes were observed: \u003cem\u003eC. eximium\u003c/em\u003e with a distance of 0.00003181, and the other four \u003cem\u003eC. chinense\u003c/em\u003e genomes with average distances of 0.00003422, 0.00003551, and two with 0.00003822. Thanks to these results, the distributions and densities between the distances within the Capsiceae tribe can be observed. Similarly, as seen in the phylogenetic results, the five \u003cem\u003eC. chinense\u003c/em\u003e genomes, \u003cem\u003eC. galapagoense\u003c/em\u003e, and \u003cem\u003eC. eximium\u003c/em\u003e exhibit a similar distribution and probability density trend, in contrast to the other plastid genomes of their tribe.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eAnalysis of repetitive sequences\u003c/p\u003e \u003cp\u003eThe analysis detected different types of repetitive sequences within the genome of the Arnaucho chili pepper, as well as across the entire tribe, consisting of 14 cp genome sequences. These simple sequence repeats (SSRs) are tandemly repeated DNA of 1 to 6 base pairs in length, commonly used as molecular markers to identify species, revealing gene rearrangements and losses during their evolution (Nashima et al. \u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e2020\u003c/span\u003e; Mcdonald et al. \u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e2011\u003c/span\u003e). The results obtained in the ACP genome predicted a total of 36 SSRs, consisting of 33 mononucleotides, 1 trinucleotide, and 2 pentanucleotides, revealing a significantly different pattern compared to all fourteen cp genomes of the Capsicum tribe, including the cp genomes of the four \u003cem\u003eC. chinense\u003c/em\u003e and \u003cem\u003eC. galapagoense\u003c/em\u003e, which belong to the same clade (Raveendar et al. \u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e2015\u003c/span\u003e). In addition, Reputter, RepEX, and Tandem Repeats Finder characterized a total of 172 palindromic sequences, 41 forward sequences, 3 reverse sequences, 0 complementary sequences, and 55 tandem repeats, maintaining similarity with the other genomes in these repetitive sequences (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e). Additionally, the other repetitive sequences from the 14 chloroplast genomes were also characterized and subsequently compared in a balloon plot. These results can be seen in (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e07\u003c/span\u003e) and (Table\u0026nbsp;\u003cspan refid=\"Tab3\" class=\"InternalRef\"\u003e03\u003c/span\u003e).\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\u003eThe different types of repetitive sequences and SSRs in the 14 chloroplast genomes of the Capsiceae tribe\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"7\"\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=\"char\" char=\".\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eScientific name\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eGenbank Number\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003ePalindromos\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eForward\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eReverse\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003eTandem\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003eSSR\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eC. annun\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eNC_018552\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e175\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e44\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e62\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e44\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eC. tovarii\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eKX913219\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e175\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e39\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e62\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e50\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eC. frutescens\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eKR078312\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e175\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e29\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e62\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e50\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eC. chinense\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMZ379791\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e172\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e41\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e55\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e36\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eC. galapogense\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eNC_033524\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e172\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e39\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e59\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e50\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eC. chinense\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eKX913217\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e172\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e39\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e57\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e50\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eC. chinense\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eKU041709\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e163\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e32\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e57\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e49\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eC. eximium\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eKX913220\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e172\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e45\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e59\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e50\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eC. baccanturn\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMH559320\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e174\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e49\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e64\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e50\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eC. pubescens\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eNC_039694\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e173\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e49\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e66\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e52\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eC. lycianthoides\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eNC_026551\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e181\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e31\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e50\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e54\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eC. chacoense\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eNC_033525\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e178\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e41\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e60\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e55\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eC. chinense\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMH559321\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e172\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e33\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e57\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e50\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eC. chinense\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eNC_030543\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e172\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e57\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e51\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 \u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eIn the detection of simple sequence repeats (SSRs), a heatmap was created for the comparative analysis of SSR motif frequencies. There was a higher frequency of the thymine (T) motif in the Capsiceae tribe, ranging from 14 in \u003cem\u003eC. annuum\u003c/em\u003e to 26 in \u003cem\u003eC. lycianthoides\u003c/em\u003e, followed by the adenine (A) motif. It was noted that its frequency was identical across all genomes, except for \u003cem\u003eC. annuum\u003c/em\u003e, which had a total of 11, and \u003cem\u003eC. lycianthoides\u003c/em\u003e, which had 14. This result can also be observed with the TTA (trimer) motifs, where the cp genomes of \u003cem\u003eC. baccatum\u003c/em\u003e and \u003cem\u003eC. lycianthoides\u003c/em\u003e do not show these motifs, while the others all exhibited the same frequency of 1. Studies on SSR in plants indicate that trimers are the most frequent in most groups of higher plants, such as monocots and dicots. This is consistent with the results described for this tribe, confirming studies outlined by Victoria et al. (\u003cspan citationid=\"CR61\" class=\"CitationRef\"\u003e2011\u003c/span\u003e). In addition, the frequency of motifs such as AT, CT, TA, TTC, AAAC, AAAT, AATT, ATAA, CTAT, TTTG, TTATT, TTTTA, TATAG, TTCATT, TAAT, G, and TTTTAA in the identified SSRs was entirely different, where all exhibited varying frequencies, except for the ACP, as previously described in the analysis. In the predicted number of SSRs, Arnaucho chili pepper showed the lowest amount of SSRs according to MISAweb, compared to \u003cem\u003eC. galapagoense\u003c/em\u003e and the other two \u003cem\u003eC. chinense\u003c/em\u003e individuals, which exhibited similar quantities ranging from 51 to 49 SSRs (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eComparative analysis in the binding regions\u003c/p\u003e \u003cp\u003eThe chloroplast genomes of the Capsiceae tribe showed a magnitude of displacement between the unique copy regions and the inverted repeats, considering their position relative to the nearest genes (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e). These boundaries were named JLB (LSC-IRB), JSB (IRB-SSC), JSA (SSC-IRA), and JLA (IRA-LSC) (Caycho et al. \u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e2023\u003c/span\u003e). The length of the IR in the Capsiceae tribe varies from 156,583 bp to 157,390 bp across the 14 plastid genomes. Our Arnaucho chili pepper possesses a length of 156,931 bp, similar to \u003cem\u003eC. galapagoense\u003c/em\u003e with 156,959 bp and \u003cem\u003eC. chinense\u003c/em\u003e (KU041709) with 156,936 bp, respectively. This indicates that the IR expansion was almost identical, with no significant expansion observed among these plastid genomes. It was very different with the other three \u003cem\u003eC. chinense\u003c/em\u003e genomes, which have 156,858 bp (MH559321) and two with 156,807 bp (KU041709 and NC_030543), where there were apparently only two small contractions of 124 bp and 73 bp. These expansions and contractions of the IR boundary contribute to the size and variations of the plastid genomes (Zhang et al., \u003cspan citationid=\"CR67\" class=\"CitationRef\"\u003e2023\u003c/span\u003e). Within the 14 plastid genomes of the Capsiceae tribe examined, the four distinct boundaries and their genes located near these boundaries were identified, showing consistent patterns, as well as some absences in the analyzed genomes (Fig.\u0026nbsp;\u003cspan refid=\"Fig8\" class=\"InternalRef\"\u003e08\u003c/span\u003e). Specifically, regarding the junction between LSC and IRb (JLB), where all plastid genomes showed the structure of the rps19 gene spanning from the LSC region to IRb, there was a difference in length ranging from 206 bp to 218 bp. Additionally, Arnaucho chili pepper and the other four \u003cem\u003eC. chinense\u003c/em\u003e species, including \u003cem\u003eC. galapagoense\u003c/em\u003e, exhibited the same position and size for the \u003cem\u003erps19\u003c/em\u003e gene. The \u003cem\u003erpl22\u003c/em\u003e and \u003cem\u003erpl2\u003c/em\u003e genes are located in the LSC and IRB regions.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eSimilarly, for the JSB boundary, where the union between the SSC and IRB regions occurs, two genes, \u003cem\u003eycf1\u003c/em\u003e and \u003cem\u003endhF\u003c/em\u003e, were positioned. The \u003cem\u003endhF\u003c/em\u003e gene was located in the SSC regions, while it was observed that \u003cem\u003eycf1\u003c/em\u003e crossed from the SSC region to the IRB region, except in Arnaucho chili pepper and \u003cem\u003eC. lycianthoides\u003c/em\u003e. Additionally, it was absent in \u003cem\u003eC. pubescens\u003c/em\u003e, \u003cem\u003eC. baccatum\u003c/em\u003e, and \u003cem\u003eC. chinense\u003c/em\u003e (MH559321). The \u003cem\u003eycf1\u003c/em\u003e genes that spanned both the SSC and IRB regions had the same size of 1160 bp, while those located only in the IRB region had a size of 1127 bp in \u003cem\u003eC. chinense\u003c/em\u003e and 1043 bp in \u003cem\u003eC. lycianthoides\u003c/em\u003e. The \u003cem\u003endhF\u003c/em\u003e gene (2222 bp) in the plastid of Arnaucho chili pepper showed a slight positional difference compared to \u003cem\u003eC. galapagoense\u003c/em\u003e and the other four \u003cem\u003eC. chinense\u003c/em\u003e genomes, and it was located adjacent to the JSB boundary. At the JSA boundary between SSC and IRA, the closest genes in the Capsiceae tribe showed that the \u003cem\u003eycf1\u003c/em\u003e gene was intact at the JSA boundary and crossed from SSC to the IRA region. However, the length of this gene varied from 5693 bp in \u003cem\u003eC. lycianthoides\u003c/em\u003e to 5735 bp in \u003cem\u003eC. baccatum\u003c/em\u003e. Additionally, four \u003cem\u003eC. chinense\u003c/em\u003e showed the same length for the gene \u003cem\u003eycf1\u003c/em\u003e with a size of 5720 bp, except for \u003cem\u003eC. chinense\u003c/em\u003e which had 5675 bp and \u003cem\u003eC. galapagoense\u003c/em\u003e with 5726 bp. Finally, the analysis of the junction between the IRA and LSC regions (JLA) showed that the gene \u003cem\u003erpl2\u003c/em\u003e was present in IRA, except in \u003cem\u003eC. lycianthoides\u003c/em\u003e, which did not contain this gene. The genes \u003cem\u003etrnH\u003c/em\u003e and \u003cem\u003epsbA\u003c/em\u003e were located at the LSC boundary and were present in all the chloroplast genomes.\u003c/p\u003e"},{"header":"Discussion","content":"\u003cp\u003eThe native Arnaucho pepper, also known as \u0026ldquo;supano\u0026rdquo;, \u0026ldquo;campi\u0026ntilde;ero\u0026rdquo; or \u0026ldquo;arnaucho campi\u0026ntilde;ero\u0026rdquo;, is an ecotype from the Supe Valley in the Barranca province, and is very important in the Peruvian gastronomy, especially in the Lima. This \u003cem\u003eCapsicum chinense\u003c/em\u003e cultivar has been cultivated since in family gardens for self-consumption sin the 1960s. Starting in the 1980s, it began to be cultivated in small plots with marketing intentions, where its distribution was through seeds and seedlings, from farmer to farmer, via family members or neighbors, and it continues to be distributed this way to this day (Aliaga et al. \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). Currently, the first chloroplast genome sequencing has been carried out, with the objectives of characterizing the species and understanding its phylogenetic evolution (Arbizu et al. \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). In this study, we collected the chloroplast genomes of different \u003cem\u003eCapsicum\u003c/em\u003e species from the Organelle Genome Resources database of NCBI. The collected genomes were then annotated using the Geseq tool, and the chloroplast genomes were compared using the Arnaucho chili pepper as the reference genome to further study its evolution, structure, and comparison of its cp genome. The cp genome of \u003cem\u003eC. chinense\u003c/em\u003e Arnaucho chili pepper was 156,931 bp (156.9 Kb) in length, also exhibiting a classic quadripartite circular structure: a large single-copy region (LSC), a small single-copy region (SSC), and two inverted repeats (IRA and IRB). These regions were also present in the other \u003cem\u003eCapsicum\u003c/em\u003e species. Additionally, we found that the cp genomes of the Capsiceae tribe varied slightly in size but maintained a GC content of 37%. This finding aligns with previous reports indicating that the chloroplast genome structure in most angiosperms is typically maternally inherited and remains largely unchanged (Birky, \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e1995\u003c/span\u003e). The lengths of the LSC region ranged from 86,813 bp (\u003cem\u003eC. lycianthoides\u003c/em\u003e) to 87,688 bp (\u003cem\u003eC. pubescens\u003c/em\u003e), while the SSC region ranged from 17,849 bp (\u003cem\u003eC. annum\u003c/em\u003e) to 18,522 bp (\u003cem\u003eC. lycianthoides\u003c/em\u003e), and the IR region ranged from 25,624 bp (\u003cem\u003eC. lycianthoides\u003c/em\u003e) to 25,910 bp (\u003cem\u003eC. baccatum\u003c/em\u003e). These results were similar to studies reported by Raveendar et al. (2024). The same has been found in other important Solanaceae crop species, such as \u003cem\u003eS. lycopersicum\u003c/em\u003e, \u003cem\u003eS. tuberosum\u003c/em\u003e, and \u003cem\u003eP. peruviana\u003c/em\u003e (Zhao et al. \u003cspan citationid=\"CR68\" class=\"CitationRef\"\u003e2019\u003c/span\u003e; Chen et al. \u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e2021\u003c/span\u003e; Feng et al. \u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). The chloroplast genomic regions of Solanaceae maintain a similar size among closely related species, as in the case of the Arnaucho chili pepper, an important crop for human consumption.\u003c/p\u003e \u003cp\u003eAdditionally, in another exotic Solanaceae plant, \u003cem\u003eN. physalodes\u003c/em\u003e, studies described by Chen \u0026amp; Zhang (\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e2019\u003c/span\u003e) revealed that the total length of its chloroplast genome was 156,729 bp (157.7 kb), showing a similar length to \u003cem\u003eCapsicum\u003c/em\u003e species. However, some Solanaceae species exhibit regions of varying lengths. For example, studies conducted on other Solanaceae species reported \u003cem\u003eDatura stramonium\u003c/em\u003e with a size of 155,871 bp and the African boxwood shrub \u003cem\u003eLycium ferocissimum\u003c/em\u003e with 155,894 bp, showing a contraction of around 1,000 bp (Yang et al. 2014 \u0026amp; Li et al. 2019). However, these species exhibited similar boundary regions to the Capsiceae tribe, specifically in the IR region, which measured 25,601 bp in \u003cem\u003eD. stramonium\u003c/em\u003e and 25,476 bp in \u003cem\u003eL. ferocissimum\u003c/em\u003e, and in the LSC region, which measured 86,302 bp in \u003cem\u003eD. stramonium\u003c/em\u003e and 86,536 bp in \u003cem\u003eL. ferocissimum\u003c/em\u003e. This suggests that the reduction in chloroplast genomes of these species occurs in the SSC regions, possibly due to genetic variations present in this family (Su et al. \u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). Additionally, in the annotated chloroplast genome of \u003cem\u003eC. chinense\u003c/em\u003e, 133 genes were identified, including a total of 86 CDS, 8 rRNA, 37 tRNA, and 2 pseudogenes. Compared to other \u003cem\u003eCapsicum\u003c/em\u003e species, this variety has more genes in its chloroplast but fewer protein-coding sequences. Most of the genes are present as a single copy, except for 18 genes that are duplicated in the IR regions. These 18 duplicated genes in the IR region have also been found in other Solanaceae species that are not \u003cem\u003eCapsicum\u003c/em\u003e (Asaf et al. \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e2016\u003c/span\u003e). In the genomic sequence comparison analysis conducted by mVISTA, it was revealed that \u003cem\u003eC. lycianthoides\u003c/em\u003e exhibited the greatest divergence in relation to \u003cem\u003eC. chinense\u003c/em\u003e Arnaucho chili pepper. The analysis showed that the greatest variation occurred in the non-coding regions compared to the coding regions present in all genomes of the Capsiceae tribe. Additionally, the variations observed in the coding regions were present in all the genomes, specifically in the genes \u003cem\u003eaccD\u003c/em\u003e, \u003cem\u003erpl20\u003c/em\u003e, \u003cem\u003eycf1\u003c/em\u003e, \u003cem\u003eycf2\u003c/em\u003e, and \u003cem\u003endhA\u003c/em\u003e. On the other hand, the alignment between the Arnaucho chili pepper and \u003cem\u003eC. galapagoense\u003c/em\u003e showed only one significant variation, which occurred in the \u003cem\u003erpl20\u003c/em\u003e gene. Meanwhile, the alignment between the ACP and the other four \u003cem\u003eC. chinense\u003c/em\u003e individuals showed variations in the \u003cem\u003eaccD\u003c/em\u003e gene (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e02\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eThe analysis of codon usage is essential for understanding the complexities of genomic structure, dynamic evolution, and the selective pressure imposed on genes (Morton, \u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e1998\u003c/span\u003e). We found that the most commonly used codon in the \u003cem\u003eC. chinense\u003c/em\u003e genome was AAA, which codes for the amino acid lysine, followed by UUU, which codes for phenylalanine, and finally AUU, which codes for isoleucine. These patterns indicate a preference for codons that end in A or T/U. Previous studies have shown that higher RSCU values indicate similar results in extensive research on Solanaceae species, with a tendency to be rich in A/U or A/T in chloroplast genomes (Mehmetoğlu et al. \u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e2023\u003c/span\u003e and Wang et al. \u003cspan citationid=\"CR62\" class=\"CitationRef\"\u003e2023\u003c/span\u003e). This means that there is already a selective pressure favoring the use of codons in chloroplast genomes, commonly detected at the third position of codons.\u003c/p\u003e \u003cp\u003ePhylogenetic trees are used to understand the evolutionary relationships between species, and they can be based on genomic regions or the complete genome sequence. The angiosperm tree of life has been primarily determined through plastid genome analysis. These chloroplast genomes are highly conserved in both sequence and structure, making them highly valuable for taxonomic studies and plant classification (Amenu et al. \u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e2022\u003c/span\u003e; Zuntini et al. \u003cspan citationid=\"CR69\" class=\"CitationRef\"\u003e2024\u003c/span\u003e). Here, a phylogenetic tree reconstruction was performed using the complete genome sequence of the pepper along with 14 additional Capsicum genomes. The goal was to classify it within its corresponding tribe and determine its phylogenetic position. The tribe was divided into six groups (green, mustard, light blue, purple, red, and yellow), along with one additional group (pink) representing two Solanaceae genome sequences used to root the tree. The analysis revealed that the Arnaucho chili pepper and \u003cem\u003eC. galapagoense\u003c/em\u003e clustered in the corresponding group alongside other \u003cem\u003eC. chinense\u003c/em\u003e and \u003cem\u003eC. eximium\u003c/em\u003e, showing a genetic relationship among these species. This previous result had already been reported in a study described by Arbizu et al. (\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). To determine the pairwise distance between chloroplast genomes, an analysis was conducted using Mega11. This analysis was performed using the p-distance method with complete removal of missing data. The results showed that the p-distance values ranged from 0.00002733 for the closest species, \u003cem\u003eC. galapagoense\u003c/em\u003e, to 0.00021523 for the most distant species, \u003cem\u003eC. lycianthoides\u003c/em\u003e, respectively. These p-distance studies have also been conducted in other families, such as the Styracaceae. Here, we present one of the first results of p-distance analysis in the Capsicum tribe (Song et al. \u003cspan citationid=\"CR56\" class=\"CitationRef\"\u003e2022\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eWithin each genome, a large number of repetitive sequences, also known as SSRs (Simple Sequence Repeats), are present. These repetitive sequences exhibit high sequence repeatability, high variability, and co-dominant heterozygous inheritance. These sequences are molecular genetic markers suitable for species identification, as well as for ecological and evolutionary studies (Yang et al. 2017; Li et al. \u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e2014\u003c/span\u003e). Analyses of these SSR sequences offer a perspective as potential markers specific to each genus (Shirasawa et al. \u003cspan citationid=\"CR54\" class=\"CitationRef\"\u003e2010\u003c/span\u003e). In general, the most abundant nucleotides in chloroplast genomes are A and T, or A/T repeats, which are prevalent in angiosperms, rather than G and C or G/C repeats (Kurt et al. \u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e2023\u003c/span\u003e). In this SSR analysis of Arnaucho chili pepper, a total of 36 SSR markers were identified, comprising 33 mononucleotides, 1 trinucleotide, and 2 pentanucleotides. This revealed a lower pattern compared to the different types of \u003cem\u003eCapsicum\u003c/em\u003e species present in this study. The repetitive sequence repetitions, including palindromic sequences, reverse sequences, forward sequences, and tandem repeats, showed values of 172, 41, 3, and 55, respectively. In the comparison of the number of repetitive sequences across the 14 cp genomes, it was observed that none of the genomes contained complementary sequences. There was a variation in the number of reverse sequences, ranging from 1 to 5 in relative magnitude, with the exception of \u003cem\u003eC. baccatum\u003c/em\u003e and \u003cem\u003eC. pubescens\u003c/em\u003e, which did not present these repetitive sequences (shown in red). For forward sequences, the relative magnitude of repetitive sequences ranged from 16 to 49. In the complementary sequences, a relative magnitude of repetitive sequences was observed between 50 and 66 (shown in light blue), and lastly, for tandem sequences, the relative magnitude was greater than 150, ranging from 163 to 181. In comparison to the SSR sequences, these repetitive sequences appeared similarly to the repetitive sequences found in the other genomes, corroborating that this particular chili variety has fewer SSR sequences in its genome compared to the other Capsicum species detailed in this research.\u003c/p\u003e \u003cp\u003eThe IR regions can indicate the size of cp genomes because they expand or contract, reflecting the distance between species to some extent (Zhao et al., 2023). These highly variable IR regions can provide molecular marker studies in cp genomes, which are important for research related to species identification, phylogeny, and population genetics (Xiao et al., \u003cspan citationid=\"CR64\" class=\"CitationRef\"\u003e2024\u003c/span\u003e). Our analysis of the ACP genome revealed that it retains an IR region of 25,847 bp (25 kb), leading to a total genome length of 156,931 bp. It is important to highlight that the chloroplast genome length of this Peruvian landrace closely resembles that of \u003cem\u003eC. galapagoense\u003c/em\u003e and \u003cem\u003eC. chinense\u003c/em\u003e (GenBank KU041709), indicating similar IR expansion. However, its structure is distinctly different. In the Arnaucho chili pepper, the JSB boundary composed of IRb and SSC contains the \u003cem\u003eycf1\u003c/em\u003e gene, which is located exclusively within the IRb structure. In contrast, \u003cem\u003eC. galapagoense\u003c/em\u003e and \u003cem\u003eC. chinense\u003c/em\u003e possess the \u003cem\u003eycf1\u003c/em\u003e gene spanning both the IRb and SSC structures at the JSB boundary. The current taxonomy of this Peruvian landrace is questioned based on the present work, and also by Arbizu et al. (\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). The \u003cem\u003eycf1\u003c/em\u003e gene in the ACP is 1127 bp long, similar in size to the 1043 bp \u003cem\u003eycf1\u003c/em\u003e gene in \u003cem\u003eC. lycianthoides\u003c/em\u003e, positioned solely at the junction. This gene's variation plays a key role in the structural variation of chloroplast genomes within the Capsiceae tribe. This result regarding the IR structure indicates that the \u003cem\u003eycf1\u003c/em\u003e gene in most angiosperms is generally larger and more diverse. In some cases, the \u003cem\u003eycf1\u003c/em\u003e gene may be absent, which could lead to a reduction in protein-coding capacity and variation in the IRb/SSC boundary structure. As noted by Ge et al. (\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e2019\u003c/span\u003e), this variation can influence the overall stability and function of the chloroplast genome, potentially affecting the plant's metabolic processes and adaptation to different environments. The presence of \u003cem\u003eycf1\u003c/em\u003e and its position within the IR regions plays a significant role in the genomic architecture and evolutionary dynamics of angiosperms.\u003c/p\u003e"},{"header":"Conclusion","content":"\u003cp\u003eHere, we report the in-silico analysis of the Arnaucho chili pepper along with 13 chloroplast genomes from the Capsiceae tribe, including both hot and sweet peppers, obtained from the NCBI database. We compared the 14 chloroplast genome sequences. In this comparative analysis, highly variable sites were identified, specifically non-coding regions, as well as coding regions of genes that could serve as potential markers for species identification. In this case, \u003cem\u003erpl20\u003c/em\u003e, \u003cem\u003eaccD\u003c/em\u003e, \u003cem\u003eycf1\u003c/em\u003e, \u003cem\u003eycf2\u003c/em\u003e, and \u003cem\u003endhA\u003c/em\u003e were highlighted. It was also observed that this Arnaucho chili pepper exhibited patterns of codons A (adenine) and U (uracil), similar to the other types of peppers present. It was discovered in its phylogenetic reconstruction and p-distance analysis that this \u003cem\u003eCapsicum\u003c/em\u003e species is closely related in evolutionary terms to \u003cem\u003eC. galapagoense\u003c/em\u003e. All the genomes of the Capsiceae tribe were highly conserved, except in the IRB region at the JSB boundary. This complete cp genome of Arnaucho pepper showed different genetic characteristics regarding its SSR sequence identification compared to the other genomes. It was found to possess 36 SSR sequences, which is fewer than the other pepper genomes used in the present study. Additionally, in the other repetitive sequences, it was completely different, displaying similarities to the other types of chloroplast genomes of peppers studied. These studies may be useful for future research on the diversity or genetic improvement of this Peruvian chili pepper landrace.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgments\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe would like to thank the Vicerrectorado de Investigaci\u0026oacute;n of UNTRM.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthor contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eGC: Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Software, Validation, Visualization, Writing \u0026ndash; original draft. KRQ-H: Data curation, Formal analysis, Investigation, Software, Validation, Visualization, Writing \u0026ndash; original draft. DHT-I: Data curation, Formal analysis, Investigation, Software, Validation, Visualization, Writing \u0026ndash; original draft. JEB-G: Data curation, Formal analysis, Investigation, Software, Validation, Visualization, Writing \u0026ndash; original draft. YAC-R: Data curation, Formal analysis, Investigation, Software, Validation, Visualization, Writing \u0026ndash; original draft. SC-L: Conceptualization, Formal analysis, Investigation, Methodology, Project administration, Supervision, Validation, Visualization, Writing \u0026ndash; review \u0026amp; editing. CIA: Conceptualization, Data curation, Investigation, Resources, Supervision, Validation, Visualization, Writing \u0026ndash; review \u0026amp; editing. PMR-G: Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing \u0026ndash; review \u0026amp; editing.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis research received not external funding.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConflict of interest\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare that they have no conflicts of interest in this research.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData Availability\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNo datasets were generated during the current study.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConflicts of interest\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare no competing interests.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eAguilar-Meléndez A, Morrell PL, Roose ML, Kim SC. Genetic diversity and structure in semiwild and domesticated chiles (\u003cem\u003eCapsicum annuum\u003c/em\u003e; Solanaceae) from Mexico. Am J Bot. 2009;96(6):1190–202\u003c/li\u003e\n\u003cli\u003eAliaga, J., Portalatino, E., Obregon, K., Rodriguez, A. \u0026amp; Jimenez, J. (2020). Presencia del \"aji nativo supano\" (Capsicum chinense Jacq.) en el valle de Supe, Peru. Peruvian Agricultural Research. (1). 58-63. DOI: 10.51431/par.v1i2.584\u003c/li\u003e\n\u003cli\u003eAmenu, S.G., Wei, N., Wu, L. et al. Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution. BMC Plant Biol 22, 88 (2022). https://doi.org/10.1186/s12870-022-03480-5\u003c/li\u003e\n\u003cli\u003eAmiryousefi, A., Hyvönen, J., Poczai, P. IRscope: an online program to visualize the junction sites of chloroplast genomes, Bioinformatics, Volume 34, Issue 17, September 2018, Pages 3030–3031, https://doi.org/10.1093/bioinformatics/bty220\u003c/li\u003e\n\u003cli\u003eÁngel Gaviria, I.J. (2023). La bioinformática como herramienta para el conocimiento de microorganismos edáficos con potencial para la producción agrícola sostenible, recuperación y conservación de suelos [Tesis de maestría, Universidad Libre].\u003c/li\u003e\n\u003cli\u003eAntonio, A.S., Wiedermann, L.S.M. \u0026amp; Veiga, F.J. (2018). The genus Capsicum: a phytochemical review of bioactive secondary metabolites. RSC Advances. 25767-25784. DOI: 10.1039/c8ra02067a\u003c/li\u003e\n\u003cli\u003eArbizu, C. I., Saldaña, C. L., Ferro-Mauricio, R. D., Chávez-Galarza, J. C., Herrera, J., Contreras-Liza, S., … Maicelo, J. L. (2022). Characterization of the complete chloroplast genome of a Peruvian landrace of \u003cem\u003eCapsicum chinense\u003c/em\u003e Jacq. (Solanaceae), arnaucho chili pepper. \u003cem\u003eMitochondrial DNA Part B\u003c/em\u003e, \u003cem\u003e7\u003c/em\u003e(1), 156–158. https://doi.org/10.1080/23802359.2021.2014366\u003c/li\u003e\n\u003cli\u003eAsaf, S., Khan, A.L., Khan, A.R., Waqas, M., Kang, S., Khan, M., Lee, S. \u0026amp; Lee, I. (2016). Complete Chloroplast Genome of Nicotiana otophora and its Comparison with Related Species. Front Plant Sci. Sec. Evolutionary and Population Genetics. https://doi.org/10.3389/fpls.2016.00843\u003c/li\u003e\n\u003cli\u003eBeier S, Thiel T, Münch T, Scholz U, Mascher M (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics 33 2583–2585. dx.doi.org/10.1093/bioinformatics/btx198\u003c/li\u003e\n\u003cli\u003eBenson 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research. Vol 27. Pages 573-580. https://doi.org/10.1093/nar/27.2.573\u003c/li\u003e\n\u003cli\u003eBirky Jr, C.W. (1995). Uniparental inheritance of mitochndrial and chloroplast genes: mechanisms and evolution. PNAS. Vol 92. 11331-11338. https://doi.org/10.1073/pnas.92.25.11331\u003c/li\u003e\n\u003cli\u003eBrudno, M., Malde, S., Poliakov, A., Do, C.B., Couronne, O., Dubchak, I., and Batzoglou, S. Glocal Alignment: Finding Rearrangements During Alignment, 2003. Bioinformatics, 19S1: i54-i62.\u003c/li\u003e\n\u003cli\u003eCaycho, E., La Torre, R. \u0026amp; Orjeda, G. Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree \u003cem\u003eNeltuma pallida\u003c/em\u003e (subfamily: Caesalpinioideae). \u003cem\u003eBMC Plant Biol\u003c/em\u003e\u003cstrong\u003e23\u003c/strong\u003e, 570 (2023). https://doi.org/10.1186/s12870-023-04581-5\u003c/li\u003e\n\u003cli\u003eChan, P.P., Lin, B.Y., Mak, A.J., and Lowe, T.M. (2021)tRNAscan-SE 2.0: Improved Detection and Functional Classification of Transfer RNA Genes.\u003cem\u003eNucl. Acids Res. \u003c/em\u003e\u003cstrong\u003e49\u003c/strong\u003e:9077–9096.\u003c/li\u003e\n\u003cli\u003eChen, Q., \u0026amp; Zhang, D. (2019). The complete chloroplast genome sequence of the medicinal plant Nicandra physalodes (Linn.) Gaertn. (Solanaceae). Mitochondrial DNA Part B, 4(2), 3053–3054. https://doi.org/10.1080/23802359.2019.1666674\u003c/li\u003e\n\u003cli\u003eChen, S., Zhao, Y., Zhang, J. Y., Zhang, J. Y., Wang, Y. P., Mou, B., … Han, Y. Z. (2021). Characterization of the complete chloroplast genome of the \u003cem\u003eSolanum tuberosum\u003c/em\u003e L. cv. Shepody (Solanaceae). Mitochondrial DNA Part B, 6(8), 2342–2344. https://doi.org/10.1080/23802359.2021.1934135\u003c/li\u003e\n\u003cli\u003eDarriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9(8), 772.\u003c/li\u003e\n\u003cli\u003eDong, X., Li, X., Ding, L., Cui, F., Tang, Z., Liu, Z., Stage Extraction of Capsaicinoids and Red Pigments from Fresh Red Pepper (Capsicum) Fruits with Ethanol as Solvent, LWT - Food Science and Technology (2014), doi: 10.1016/j.lwt.2014.04.051.\u003c/li\u003e\n\u003cli\u003eEstrada, R., Tantalean, J.F.C., Saldaña, C.L. \u003cem\u003eet al.\u003c/em\u003e Draft genome and SSR data mining of a Peruvian landrace of \u003cem\u003eCapsicum chinense,\u003c/em\u003e the arnaucho chili pepper. \u003cem\u003eGenet Resour Crop Evol\u003c/em\u003e (2024). https://doi.org/10.1007/s10722-024-01941-4\u003c/li\u003e\n\u003cli\u003eFeng, S., Zheng, K., Jiao, K., Cai, Y., Chen, C., Mao, Y., Wang, L., Zhan, X., Ying, Q. \u0026amp; Wang, H. (2020). Complete chloroplast genomes of four Physalis species (Solanaceae): lights into genome structure, comparative analysis, and phylogenetic relationships. BMC Plant Biol 20, 242. \u003cu\u003ehttps://doi.org/10.1186/s12870-020-02429-w\u003c/u\u003e\u003c/li\u003e\n\u003cli\u003eFlorencio, V. \u0026amp; Valdir, Jr. (2022). Chapter 1: Origin and Evolution of Capsicum. Chemistry and Nutritional Effects of \u003cem\u003eCapsicum\u003c/em\u003e. Page: 1-14. https://doi.org/10.1039/9781839160646-00001\u003c/li\u003e\n\u003cli\u003eFrazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9. \u003c/li\u003e\n\u003cli\u003eGe, Y., Dong, X., Wu, B., Wang, N., Chen, D., Chen, H., Zou, M., Xu, Tan, L. \u0026amp; Zhan, R. (2019). Evolutionary analysis of six chloroplast genomes from three \u003cem\u003ePersea americana\u003c/em\u003e ecological races: Insights into sequence divergences and phylogenetic relationships. PLoS ONE 14(9): e0221827. https://doi.org/10.1371/journal.pone.0221827\u003c/li\u003e\n\u003cli\u003eGreiner S, Lehwark P and Bock R (2019) OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Research 47: W59-W64. https://doi.org/10.1093/nar/gkz238\u003c/li\u003e\n\u003cli\u003eHernandez, A.A., Pineda, A.L., Rojas, J.C. \u0026amp; Diaz, H.P. (2022). In vitro regeneration of arnaucho (Capsicum chinense Jacq.) from apical buds. \u003cem\u003eManglar.\u003c/em\u003e (1). 71-75. DOI: http://dx.doi.org/10.17268/manglar.2021.009\u003c/li\u003e\n\u003cli\u003eIbiza, V.P.; Blanca, J.; Cañizares, J.; Nuez, F. Taxonomy and genetic diversity of domesticated Capsicum species in the Andean region. Genet. Resour. Crop Evol. 2012, 59, 1077−1088. DOI 10.1007/s10722-011-9744-z\u003c/li\u003e\n\u003cli\u003eKatoh, K., Standley, D. (2013). MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution. Vol4. Pág 772-780. doi: 10.1093/molbev/mst010\u003c/li\u003e\n\u003cli\u003eKurtz, S. and Choudhuri, Jomuna V. and Ohlebusch, Enno and Schleiermacher, Chris and Stoye, Jens and Giegerich, Robert (2001) REPuter: The Manifold Applications of Repeat Analysis on a Genomic Scale, Nucleic Acids Res., Nucleic Acids Res., 29(22):4633-4642.\u003c/li\u003e\n\u003cli\u003eKurt, S., Kaymaz, Y., Ateş, D. et al. Complete chloroplast genome of Lens lamottei reveals intraspecies variation among with Lens culinaris. Sci Rep 13, 14959 (2023). https://doi.org/10.1038/s41598-023-41287-y\u003c/li\u003e\n\u003cli\u003eLarsson, A. (2014). AliView: a fast and lightweight alignment viewer and editor for large data sets. \u003cem\u003eBioinformatics\u003c/em\u003e30(22): 3276-3278.http://dx.doi.org/10.1093/bioinformatics/btu531\u003c/li\u003e\n\u003cli\u003eLetunic I and Bork P (2024) Nucleic Acids Res doi: 10.1093/nar/gkae268 Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool\u003c/li\u003e\n\u003cli\u003eLi, M., Qi, X.M., Lam, H. (2013). Silicon Era of Carbon-Based Life: Application of Genomics and Bioinformatics in Crop Stress Research. Mol. Sci. 14. 11444-11483. https://doi.org/10.3390/ijms140611444\u003c/li\u003e\n\u003cli\u003eLi, X. et al. Plant DNA barcoding: From gene to genome. Biol. Rev. Camb. Philos. Soc. 90, 157–166 (2014).\u003c/li\u003e\n\u003cli\u003eLi, Z., Zhang, X., Zhang, Q., \u0026amp; Yisilam, G. (2020). Complete chloroplast genome of Lycium ferocissimum (Solanaceae), a species native to South Africa. Mitochondrial DNA Part B, 5(1), 756–757. https://doi.org/10.1080/23802359.2020.1715301\u003c/li\u003e\n\u003cli\u003eLiu H, Liu X, Sun C, Li HL, Li ZX, Guo Y, Fu XQ, Liao QH, Zhang WL, Liu YQ. Chloroplast Genome Comparison and Phylogenetic Analysis of the Commercial Variety \u003cem\u003eActinidia chinensis\u003c/em\u003e 'Hongyang'. Genes (Basel). 2023 Nov 27;14(12):2136. doi: 10.3390/genes14122136. PMID: 38136958; PMCID: PMC10743354.\u003c/li\u003e\n\u003cli\u003eLópez Medina, E., López Zabaleta, A., Gil Rivero, A. E., Mostacero, J., De La Cruz, A.J. y Villena, L. (2020) Morfometría de frutos y semillas del “ají mochero” Capsicum chinense Jacq. Ciencia \u0026amp; Tecnología Agropecuaria, 21(3), 1-11. https://doi.org/10.21930/rcta.vol21_num3_art:1598.\u003c/li\u003e\n\u003cli\u003eMansoor, S., Hamid, S., Thanh, T.T., Park, J. Suk, Y.C. (2024). Advance computational tools for multiomics data learning. Biotechnol Adv. Vol 77. https://doi.org/10.1016/j.biotechadv.2024.108447\u003c/li\u003e\n\u003cli\u003eMcDonald MJ, Wang W-C, Huang H-D, Leu J-Y (2011) Clusters of Nucleotide Substitutions and Insertion/Deletion Mutations Are Associated with Repeat Sequences. PLoS Biol 9(6): e1000622. https://doi.org/10.1371/journal.pbio.1000622\u003c/li\u003e\n\u003cli\u003eMeckelmann, S., Riegel, D.W., Zonneveld, M.J., Rios, L., Pe;a, K., Ugas, R., Quinonez, L., Mueller-Seitz, E. \u0026amp; Petz, M. (2013). Compositional Characterization of Native Peruvian Chili Peppers (Capsicum spp.). Agric Food Chem. Vol 61. Pages: 2530-2537. DOI: 10.1021/jf304986q \u003c/li\u003e\n\u003cli\u003eMehmetoğlu, E., Kaymaz, Y., Ateş, D. et al. The complete chloroplast genome of Cicer reticulatum and comparative analysis against relative Cicer species. Sci Rep 13, 17871 (2023). https://doi.org/10.1038/s41598-023-44599-1\u003c/li\u003e\n\u003cli\u003eMichael, D., Gurusaran, M., Santhosh, R., Khaja, Md.H., Satheesh, S.N., Suhan, S., Sivaranjan, P., Jaiswal, A. \u0026amp; Sekar, K. (2019). RepEx: A web server to extract sequence repeats from protein and DNA sequences. Computational Biology and Chemistry. Vol: 78. Pages: 424-430. https://doi.org/10.1016/j.compbiolchem.2018.12.015\u003c/li\u003e\n\u003cli\u003eMinguez-Mosquera, M.I., Jaren-Galan, M. and Garrido-FErnandez, J. (1992). Color Quality in Paprika. J. Agric. Food Cherm. Vol:40. Pages 2384-2388. https://doi.org/10.1021/jf00024a012\u003c/li\u003e\n\u003cli\u003eMorton, B.R. (1998). Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages. J Mol Evol.;46(4):449–59.\u003c/li\u003e\n\u003cli\u003eMcGowan, J. (2024). RSCU calculator. Online Bioinformatics Tools. https://jamiemcgowan.ie/bioinf/rscu.html\u003c/li\u003e\n\u003cli\u003eNashima K, Hosaka F, Terakami S, et al. SSR markers developed using next-generation sequencing technology in pineapple, Ananas comosus (L.) Merr. Breed Sci. 2020;70(3):415–21.\u003c/li\u003e\n\u003cli\u003ePark, H. S., Lee, J., Lee, S. C., Yang, T. J., \u0026amp; Yoon, J. B. (2016). The complete chloroplast genome sequence of \u003cem\u003eCapsicum chinense\u003c/em\u003e Jacq. (Solanaceae). \u003cem\u003eMitochondrial DNA Part B\u003c/em\u003e, \u003cem\u003e1\u003c/em\u003e(1), 164–165. https://doi.org/10.1080/23802359.2016.1144113\u003c/li\u003e\n\u003cli\u003ePerry L, Dickau R, Zarrillo S et al (1979) (2007) Fósiles de almidón y la domesticación y dispersión de chiles (\u003cem\u003eCapsicum\u003c/em\u003e spp. L.) en las Américas. Ciencia 315:986–988.https://doi.org/10.1126/science.1136914\u003c/li\u003e\n\u003cli\u003eRay, S. \u0026amp; Saty, P. (2014). Next generation sequencing technologies for next generation plant breeding. Front Plant Sci. Vol 5. https://doi.org/10.3389/fpls.2014.00367\u003c/li\u003e\n\u003cli\u003eRaveendar, S., Jeon, Y., Lee, J., Lee, G., Lee, K.J., Cho, G., Ma, K., Lee, S. and Chung, J. (2015). The Compmplete Chloroplast Genome Sequence of Korean Landrace “Subicho” Pepper (\u003cem\u003eCapsicum annuum\u003c/em\u003e var. \u003cem\u003eannuum\u003c/em\u003e). Plant breeding and Biotechnology. Vol 3. 88-94https://doi.org/10.9787/PBB.2015.3.2.08888\u003c/li\u003e\n\u003cli\u003eRoychowdhury, R., Prakash, S.D., Gupta, A., Parihar, P., Chandrasekhar, K., Sarker, U., Kumar, A., Pandurang, D.R. \u0026amp; Sudhakar, C. (2023). Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant's Abiotic Stress Tolerance Responses. Genes. Vol 14. https://doi.org/10.3390/genes14061281 \u003c/li\u003e\n\u003cli\u003eSharp, P.M. \u0026amp; Li, W.H. (1987). The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research. Vol 3. Pages: 1281-1295. doi: 10.1093/nar/15.3.1281\u003c/li\u003e\n\u003cli\u003eSebastin, R., Lee, K. J., Cho, G. T., Shin, M. J., Kim, S. H., Hyun, D. Y., \u0026amp; Lee, J. R. (2019). The complete chloroplast genome sequence of a Bolivian wild chili pepper, \u003cem\u003eCapsicum eximium\u003c/em\u003e Hunz. (Solanaceae). \u003cem\u003eMitochondrial DNA Part B\u003c/em\u003e, \u003cem\u003e4\u003c/em\u003e(1), 1634–1635. https://doi.org/10.1080/23802359.2019.1601533\u003c/li\u003e\n\u003cli\u003eSebastin, R., Kim, J., Jo, IH. \u003cem\u003eet al.\u003c/em\u003e Comparative chloroplast genome analyses of cultivated and wild \u003cem\u003eCapsicum\u003c/em\u003e species shed light on evolution and phylogeny. \u003cem\u003eBMC Plant Biol\u003c/em\u003e\u003cstrong\u003e24\u003c/strong\u003e, 797 (2024). https://doi.org/10.1186/s12870-024-05513-7 \u003c/li\u003e\n\u003cli\u003eShirasawa, K., Asamizu, E., Fukuoka, H., Ohyama, A., Sato, S., Nakamura, Y., Tabata, S., Sasamoto, S., Wada, T., Kishida, Y., Tsuruoka, H., Fujishiro, T., Yamada, M. \u0026amp; Isobe, S. (2010). An interspecific linkage map of SSR and intronic polymorphism markers in tomato. Theor Appl Genet. Vol 121. Pages 731-739. https://doi.org/10.1007/s00122-010-1344-3\u003c/li\u003e\n\u003cli\u003eShiragaki K, Yokoi S, Tezuka T. 2020. Phylogenetic analysis and molecular diversity of capsicum based on rDNA-ITS region. Horticulturae. 6(4):87. \u003c/li\u003e\n\u003cli\u003eSong, F., Zhao, W., Xu, J., Li, M. \u0026amp; Zhang, Y. (2022). Chloroplast Genome Evolution and Species Identification of \u003cem\u003eStyrax\u003c/em\u003e (Styracaceae). BioMed Research International. https://doi.org/10.1155/2022/5364094\u003c/li\u003e\n\u003cli\u003eSu Q, Liu L, Zhao M, Zhang C, Zhang D, Li Y, et al. Los genomas completos del cloroplasto de diecisiete \u003cem\u003eAegilops tauschii\u003c/em\u003e: análisis comparativo del genoma e inferencia filogenética. PeerJ. 2020;8:e8678.\u003c/li\u003e\n\u003cli\u003eTamura, K., Stecher, G., and Kumar, S. (2021) MEGA11: Molecular Evolutionary Genetics Analysis version 11. Molecular Biology and Evolution 38:3022-3027\u003c/li\u003e\n\u003cli\u003eTillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R and Greiner S (2017). GeSeq – versatile and accurate annotation of organelle genomes. Nucleic Acids Research 45: W6-W11. https://doi.org/10.1093/nar/gkx391\u003c/li\u003e\n\u003cli\u003eTripodi P, Rabanus-Wallace MT, Barchi L, Kale S, Esposito S, Acquadro A, Schafleitner R, van Zonneveld M, Prohens J, Diez MJ. 2021. Global range expansion history of pepper (Capsicum spp.) revealed by over 10,000 genebank accessions. Proc Natl Acad Sci USA. 118(34):e2104315118.\u003c/li\u003e\n\u003cli\u003eVictoria, F.C., Maia, L.C., Oliveira, A.C. (2011). In silico comparative analysis of SSR markers in plants. BMC Plat Biology. 11-15. https://doi.org/10.1186/1471-2229-11-15\u003c/li\u003e\n\u003cli\u003eWang, X., Bai, S., Zhang, Z., Zheng, F., Song, L., Wen, L., Guo, M., Cheng, G., Yao, W., Gao, Y. \u0026amp; Li, J. (2023). Front Plant Sci. Sec. Plant Bioinformatics. Vol 13. https://doi.org/10.3389/fpls.2023.1179009\u003c/li\u003e\n\u003cli\u003eWrite, F. (1990). The 'effective number of codons' used in a gene. Gene. Vol 87. Pages: 23-29. https://doi.org/10.1016/0378-1119(90)90491-9\u003c/li\u003e\n\u003cli\u003eXiao, F., Zhao, Y., Wang, X. et al. Characterization of the chloroplast genome of Gleditsia species and comparative analysis. Sci Rep 14, 4262 (2024). https://doi.org/10.1038/s41598-024-54608-6\u003c/li\u003e\n\u003cli\u003eYang, Y., Yuanye, D., Qing, L., Jinjian, L. \u0026amp; Xiwen, L. (2015). Complete Chloroplast Genome Sequence of Poisonous and Medicinal Plant Datura stramonium: Organizations and Implications for Genetic Engineering. PLOS ONE 10(2): e0118236. https://doi.org/10.1371/journal.pone.0118236\u003c/li\u003e\n\u003cli\u003eYang, Z. \u0026amp; Ji, Y. Comparative and Phylogenetic Analyses of the Complete Chloroplast Genomes of Three Arcto-Tertiary Relicts: Camptotheca acuminata, Davidia involucrata, and Nyssa sinensis. Front. Plant. Sci. 8, 1536 (2017).\u003c/li\u003e\n\u003cli\u003eZhang, D., Tu, J., Ding, X., Guan, W., Gong, L., Qiu, X. \u0026amp; Huang, Z. (2023). Analysis of the chloroplast genome and phylogenetic evolution of Bidens pilosa. BMC Genomics.(113). https://doi.org/10.1186/s12864-023-09195-7\u003c/li\u003e\n\u003cli\u003eZhao, C., Sun, K., Chen, S., Liang, C., Meng, J., Tang, Y., \u0026amp; Song, S. (2019). Characterization the complete chloroplast genome of the tomato (Solanum lycopersicum L.) from China. Mitochondrial DNA Part B, 4(1), 1374–1376. https://doi.org/10.1080/23802359.2019.1598300\u003c/li\u003e\n\u003cli\u003eZuntini, A.R., Carruthers, T., Maurin, O. \u003cem\u003eet al.\u003c/em\u003e Phylogenomics and the rise of the angiosperms. \u003cem\u003eNature\u003c/em\u003e 629, 843–850 (2024). https://doi.org/10.1038/s41586-024-07324-0\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":"[email protected]","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":"In-silico, Germplasm, Chili pepper, Bioinformatics","lastPublishedDoi":"10.21203/rs.3.rs-5657151/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5657151/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eAlthough many complete chloroplast (cp) genomes of different types of peppers have already been published, there has been no comprehensive study that summarizes all the characteristics of the Peruvian landrace “arnaucho” chili pepper (ACP) comparing it with other types of genomes in its Capsiceae tribe. In this study, a comprehensive analysis was conducted using data from cp genomes obtained from NCBI GenBank. These 14 genomes were annotated using Geseq, followed by genomic comparisons, chloroplast structure analysis, phylogeny, and repetitive sequence analysis, employing a variety of bioinformatics tools. The findings revealed length variations among the cp genomes, ranging from 156,583 bp in \u003cem\u003eC. lycianthoides\u003c/em\u003e to 157,390 bp in \u003cem\u003eC. pubescens\u003c/em\u003e, with a GC content of 37% across all genomes. The comparative genome analysis revealed that the greatest variation among the 14 genomes occurred in the non-coding regions. Arnaucho chili pepper exhibited greater divergence in coding regions with \u003cem\u003eC. lycianthoides\u003c/em\u003e, specifically in the genes \u003cem\u003eaccD\u003c/em\u003e, \u003cem\u003erpl20\u003c/em\u003e, \u003cem\u003erps12\u003c/em\u003e, \u003cem\u003eclpP\u003c/em\u003e, \u003cem\u003eycf2\u003c/em\u003e, \u003cem\u003endhF\u003c/em\u003e, \u003cem\u003endhA\u003c/em\u003e, \u003cem\u003eycf1\u003c/em\u003e, and \u003cem\u003erpl2\u003c/em\u003e. The results of the phylogeny and pairwise distance analysis in this study support that the arnaucho chili pepper clusters with \u003cem\u003eC. galapagoense\u003c/em\u003e, with an average distance value of 0.00002733. Additionally, the repetitive sequence analysis determined that ACP maintains a number of repetitive sequences similar to other \u003cem\u003eCapsicum \u003c/em\u003especies but possesses a lower number of SSRs (33). Finally, it was determined that the junction regions of ACP have a total length of 156,931 bp, similar to \u003cem\u003eC. galapagoense\u003c/em\u003e with 156,959 bp. The four boundary regions exhibited consistent gene patterns, except for the JSB region, where the \u003cem\u003eycf1\u003c/em\u003e gene in ACP was located only in the IRb region, whereas it was absent in other \u003cem\u003eCapsicum\u003c/em\u003e species. This research provides additional effective evidence for characterizing the entire cp genome and classifying species and genera within the Capsiceae tribe.\u003c/p\u003e","manuscriptTitle":"Comparative analysis of complete chloroplast genome of the Peruvian landrace of Capsicum chinense, arnaucho chili pepper, and related species of the Capsiceae tribe","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-12-21 15:37:59","doi":"10.21203/rs.3.rs-5657151/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","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":"6290c630-7b89-4d39-903d-cb67fa248c11","owner":[],"postedDate":"December 21st, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2025-01-08T04:53:18+00:00","versionOfRecord":[],"versionCreatedAt":"2024-12-21 15:37:59","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-5657151","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5657151","identity":"rs-5657151","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}