High-Resolution Genome of Temperate Acropora hyacinthus Reveals Regional Divergence and Resolves Co- localized Gene Paralogs

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MANALILI, Takuma MEZAKI, Takahiro TAGUCHI, Satoshi KUBOTA This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6428194/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 12 Feb, 2026 Read the published version in Conservation Genetics → Version 1 posted 9 You are reading this latest preprint version Abstract Reef-building Acropora corals face climate change threats, necessitating genomic resources to understand adaptation, particularly at range edges. Temperate populations of Acropora hyacinthus , like those in Kochi, Japan, are genetically distinct but lack a high-quality reference genome, hindering comparative studies. We generated a 480.16 Mb, highly contiguous (N50 6.99 Mb) PacBio HiFi genome assembly for Kochi A. hyacinthus , achieving 94.0% BUSCO completeness. Phylogenomic analysis using 588 single-copy orthologs confirmed significant divergence between the Kochi and subtropical Okinawa populations, placing Kochi within Acropora Clade IV but on a distinct, longer branch. The enhanced contiguity resolved complex genomic regions; notably, we identified and characterized two distinct, co-localized FOX gene paralogs (AhyaKCZ.442 and the divergent AhyaKCZ.437) within an orthogroup (OG0009671) significantly expanded in Kochi (Z = 3.881) and typically containing a single copy in other Acropora . The divergent paralog (AhyaKCZ.437) exhibits unique structural features, including an ammonium transporter motif, and a basal phylogenetic position, suggesting potential functional novelty relevant to temperate adaptation. While comparative analysis revealed substantial gene count differences in expanded orthogroups relative to a short-read reference (e.g., 21.89 vs 2.445 mean genes), methodological differences in sequencing and assembly likely contribute significantly to this disparity. This first high-quality temperate A. hyacinthus genome provides a critical resource for investigating regional adaptation, demonstrates the power of long-read sequencing for resolving paralogs, and underscores the need for comparable datasets in comparative genomics. Temperate Coral Comparative Genomics Long-read Sequencing Kuroshio Current Gene Paralog Figures Figure 1 Figure 2 Figure 3 Introduction Coral reefs are among the most biodiverse marine ecosystems, providing invaluable services such as fisheries, coastal protection, and tourism. Reef-building corals (Order Scleractinia) create this structure by depositing calcium carbonate and forming habitat for diverse organisms (Tortolero-Langarica et al., 2022 ). Acropora spp. (staghorn and tabular corals) are particularly important framework builders as the most diverse and abundant corals on many reefs (Rodríguez-Zaragoza & Arias-González, 2015 ). However, rapid climate change and ocean acidification threaten reefs globally by compromising coral calcification and survival (Hoegh-Guldberg et al., 2007 ). Understanding the biology and genetic basis of adaptation in key reef-builders like Acropora is therefore critical for reef conservation. Acropora hyacinthus , a widespread Indo-Pacific tabular coral, is a model for coral population genomics and adaptive variation. Although considered a single species, A. hyacinthus encompasses multiple cryptic lineages that are morphologically similar yet genetically distinct (Ladner & Palumbi, 2012 ). Studies across the Pacific reveal extensive cryptic diversity and introgression within A. hyacinthus populations (Ladner & Palumbi, 2012 ). In the Western Pacific, particularly around Japan, A. hyacinthus populations show regional genetic divergence. High-latitude temperate populations in Japan are genetically depauperate and isolated compared to tropical ones (Suzuki et al., 2016 ). Mitochondrial and nuclear markers identified at least three distinct A. hyacinthus lineages across Japanese waters, reflecting limited gene flow between southern (Ryukyu Archipelago) and northern (mainland Japan) reefs (Nakabayashi et al., 2019 ). Oceanographic features like the Kuroshio Current likely shape these patterns by facilitating northward larval transport while limiting return dispersal. This partial isolation suggests that temperate Japanese reefs may serve as refugia for A. hyacinthus under climate change (Nakabayashi et al., 2019 ). Thus, A. hyacinthus is an ideal system to investigate population genomics, cryptic diversity, and regional adaptation in reef corals. Coral genomics has progressed significantly over the past decade, providing resources to explore adaptation. The first coral genome sequenced was Acropora digitifera (a close relative of A. hyacinthus ) from Okinawa, assembled using short reads (~ 420 Mb genome) (Shinzato et al., 2011 ). This landmark genome provided ~ 23,700 gene models and initial insights into coral-specific genes for symbiosis and calcification (Shinzato et al., 2011 ). Subsequently, Shinzato et al. ( 2021 ) reported draft genomes for 18 acroporids (15 Acropora spp., 3 relatives), revealing the genus's genomic diversity. A high-quality, chromosome-level reference genome for A. hyacinthus (Palau population) was also released (NCBI Assembly GCA_020536085.1). This assembly (~ 450 Mb) achieved near chromosome-scale contiguity, a significant improvement over earlier short-read assemblies. These resources from Okinawan and other tropical Acropora have advanced our understanding of coral genomes. However, no genome exists for A. hyacinthus from its temperate range limit. Lacking a high-quality temperate genome, such as from Kochi (Shikoku, Japan), limits discerning the genomic divergence associated with high-latitude adaptation. Key genomic differences (structural variants, unique alleles, divergent repeats) may be missed using only tropical references for comparison. Therefore, a population-specific reference genome is needed to characterize the genomic basis of regional divergence in A. hyacinthus . Here, we generate a high-quality de novo genome assembly for A. hyacinthus from the temperate Kochi population to address this gap. We used PacBio HiFi long-read sequencing (producing accurate ~ 15–20 kb reads) to resolve complex and repetitive genomic regions problematic in short-read assemblies. We assembled the new Kochi genome to near-chromosome scale and comprehensively annotated its gene repertoire. We then compared the Kochi genome and gene set with existing tropical Acropora references ( A. digitifera from Okinawa, A. hyacinthus from Palau) to identify genomic differences between temperate and tropical lineages. Using single-copy orthologs (SCOs), we quantified genetic divergence and performed phylogenomic analyses placing the Kochi population within Acropora . This PacBio-based assembly resolves complex genomic loci (e.g., repetitive gene families, structural variants) previously collapsed or ambiguous. Our objectives were to: (1) produce a near chromosome-level reference genome for A. hyacinthus from Kochi and assess its completeness and gene content; (2) compare this temperate genome to existing tropical A. hyacinthus / A. digitifera assemblies to identify genomic differences; (3) evaluate population divergence via genome-wide ortholog analyses and phylogeny; and (4) illustrate the assembly's improved resolution of complex regions. This work provides the first high-quality genome for a high-latitude Acropora population, offering insight into the genomic basis of local adaptation and a crucial resource for coral genomics. A Kochi A. hyacinthus reference will facilitate future studies on coral resilience and evolution across environmental gradients, aiding conservation for reef-builders in a changing climate. Materials and Methods Sample Preparation and Sequencing We collected morphologically identified Acropora hyacinthus fragments from Nishidomari Bay, Japan (Figure 1), fixed them in 70% ethanol, and transferred them to CHAOS solution (4 M guanidine thiocyanate, 0.5% N-lauroylsarcosine sodium salt, 0.1 M 2-mercaptoethanol, 25 mM Tris-HCl pH 8.0) for storage at room temperature. For genomic DNA extraction, we combined CHAOS-solubilized material with an equal volume of 2×CTAB buffer (100 mM Tris, 20 mM EDTA, 1.4 M NaCl, 4% CTAB, pH 8.0) and incubated at 65°C for 60 minutes. We performed sequential phenol/chloroform and chloroform extractions (centrifuging at 12,000 rpm for 10 min each). We precipitated DNA from the aqueous layer using 10% volume 3 M sodium carbonate (pH 8.0) and an equal volume of 2-propanol (centrifuged 12,000 rpm, 5 min). We washed the DNA precipitate with 70% ethanol, partially dried it, and dissolved it in distilled water. We treated the solution with RNase (10 mg/ml, 1% volume) at 37°C for 60 minutes. We performed a second precipitation (10% vol 3 M sodium carbonate pH 8.0, equal volume ethanol; centrifuged 12,000 rpm, 10 min), washed the pellet with 70% ethanol, briefly centrifuged, partially dried, and dissolved it in distilled water. We further purified the DNA using the DNeasy PowerClean Pro Cleanup Kit (Qiagen). We evaluated DNA concentration/purity (NanoVue spectrophotometer) and integrity (agarose gel electrophoresis, Agilent Bioanalyzer 2100). We then quantified the high-quality extracted DNA (QuantiFluor dsDNA System, Quantus Fluorometer; Promega) and assessed fragment size distribution (5200 Fragment Analyzer System, Agilent HS Genomic DNA 50 kb Kit; Agilent Technologies). We purified the DNA using 1.8× DNA Clean Beads (MGI Tech), processed it with Short Read Eliminator XS (PacBio), and cleaned it again with 0.96× DNA Clean Beads. We constructed sequencing libraries using the SMRTbell Express Template Prep Kit 2.0 (PacBio). We performed sequencing on a PacBio Revio Sequencing System with the Revio Polymerase Kit to generate high-fidelity (HiFi) reads. Genome Assembly and Annotation We generated HiFi reads using SMRT Link software (v13.0.0.207600), which performed adapter removal, subread alignment, consensus calling (CCS), and quality filtering (removing reads < QV 20). We assembled the filtered HiFi reads using HiFi-asm (default conditions), retaining primary contigs and alternate haplotypes. We identified and removed mitochondrial contigs using MitoHIFI. Potential non-coral sequence contaminants were removed via DIAMOND alignment against an A. hyacinthus reference genome (Shinzato et al., 2021) followed by a custom filtering script. We evaluated the final primary assembly metrics (genome size, contig number, N50, GC content) using QUAST. We assessed genome completeness using BUSCO (v5) against the metazoa_odb10 lineage dataset. To prepare for annotation, we identified tandem repeats on the primary assembly using Tandem Repeat Finder (TRF) with parameters "2 5 7 80 10 50 2000 -d -h" and generated a repeat-masked version of the genome. We then predicted protein-coding genes using MAKER (v3.01.04) in two iterations (Rnd1, Rnd2). Input evidence included transcript alignments from Acropora ESTs (Moya et al., 2012), protein alignments from existing Acropora annotations (Shinzato et al., 2021), and ab initio predictions. We trained SNAP and AUGUSTUS on high-confidence gene models identified within the MAKER pipeline. We retained gene models meeting stringent criteria (Annotation Edit Distance [AED] < 0.5, transcript or protein support). We generated a final consensus gene set using EVidenceModeler (EVM) by merging ab initio predictions with transcript and protein alignments. We assessed the quality of the final predicted proteome using BUSCO (metazoa_odb10). We identified and consolidated redundant protein isoforms using Clusterize (Wright, 2024) and updated the final GFF annotation file using agat_sp_filter_feature_from_keep_list.pl to retain only primary, non-redundant gene models. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JBMUIC000000000. The version described in this paper is version JBMUIC010000000. Comparative and Phylogenetic Analyses We performed pairwise genome alignments using NUCMER (MUMmer suite) to compare the Kochi genome structure and determine alignment rates against other Acropora assemblies. We conducted protein-level homology and similarity searches using BLASTp. To investigate gene family evolution, we detected orthologous gene clusters (orthogroups) among 21 initial cnidarian species using OrthoFinder (v2.5.5). We inferred a species phylogeny using the STAG algorithm (unrooted) and STRIDE (rooting) within OrthoFinder. In a focused secondary analysis of 16 Acropora species, we identified significantly expanded or contracted orthogroups based on gene count variation Z-scores (|Z| > 2). We selected significantly expanded families for detailed characterization, inspecting gene trees (FigTree), aligning sequences (Clustal Omega via EMBL-EBI MSA), and visualizing alignments (Jalview). We functionally annotated selected orthogroups using BLASTp against UniProt (Jan 2025 release) and domain identification with InterProScan, retaining only those with clear phylogenetic patterns and functional annotation. Specifically for the FOX gene family, we performed two separate Maximum Likelihood (ML) phylogenetic analyses using MEGA12. The first analysis aligned 28 representative FOX sequences and inferred phylogeny using the LG+G+I (5 categories) model. The second re-analyzed the target FOX orthogroup (19 sequences, 295 positions) using the JTT+I model. Both analyses used Nearest-Neighbor-Interchange (NNI) search, automatic initial tree generation (NJ/MP), and fast adaptive bootstrap (1000 replicates, threshold 5.0) with no branch swap filter, including gaps/missing data and utilizing 18 threads. We visualized gene locations and structures using IGV and examined specific protein domain features (e.g., FOXA2-DBD residues 157–258) using sequence alignments in Jalview. This integrated workflow allowed us to characterize comparative genomics, orthogroup evolution, and specific gene family phylogenetics. Results Genome Assembly and Quality Assessment De novo assembly of the Acropora hyacinthus Kochi population yielded a 480.16 Mb genome partitioned into 189 contigs (Table 1), with a GC content of 39.03%. Contiguity was high (N50 = 6.99 Mb, L50 = 22). BUSCO analysis showed 94.0% genome completeness against the metazoa_odb10 dataset (Table 2), with 93.1% identified as complete and single-copy, 0.9% duplicated, 3.2% fragmented, and 2.8% missing. Gene Prediction and Proteome Completeness Gene prediction identified 35,721 protein-coding genes in the A. hyacinthus (Kochi) genome compared to what was predicted by Shinzato et al. (2021) at 27,215 in the A. hyacinthus (Okinawa) genome. Protein-level BUSCO assessment for A. hyacinthus (Kochi) showed 86.8% of BUSCOs were complete within the predicted proteome (Table 3), with 4.5% fragmented and 8.7% missing. For comparison, the A. hyacinthus (Okinawa) proteome showed 83.5% complete BUSCOs, 7.8% fragmented and 8.7% missing. Comparative Genomic Divergence within Acropora Genome-wide alignment analysis of the A. hyacinthus (Kochi) genome against other Acropora species revealed varying alignment rates. The alignment rate against A. hyacinthus (Okinawa) was 51.18%. Alignment rates against other Acropora species were: A. tenuis (Clade I): 1.03%, A. gemmifera (II): 6.67%, A. acuminata (III): 13.52%, A. digitifera (III): 23.36%, and A. echinata (IV): 3.87%. These alignment patterns are consistent with previously established clade divisions within Acropora . Additionally, protein similarity analysis showed high sequence identity between A. hyacinthus (Kochi and Okinawa) and A. acuminata , with median identities of 66.4%, 66.4%, and 65.9% respectively. Table 1. Genome assembly metrics for Acropora species. The Acropora hyacinthus assembly from Kochi is from this study, while all other assemblies, including the Acropora hyacinthus assembly from Okinawa, are sourced from Shinzato et al. (2021). Species Contigs Total Length MBP GC (%) N50 L50 Acropora hyacinthus (Kochi, This study) 189 480,158,887 480.16 39.03 6,994,003.00 22 Acropora digitifera 943 415,831,903 415.83 39.04 1,856,312.00 69 Acropora tenuis 1825 406,855,084 406.86 38.93 1,160,220.00 103 Acropora echinata 2229 409,633,553 409.63 38.94 1,812,701.00 63 Acropora gemmifera 2309 405,175,433 405.18 38.93 1,134,581.00 103 Acropora hyacinthus (Okinawa) 2837 452,664,370 452.66 39 1,562,592.00 88 Acropora nasuta 4645 419,336,012 419.34 38.97 1,045,289.00 111 Acropora microphthalma 4855 387,847,894 387.85 38.95 1,050,196.00 117 Acropora selago 5691 393,033,298 393.03 38.96 657,172.00 173 Acropora intermedia 6073 416,762,810 416.76 38.94 577,312.00 216 Acropora muricata 6680 420,608,036 420.61 39.03 574,627.00 217 Acropora florida 6816 442,722,093 442.72 38.96 751,376.00 174 Table 2. BUSCO assessment of genome completeness for Acropora species using the metazoa_odb10 lineage dataset. Species Complete (C) Single-Copy (S) Duplicated (D) Fragmented (F) Missing (M) Total BUSCOs Acropora hyacinthus (Kochi) 94.00% 93.10% 0.90% 3.20% 2.80% 954 Acropora digitifera 92.60% 92.20% 0.40% 3.90% 3.50% 954 Acropora echinata 87.50% 87.30% 0.20% 7.50% 5.00% 954 Acropora acuminata 91.90% 91.00% 0.90% 5.20% 2.90% 954 Acropora gemmifera 87.50% 86.70% 0.80% 7.20% 5.30% 954 Acropora tenuis 92.00% 91.30% 0.70% 4.50% 3.50% 954 Acropora hyacinthus (Okinawa) 92.40% 90.00% 2.40% 3.90% 3.70% 954 Table 3. BUSCO assessment of protein completeness for Acropora hyacinthus (Okinawa) and Acropora hyacinthus (Kochi) using the metazoa_odb10 lineage dataset. Species Complete (C) Single-Copy (S) Duplicated (D) Fragmented (F) Missing (M) Total BUSCOs Acropora hyacinthus (Okinawa) 83.50% 71.20% 12.30% 7.80% 8.70% 954 Acropora hyacinthus (Kochi) 86.80% 86.40% 0.40% 4.50% 8.70% 954 Regional Phylogeny of Acropora hyacinthus Phylogenomic analysis (588 single-copy orthologs) clearly separated the Kochi and Okinawa A. hyacinthus populations (Figure 2). The longer Kochi branch length suggests an accelerated evolutionary rate relative to the Okinawa population. Proteome-based phylogeny also placed both A. hyacinthus populations within Acropora Clade IV (Figure 2, inset), consistent with taxonomic classifications. These congruent signals underscore the evolutionary distinctiveness of the Kochi population. Orthogroup Analysis and FOX Gene Expansion Orthogroup analysis across 16 Acropora species and an outgroup identified 24,959 orthogroups, encompassing 455,187 genes (97.7%). We found 2,151 species-specific orthogroups, 8,425 orthogroups present across all 17 species, and 1,489 single-copy orthologs. Comparative analysis based on Z-scores (|Z| > 2) revealed significant orthogroup expansions in Kochi A. hyacinthus compared to the other 15 Acropora species. Notably, the mean gene count in expanded orthogroups was substantially higher in Kochi (mean = 21.89, SD = 24.83) than in Okinawa (mean = 2.445, SD = 2.099). For example, orthogroup OG0000015 contains 323 genes in Kochi A. hyacinthus compared to an average of approximately 20 genes in other species. Nine of the top 20 expanded orthogroups in Kochi were functionally annotated (Table 4). We selected orthogroup OG0009671 (Forkhead domain-related) for detailed analysis due to its species tree-approximating gene tree, clear annotation, and significant expansion in Kochi (Z=3.881; Kochi count=2 vs. mean=1.059). Within this group, we characterized two A. hyacinthus isoforms: AhyaKCZ.442 and AhyaKCZ.437. Both isoforms are located on contig ptg000050l (~6,994 kb), separated by 44,945 bp containing intervening genes (Exocyst complex component 8-like, Exosome complex component 10-like). This indicates the isoforms are distinct gene copies, not tandem duplicates. Phylogenetic analysis (Figure 3) showed AhyaKCZ.442 clusters robustly within the main Acropora FOX clade, while AhyaKCZ.437 occupies a basal position with a long branch (0.38623), suggesting greater divergence and a potential paralogous/specialized role. Cnidarian FOX sequences formed an intermediate clade between vertebrate FOXJ and FOXF subfamilies. Table 4. Top expanded orthogroups in Acropora hyacinthus (Kochi) compared to 15 other Acropora species, identified through OrthoFinder analysis. The table displays orthogroups with high Z-scores indicating significant expansion, along with the mean gene count across other species, standard deviation, gene count in the Kochi assembly, and the top UniProt BLAST match for functional annotation. Orthogroup Z-score Mean_Count Standard_Deviation Kochi Gene_Count uniprot BLAST Match (Top %id, E-value) OG0001291 3.881 2.529 10.429 43 not curated OG0001548 3.881 2.353 9.701 40 not curated OG0006919 3.881 1.176 4.851 20 not curated OG0007423 3.881 1.176 0.728 4 sp|A2A9A2|DMTA2_MOUSE OG0008061 3.881 1.118 0.485 3 sp|O73823|TAL1_XENLA OG0009241 3.881 1.059 4.366 18 not curated OG0009671 3.881 1.059 0.243 2 sp|Q63245|FOXD3_RAT OG0009784 3.881 1.059 0.243 2 NO MATCH OG0010077 3.881 1.059 0.243 2 sp|Q9D411|TSSK4_MOUSE OG0010119 3.881 1.059 0.243 2 sp|Q6DBY9|CHST1_DANRE OG0010189 3.881 1.059 0.243 2 sp|Q3SZ21|RPP30_BOVIN OG0010327 3.881 1.059 0.243 2 sp|F4K2M8|JMJ31_ARATH OG0000015 3.88 19.941 78.099 323 not curated OG0000021 3.88 17.412 58.145 243 not curated OG0000048 3.88 10.824 43.087 178 not curated OG0000107 3.88 7.706 29.459 122 sp|Q86TV6|TTC7B_HUMAN OG0000201 3.88 5.706 22.756 94 not curated OG0000018 3.878 18.588 51.163 217 not curated OG0000026 3.878 15.529 47.309 199 not curated OG0000052 3.878 10.294 38.6 160 not curated Preliminary analysis of domain architecture using InterProScan revealed that both isoforms contain the Forkhead domain (IPR001766; PF00250). However, AhyaKCZ.442 exhibits a more conserved domain structure, featuring multiple ProSitePatterns—indicative of potential phosphorylation and myristoylation sites—and predicted intrinsically disordered regions (IDRs). In contrast, while AhyaKCZ.437 retains the Forkhead domain, it lacks several of these conserved motifs and displays a notable substitution in helix 3 (a glutamic acid replacing the conserved glycine), as determined by alignment with the human FOXA2 DNA-binding domain (Li et al., 2017). Complementary analysis using the NCBI Conserved Domain Database confirmed that both proteins are classified as forkhead box transcription factors (CDD ID 15331620), with significant hits for FH_FOXQ2-like, Forkhead, FH, and COG5025. These domains, localized in the N-terminal region, are associated with DNA binding (GO:0003677) and transcription factor activity (GO:0003700). FIMO motif scanning (Table 5) further identified high-confidence occurrences of the FORK_HEAD_2 motif (PS00658) in both isoforms. The motif “WRNSIRH” was detected at positions 139–145 in AhyaKCZ.442 and 140–146 in AhyaKCZ.437, each with a p-value of 1.4×10^–9 and a q-value of 3×10^–7. In addition, AhyaKCZ.442 harbors several motifs related to metabolic and transport functions (including motifs for MIP, CPSASE_2, COA_TRANSF_2, and AIPM_HOMOCIT_SYNTH_2), as well as motifs corresponding to REACTION_CENTER, CYTOCHROME_B559, HEMOCYANIN_1, TYROSINASE_2, SULFATASE_1, MACPF_1, GLYCO_HORMONE_BETA_1, BTG_1, and RIBOSOMAL_L16_2. Conversely, AhyaKCZ.437 uniquely exhibits an ammonium transport motif (PS01219) and additional motifs linked to enzyme-related domains such as CARBOXYPEPT_SER_SER, PEROXIDASE_2, and HSP70_3. Sequence analysis confirmed that both isoforms conserve critical DNA-binding residues (Arg140, Asn141, and Ser142) within the FORK_HEAD_2 motif, although the “WRNSIRH” sequence deviates from the canonical motifs observed in vertebrate FOXJ and FOXF subfamilies. Table 5. Motif analysis of the FOX paralogs AhyaKCZ.442 and AhyaKCZ.437 from Acropora hyacinthus (Kochi) using FIMO motif scanning. The table lists identified motifs, their IDs, matched sequences, start and end positions, strand, p-values, and q-values. Both paralogs contain the FORK HEAD_2 motif, while AhyaKCZ.437 uniquely possesses an ammonium transport motif. Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence PS00658 FORK_HEAD_2 evm.model.ptg000050l.442 + 139 145 1.4e-09 3e-07 WRNSIRH PS00658 FORK_HEAD_2 evm.model.ptg000050l.437 + 140 146 1.4e-09 3e-07 WRNSIRH PS01219 AMMONIUM_TRANSP evm.model.ptg000050l.437 + 41 64 2.71e-06 0.00101 DPAVSPCVPYWGASYASPNMFPLR PS00221 MIP evm.model.ptg000050l.442 + 37 45 1.09e-05 0.00472 NSVPAFSFA PS00537 CYTOCHROME_B559 evm.model.ptg000050l.442 + 26 40 1.32e-05 0.00586 LTSGRFYLPGTNSVP PS00117 GAL_P_UDP_TRANSF_I evm.model.ptg000050l.442 + 132 149 1.38e-05 0.00516 FRNRGPGWRNSIRHNLSL PS00353 HMG_BOX_1 evm.model.ptg000050l.437 + 178 189 1.73e-05 0.00754 FSRGEYKRKRRV PS00867 CPSASE_2 evm.model.ptg000050l.442 + 217 224 1.88e-05 0.0087 VIPLNTRC PS00131 CARBOXYPEPT_SER_SER evm.model.ptg000050l.437 + 50 57 1.96e-05 0.00839 YWGASYAS PS00197 2FE2S_FER_1 evm.model.ptg000050l.442 + 72 80 2.55e-05 0.0116 CHTGHCYQP PS00244 REACTION_CENTER evm.model.ptg000050l.442 + 65 91 3.18e-05 0.0115 DMRGLPACHTGHCYQPPFQGVMSYHGN PS00229 TAU_MAP_1 evm.model.ptg000050l.437 + 189 201 3.26e-05 0.0129 VSRRNHGFFAAGI PS00496 PII_GLNB_UMP evm.model.ptg000050l.437 + 50 55 3.31e-05 0.0148 YWGASY PS01036 HSP70_3 evm.model.ptg000050l.437 + 201 215 4.15e-05 0.0187 ISIEGGSGQVDEMKR PS00209 HEMOCYANIN_1 evm.model.ptg000050l.442 + 61 80 4.72e-05 0.0178 HRDKDMRGLPACHTGHCYQP PS00701 RIBOSOMAL_L16_2 evm.model.ptg000050l.442 + 158 169 4.76e-05 0.00982 RSPNGKGHFWAI PS00701 RIBOSOMAL_L16_2 evm.model.ptg000050l.437 + 159 170 4.76e-05 0.00982 RSPNGKGHFWAI PS01152 HESB evm.model.ptg000050l.442 + 217 234 5.32e-05 0.0174 VIPLNTRCSNKGAENRSF PS00504 FRD_SDH_FAD_BINDING evm.model.ptg000050l.437 + 192 201 5.4e-05 0.021 RNHGFFAAGI PS00876 IDO_1 evm.model.ptg000050l.442 + 104 114 5.84e-05 0.0154 IGKAILSSPQQ PS00498 TYROSINASE_2 evm.model.ptg000050l.442 + 54 65 5.92e-05 0.0247 SPQMYSPHRDKD PS00279 MACPF_1 evm.model.ptg000050l.442 + 41 52 6.03e-05 0.0207 AFSFAPYFGTGY PS00436 PEROXIDASE_2 evm.model.ptg000050l.437 + 65 76 6.26e-05 0.0266 SDADIRVFSHGS PS00816 AIPM_HOMOCIT_SYNTH_2 evm.model.ptg000050l.442 + 86 99 6.82e-05 0.0268 MSYHGNNDDKPTQS PS00261 GLYCO_HORMONE_BETA_1 evm.model.ptg000050l.442 + 73 79 7.02e-05 0.0299 HTGHCYQ PS01274 COA_TRANSF_2 evm.model.ptg000050l.442 + 97 105 7.25e-05 0.0329 TQSYIGLIG PS00187 TPP_ENZYMES evm.model.ptg000050l.437 + 189 208 7.47e-05 0.031 VSRRNHGFFAAGISIEGGSG PS00960 BTG_1 evm.model.ptg000050l.442 + 37 57 7.48e-05 0.0283 NSVPAFSFAPYFGTGYISPQM PS00873 NA_ALANINE_SYMP evm.model.ptg000050l.437 + 205 220 7.56e-05 0.0339 GGSGQVDEMKRQTYDG PS00876 IDO_1 evm.model.ptg000050l.437 + 105 115 7.71e-05 0.0154 IGNAILSSPRQ PS00607 PDEASE_II evm.model.ptg000050l.437 + 99 113 8.01e-05 0.0358 QPYIDLIGNAILSSP PS00448 CLOS_CELLULOSOME_RPT evm.model.ptg000050l.437 + 103 122 8.23e-05 0.0332 DLIGNAILSSPRQKLVLSDI PS00523 SULFATASE_1 evm.model.ptg000050l.442 + 56 68 8.27e-05 0.0347 QMYSPHRDKDMRG PS00997 G10_1 evm.model.ptg000050l.437 + 27 49 8.77e-05 0.0356 LPCSGRFYLLQPNADPAVSPCVP PS00647 THYMID_PHOSPHORYLASE evm.model.ptg000050l.437 + 9 24 9.56e-05 0.0414 SSRFAHTESLTTRFLS PS01288 UPF0027 evm.model.ptg000050l.442 + 52 81 9.57e-05 0.0371 YISPQMYSPHRDKDMRGLPACHTGHCYQPP PS00675 SIGMA54_INTERACT_1 evm.model.ptg000050l.442 + 153 166 9.99e-05 0.0224 FVKVGRSPNGKGHF PS00675 SIGMA54_INTERACT_1 evm.model.ptg000050l.437 + 154 167 9.99e-05 0.0224 FVKVGRSPNGKGHF Discussion Kochi A. hyacinthus Genome Assembly and Annotation This study presents the first high-quality genome assembly of Acropora hyacinthus from a temperate region (Kochi, Japan). Using PacBio HiFi sequencing, we generated an assembly that spans 480.16 Mb across 189 contigs, with a contig N50 of 6.99 Mb and a BUSCO completeness of 94.0% (Table 1; Table 2). In contrast, previous assemblies—including a draft genome from Okinawa assembled with short reads (Shinzato et al., 2021) and a chromosome-level assembly from Palau (NCBI GCA_020536085.1)—offer complementary perspectives from tropical populations. Although the Palau genome exhibits even higher continuity, our Kochi assembly is the first for a temperate A. hyacinthus and provides an essential resource for evaluating genomic differences at the species’ range edge. The high contiguity and completeness achieved here address the fragmentation issues typical of short-read assemblies (Shinzato et al., 2011) and establish a robust foundation for comparative analyses across latitudes. Gene content in the Kochi genome is in line with observations in other acroporids, with improvements arising from enhanced assembly continuity and updated annotation methods. We predicted 35,721 protein-coding genes, which is higher than the ~27,200 reported for the Okinawa genome (Shinzato et al., 2021). This difference is likely due to improved resolution of gene fragments and duplicated regions in the Kochi assembly rather than a true biological expansion of gene number. The overall genome BUSCO score of ~94% (Table 2) confirms the presence of the expected metazoan gene repertoire (Manni et al., 2021), while the proteome BUSCO score of 86.8% (Table 3) supports the effectiveness of our MAKER-based annotation. Furthermore, cross-species comparisons show that over 90% of Kochi proteins align with orthologs in other Acropora species, reinforcing the accuracy of our predictions. Notably, the enhanced continuity of the Kochi assembly has allowed for the recovery of complete gene sequences for loci that were previously partial or absent in shorter assemblies. Overall, the Kochi genome’s assembly and annotation provide a reliable temperate reference that complements existing tropical datasets, enabling detailed comparative analyses of local adaptation and evolutionary divergence. Investigating Genomic Differences in Variable Regions The Kochi genome’s enhanced contiguity enabled us to resolve subtle differences in gene family structure, exemplified by the analysis of orthogroup OG0009671, associated with FOX (Forkhead) domain proteins. While most Acropora species typically present a single copy in this group, our Kochi assembly revealed two distinct copies—namely, AhyaKCZ.442 and AhyaKCZ.437—resulting in a significant copy-number expansion (Z = 3.881; mean ≈ 1.06 in other species). Notably, these two isoforms are co-localized on contig ptg000050l , separated by approximately 45 kb. Phylogenetic analysis indicates that AhyaKCZ.442 clusters with the conventional FOX homologs of other Acropora species, while AhyaKCZ.437 occupies a basal position with a long branch. This divergence suggests that AhyaKCZ.437 has followed a distinct evolutionary trajectory, potentially reflecting neofunctionalization or subfunctionalization. Furthermore, domain analyses reveal that AhyaKCZ.437 uniquely harbors an ammonium transporter motif (PS01219) alongside the canonical forkhead domain, a feature absent in AhyaKCZ.442. Such a domain configuration is unusual among FOX proteins and may indicate a modified regulatory role or an integration of additional cellular functions. The discovery of the divergent paralog AhyaKCZ.437 is significant for several reasons. First, it underscores the ability of HiFi sequencing to differentiate highly similar, co-localized genes that might otherwise be collapsed in short-read assemblies. Second, the presence of a uniquely modified FOX isoform in the temperate Kochi genome may signal subtle adaptations in gene regulation that are specific to the temperate environment. While further functional studies are necessary to elucidate the biological role of AhyaKCZ.437, its distinct structural features and phylogenetic placement suggest that even conserved gene families can harbor hidden diversity with potential adaptive implications. Challenges in Quantifying Differences (Gene Count Disparity) A notable observation from our comparative orthogroup analysis is the marked disparity in gene count for expanded orthogroups between the Kochi HiFi assembly and the Okinawa short-read assembly. On average, expanded orthogroups in the Kochi genome contain approximately 21.89 genes, whereas the corresponding groups in the Okinawa genome average only about 2.445 genes. This roughly 9-fold difference is unlikely to represent a true biological expansion in the temperate population but rather reflects methodological differences in sequencing and assembly. The long-read HiFi technology provides superior resolution of repetitive regions and duplicated gene copies that short-read assemblies tend to collapse (Shinzato et al., 2021). In addition, the gene prediction and filtering pipelines used for the Kochi and Okinawa datasets differ, further contributing to these quantitative discrepancies. These technical factors complicate direct comparisons of gene family size and highlight the need for caution when interpreting such differences as biologically meaningful. Standardizing assembly and annotation approaches across samples would be necessary to disentangle technical bias from true genetic variation. Future work employing comparable HiFi-based sequencing for multiple individuals from different regions could resolve whether the observed gene count differences are consistent features or artifacts of differing methodologies. This challenge underscores the importance of using high-quality, uniformly generated genomic data when quantifying gene family variation across populations. Limitations and Future Perspectives While our Kochi Acropora hyacinthus genome assembly offers a valuable temperate reference, several limitations must be acknowledged. First, this study is based on a single individual from Kochi (with one Okinawan genome for comparison), which restricts our ability to capture the full range of population-level genetic variation. Some observed differences may reflect individual variation or technical artifacts rather than fixed regional traits (Ladner & Palumbi, 2012). Future studies involving population-scale sequencing across the Northwest Pacific are needed to validate and extend our findings. Our automated gene annotation, although robust, may still contain errors common to draft annotations. Manual curation of key genes—especially those involved in stress response or symbiosis—will further refine the dataset. Additionally, this study focused solely on the coral host genome; comprehensive insights into coral adaptation would also require analysis of the symbiotic algae and associated microbial communities. Looking forward, the Kochi genome opens avenues for functional and comparative genomic studies. Future work should examine genetic variants and expression differences that correlate with tolerance to cooler, more variable environments. Functional assays, such as common garden experiments and transcriptome profiling, can help determine whether temperate populations possess unique adaptations. Expanding high-quality, HiFi-based genomic resources to multiple populations and coral species will be essential to distinguish true adaptive variation from technical artifacts, ultimately enhancing our understanding of coral evolution and resilience in a changing ocean. Conclusion This work provides the first high-fidelity genome assembly for the reef-building coral Acropora hyacinthus from a temperate environment (Kochi, Japan). Leveraging this high-quality resource, our analysis of conserved single-copy orthologs confirmed substantial phylogenetic divergence relative to the subtropical Okinawa population, providing a clear genomic basis for regional differentiation. The enhanced contiguity inherent to the HiFi assembly proved critical for investigating complex genomic loci; specifically, it enabled the resolution and characterization of two distinct, co-localized FOX gene paralogs (AhyaKCZ.442 and the divergent AhyaKCZ.437) within an expanded orthogroup, revealing potential functional novelty missed in previous assemblies. While this demonstrates the value of long-read data for untangling genomic complexity, our findings also underscore the limitations of quantitatively comparing gene content (e.g., gene family sizes in expanded orthogroups) when datasets derive from different sequencing technologies and assembly methods. Future progress in comparative coral genomics, particularly for quantifying structural and gene content variation, necessitates the generation of comparable high-quality, long-read genome assemblies across diverse populations. Expanding the generation and analysis of HiFi genomes will enable deeper investigations into functionally relevant genomic divergences, such as the intriguing FOX paralog system identified here, across environmental gradients in these critical foundation species. Declarations Ethical Approval Permits for the collection of A. hyacinthus samples were obtained from the local government of Kochi Prefecture (5高漁管第123号). Funding Declaration This research was funded by the Japan Society for the Promotion of Science KAKENHI Grants-in-Aid for Scientific Research Project NOs. 21K05734, and 22K05820 Author Contribution S.E.M., T.T., and S.K. led the conceptualization. S.E.M. led the formal analysis and writing of the original draft. T.M. led the identification of the target sample. T.T. and S.K. led the project administration, with T.M. providing support. All authors reviewed the manuscript. Acknowledgement We extend our gratitude to the Division of Biological Research at the Science Research Center, Kochi University Oko Campus, for providing the essential resources for this study. Additionally, we acknowledge Bioengineering Lab. Co., Ltd. (株式会社生物技研) for performing the sequencing. Data Availability The whole genome assembly in this study has been deposited at GenBank under the accession JBMUIC000000000. References Baird, A. H., Cumbo, V. R., & Leggat, W. (2012). Poleward expansion of coral reefs in Japan: An investigation of the effects of habitat, host and symbiont. Coral Reefs , 31 (3), 607-611. Campbell, M. S., Holt, C., Moore, B., & Yandell, M. (2014). Genome annotation and curation using MAKER and MAKER-P. Current Protocols in Bioinformatics , 48 (1), 4.11.1-4.11.39. Fifer, J., Yuan, Y., Moya, A., & Davies, S. W. (2022). Genetic divergence and range expansion in a western North Pacific coral. Science of the Total Environment , 813 , 152423. 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Cite Share Download PDF Status: Published Journal Publication published 12 Feb, 2026 Read the published version in Conservation Genetics → Version 1 posted Editorial decision: Revision requested 28 Jul, 2025 Reviews received at journal 15 Jul, 2025 Reviewers agreed at journal 17 Jun, 2025 Reviews received at journal 16 Jun, 2025 Reviewers agreed at journal 10 Jun, 2025 Reviewers invited by journal 15 Apr, 2025 Editor assigned by journal 12 Apr, 2025 Submission checks completed at journal 12 Apr, 2025 First submitted to journal 11 Apr, 2025 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-6428194","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":476540068,"identity":"72a4aac6-7601-4862-b5e7-3f801af16b9b","order_by":0,"name":"Sam Edward N. MANALILI","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABFklEQVRIie3PMUvEMBTA8dRAXXJmkxwK+QqvHIhD5b5KiuB0BccODnWJk3Y98SO4VAo35wi42OJa0UEQ3A4OBLlB1KSb0NYbBfPfHrwfeUHI5frLbWGcqiWEhNpJHK9BfOyl82lytDtMLYF1CPJSTEodgrJjD+Fnd2KjPnni/qZ3qgYSk9H9dbR8BsTptmolUMY5nty+BtIcpobSJ3v1omDmsODySrQTZImvvYYEkhhS5ZYIeGwnPFsY8qnHDYkkI6NpVaz6CKrNK7HUUUNUCQTo+az3FagXuY4v9KEl8zQRhNWD2b4A1vkXnsU3L5N3fZBRrd8+4GtMs6p4WCUhpzsdh5nUz5E1m6xzvSWqfl1xuVyu/9U3SblkMHaaSFcAAAAASUVORK5CYII=","orcid":"","institution":"Kochi University","correspondingAuthor":true,"prefix":"","firstName":"Sam","middleName":"Edward N.","lastName":"MANALILI","suffix":""},{"id":476540069,"identity":"acabc85b-444f-41ab-b39b-ac6048ffd274","order_by":1,"name":"Takuma MEZAKI","email":"","orcid":"","institution":"Kuroshio Biological Research Foundation","correspondingAuthor":false,"prefix":"","firstName":"Takuma","middleName":"","lastName":"MEZAKI","suffix":""},{"id":476540070,"identity":"2f32848e-3ba3-4848-9efb-96a588073e78","order_by":2,"name":"Takahiro TAGUCHI","email":"","orcid":"","institution":"Kochi University","correspondingAuthor":false,"prefix":"","firstName":"Takahiro","middleName":"","lastName":"TAGUCHI","suffix":""},{"id":476540071,"identity":"ce295d06-1432-41dd-9373-8404332253cf","order_by":3,"name":"Satoshi KUBOTA","email":"","orcid":"","institution":"Kochi University","correspondingAuthor":false,"prefix":"","firstName":"Satoshi","middleName":"","lastName":"KUBOTA","suffix":""}],"badges":[],"createdAt":"2025-04-11 12:08:20","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-6428194/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-6428194/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1007/s10592-026-01760-3","type":"published","date":"2026-02-12T15:58:08+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":85826024,"identity":"1818aeeb-aeb0-44e6-8c53-e5e2eb2c1dd5","added_by":"auto","created_at":"2025-07-02 07:11:33","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":1435258,"visible":true,"origin":"","legend":"\u003cp\u003eSampling location and morphology of the \u003cem\u003eAcropora hyacinthus\u003c/em\u003e individual sequenced in this study. (a) Map showing the sampling site (red dot) in Nishidomari Bay, Otsuki, Kochi, Japan. Inset maps show location within Japan (top) and Kochi Prefecture (bottom). Map data © OpenStreetMap contributors. (b) \u003cem\u003eIn situ\u003c/em\u003e view of the source colony. (c, d) Close-up views illustrating coral branch structure, showing the arrangement of radial corallites and polyp detail. Scale bars: (c) 5 mm, (d) 1 cm. Map created with \u003cem\u003eMaperitive\u003c/em\u003e \u003cem\u003ev2. 4. 3.\u003c/em\u003e\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-6428194/v1/8e8c2f032e61971a077ab60b.png"},{"id":85826022,"identity":"84e8a834-c5a2-4291-aa98-5d58aa466774","added_by":"auto","created_at":"2025-07-02 07:11:33","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":212439,"visible":true,"origin":"","legend":"\u003cp\u003eSpecies tree generated by OrthoFinder based on 588 conserved single-copy orthologs (SCOs) across Cnidaria, including non-Acroporidae corals. The resolution of the Acroporidae clade within Scleractinia is consistent with Shinzato et al. (2021). Inset figure illustrates the phylogenetic relationships within \u003cem\u003eAcropora\u003c/em\u003e and the distinct separation of \u003cem\u003eA. hyacinthus\u003c/em\u003e populations from Kochi and Okinawa within \u003cem\u003eAcropora\u003c/em\u003e Clade IV. The longer branch length of the Kochi lineage suggests a potentially accelerated evolutionary rate.\u003c/p\u003e","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-6428194/v1/7522bc3a292f1d5a11b1c1d2.png"},{"id":85826027,"identity":"7961f336-560e-4da9-aee3-8639c8cb5fac","added_by":"auto","created_at":"2025-07-02 07:11:33","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":136922,"visible":true,"origin":"","legend":"\u003cp\u003ePhylogenetic analysis of FOX family proteins, including AhyaKCZ.442 and AhyaKCZ.437 from \u003cem\u003eAcropora hyacinthus\u003c/em\u003e (Kochi), along with representative sequences from vertebrates and other invertebrates. The analysis shows AhyaKCZ.442 clustering within the main \u003cem\u003eAcropora\u003c/em\u003e FOX clade, while AhyaKCZ.437 occupies a basal position with a long branch, indicating greater divergence. Phylogenetic relationships were inferred using Maximum Likelihood (ML) in MEGA12 [2] based on the Jones-Taylor-Thornton (JTT) (1992) [1] model (+F). Rate heterogeneity was modeled using a Gamma distribution (+G, 5 categories, α=0.9739) and invariant sites (+I, 0.60%). The tree with the highest log likelihood is shown, with branch support derived from adaptive bootstrapping [2]. The heuristic search employed Neighbor-Joining [3] / Maximum Parsimony starting trees. The final alignment comprised 43 sequences and 1,170 positions.\u003c/p\u003e\n\u003cp\u003e1. Jones D.T., Taylor W.R., and Thornton J.M. (1992). The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences 8: 275-282.\u003c/p\u003e\n\u003cp\u003e2. Kumar S., Stecher G., Suleski M., Sanderford M., Sharma S., and Tamura K. (2024). Molecular Evolutionary Genetics Analysis Version 12 for adaptive and green computing. Molecular Biology and Evolution 41:1-9.\u003c/p\u003e\n\u003cp\u003e3. Saitou N. and Nei M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425.\u003c/p\u003e","description":"","filename":"3.png","url":"https://assets-eu.researchsquare.com/files/rs-6428194/v1/25918a33283c14f7be3318c7.png"},{"id":102785299,"identity":"f709026f-2009-4342-a136-f91e9e0807dc","added_by":"auto","created_at":"2026-02-16 16:04:52","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":3015615,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6428194/v1/f1eb5df5-92d8-4607-95dd-2b6ff705aebe.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"High-Resolution Genome of Temperate Acropora hyacinthus Reveals Regional Divergence and Resolves Co- localized Gene Paralogs","fulltext":[{"header":"Introduction","content":"\u003cp\u003eCoral reefs are among the most biodiverse marine ecosystems, providing invaluable services such as fisheries, coastal protection, and tourism. Reef-building corals (Order Scleractinia) create this structure by depositing calcium carbonate and forming habitat for diverse organisms (Tortolero-Langarica et al., \u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). \u003cem\u003eAcropora\u003c/em\u003e spp. (staghorn and tabular corals) are particularly important framework builders as the most diverse and abundant corals on many reefs (Rodr\u0026iacute;guez-Zaragoza \u0026amp; Arias-Gonz\u0026aacute;lez, \u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e2015\u003c/span\u003e). However, rapid climate change and ocean acidification threaten reefs globally by compromising coral calcification and survival (Hoegh-Guldberg et al., \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e2007\u003c/span\u003e). Understanding the biology and genetic basis of adaptation in key reef-builders like \u003cem\u003eAcropora\u003c/em\u003e is therefore critical for reef conservation.\u003c/p\u003e \u003cp\u003e \u003cem\u003eAcropora hyacinthus\u003c/em\u003e, a widespread Indo-Pacific tabular coral, is a model for coral population genomics and adaptive variation. Although considered a single species, \u003cem\u003eA. hyacinthus\u003c/em\u003e encompasses multiple cryptic lineages that are morphologically similar yet genetically distinct (Ladner \u0026amp; Palumbi, \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2012\u003c/span\u003e). Studies across the Pacific reveal extensive cryptic diversity and introgression within \u003cem\u003eA. hyacinthus\u003c/em\u003e populations (Ladner \u0026amp; Palumbi, \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2012\u003c/span\u003e). In the Western Pacific, particularly around Japan, \u003cem\u003eA. hyacinthus\u003c/em\u003e populations show regional genetic divergence. High-latitude temperate populations in Japan are genetically depauperate and isolated compared to tropical ones (Suzuki et al., \u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e2016\u003c/span\u003e). Mitochondrial and nuclear markers identified at least three distinct \u003cem\u003eA. hyacinthus\u003c/em\u003e lineages across Japanese waters, reflecting limited gene flow between southern (Ryukyu Archipelago) and northern (mainland Japan) reefs (Nakabayashi et al., \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e2019\u003c/span\u003e). Oceanographic features like the Kuroshio Current likely shape these patterns by facilitating northward larval transport while limiting return dispersal. This partial isolation suggests that temperate Japanese reefs may serve as refugia for \u003cem\u003eA. hyacinthus\u003c/em\u003e under climate change (Nakabayashi et al., \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e2019\u003c/span\u003e). Thus, \u003cem\u003eA. hyacinthus\u003c/em\u003e is an ideal system to investigate population genomics, cryptic diversity, and regional adaptation in reef corals.\u003c/p\u003e \u003cp\u003eCoral genomics has progressed significantly over the past decade, providing resources to explore adaptation. The first coral genome sequenced was \u003cem\u003eAcropora digitifera\u003c/em\u003e (a close relative of \u003cem\u003eA. hyacinthus\u003c/em\u003e) from Okinawa, assembled using short reads (~\u0026thinsp;420 Mb genome) (Shinzato et al., \u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e2011\u003c/span\u003e). This landmark genome provided ~\u0026thinsp;23,700 gene models and initial insights into coral-specific genes for symbiosis and calcification (Shinzato et al., \u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e2011\u003c/span\u003e). Subsequently, Shinzato et al. (\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e2021\u003c/span\u003e) reported draft genomes for 18 acroporids (15 \u003cem\u003eAcropora\u003c/em\u003e spp., 3 relatives), revealing the genus's genomic diversity. A high-quality, chromosome-level reference genome for \u003cem\u003eA. hyacinthus\u003c/em\u003e (Palau population) was also released (NCBI Assembly GCA_020536085.1). This assembly (~\u0026thinsp;450 Mb) achieved near chromosome-scale contiguity, a significant improvement over earlier short-read assemblies. These resources from Okinawan and other tropical \u003cem\u003eAcropora\u003c/em\u003e have advanced our understanding of coral genomes. However, no genome exists for \u003cem\u003eA. hyacinthus\u003c/em\u003e from its temperate range limit. Lacking a high-quality temperate genome, such as from Kochi (Shikoku, Japan), limits discerning the genomic divergence associated with high-latitude adaptation. Key genomic differences (structural variants, unique alleles, divergent repeats) may be missed using only tropical references for comparison. Therefore, a population-specific reference genome is needed to characterize the genomic basis of regional divergence in \u003cem\u003eA. hyacinthus\u003c/em\u003e.\u003c/p\u003e \u003cp\u003eHere, we generate a high-quality de novo genome assembly for \u003cem\u003eA. hyacinthus\u003c/em\u003e from the temperate Kochi population to address this gap. We used PacBio HiFi long-read sequencing (producing accurate\u0026thinsp;~\u0026thinsp;15\u0026ndash;20 kb reads) to resolve complex and repetitive genomic regions problematic in short-read assemblies. We assembled the new Kochi genome to near-chromosome scale and comprehensively annotated its gene repertoire. We then compared the Kochi genome and gene set with existing tropical \u003cem\u003eAcropora\u003c/em\u003e references (\u003cem\u003eA. digitifera\u003c/em\u003e from Okinawa, \u003cem\u003eA. hyacinthus\u003c/em\u003e from Palau) to identify genomic differences between temperate and tropical lineages. Using single-copy orthologs (SCOs), we quantified genetic divergence and performed phylogenomic analyses placing the Kochi population within \u003cem\u003eAcropora\u003c/em\u003e. This PacBio-based assembly resolves complex genomic loci (e.g., repetitive gene families, structural variants) previously collapsed or ambiguous. Our objectives were to: (1) produce a near chromosome-level reference genome for \u003cem\u003eA. hyacinthus\u003c/em\u003e from Kochi and assess its completeness and gene content; (2) compare this temperate genome to existing tropical \u003cem\u003eA. hyacinthus\u003c/em\u003e/\u003cem\u003eA. digitifera\u003c/em\u003e assemblies to identify genomic differences; (3) evaluate population divergence via genome-wide ortholog analyses and phylogeny; and (4) illustrate the assembly's improved resolution of complex regions. This work provides the first high-quality genome for a high-latitude \u003cem\u003eAcropora\u003c/em\u003e population, offering insight into the genomic basis of local adaptation and a crucial resource for coral genomics. A Kochi \u003cem\u003eA. hyacinthus\u003c/em\u003e reference will facilitate future studies on coral resilience and evolution across environmental gradients, aiding conservation for reef-builders in a changing climate.\u003c/p\u003e"},{"header":"Materials and Methods","content":"\u003cp\u003e\u003cstrong\u003eSample Preparation and Sequencing\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe collected morphologically identified \u003cem\u003eAcropora hyacinthus\u003c/em\u003e fragments from Nishidomari Bay, Japan (Figure 1), fixed them in 70% ethanol, and transferred them to CHAOS solution (4 M guanidine thiocyanate, 0.5% N-lauroylsarcosine sodium salt, 0.1 M 2-mercaptoethanol, 25 mM Tris-HCl pH 8.0) for storage at room temperature. For genomic DNA extraction, we combined CHAOS-solubilized material with an equal volume of 2\u0026times;CTAB buffer (100 mM Tris, 20 mM EDTA, 1.4 M NaCl, 4% CTAB, pH 8.0) and incubated at 65\u0026deg;C for 60 minutes. We performed sequential phenol/chloroform and chloroform extractions (centrifuging at 12,000 rpm for 10 min each). We precipitated DNA from the aqueous layer using 10% volume 3 M sodium carbonate (pH 8.0) and an equal volume of 2-propanol (centrifuged 12,000 rpm, 5 min). We washed the DNA precipitate with 70% ethanol, partially dried it, and dissolved it in distilled water. We treated the solution with RNase (10 mg/ml, 1% volume) at 37\u0026deg;C for 60 minutes. We performed a second precipitation (10% vol 3 M sodium carbonate pH 8.0, equal volume ethanol; centrifuged 12,000 rpm, 10 min), washed the pellet with 70% ethanol, briefly centrifuged, partially dried, and dissolved it in distilled water. We further purified the DNA using the DNeasy PowerClean Pro Cleanup Kit (Qiagen). We evaluated DNA concentration/purity (NanoVue spectrophotometer) and integrity (agarose gel electrophoresis, Agilent Bioanalyzer 2100). We then quantified the high-quality extracted DNA (QuantiFluor dsDNA System, Quantus Fluorometer; Promega) and assessed fragment size distribution (5200 Fragment Analyzer System, Agilent HS Genomic DNA 50 kb Kit; Agilent Technologies). We purified the DNA using 1.8\u0026times; DNA Clean Beads (MGI Tech), processed it with Short Read Eliminator XS (PacBio), and cleaned it again with 0.96\u0026times; DNA Clean Beads. We constructed sequencing libraries using the SMRTbell Express Template Prep Kit 2.0 (PacBio). We performed sequencing on a PacBio Revio Sequencing System with the Revio Polymerase Kit to generate high-fidelity (HiFi) reads.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eGenome Assembly and Annotation\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe generated HiFi reads using SMRT Link software (v13.0.0.207600), which performed adapter removal, subread alignment, consensus calling (CCS), and quality filtering (removing reads \u0026lt; QV 20). We assembled the filtered HiFi reads using HiFi-asm (default conditions), retaining primary contigs and alternate haplotypes. We identified and removed mitochondrial contigs using MitoHIFI. Potential non-coral sequence contaminants were removed via DIAMOND alignment against an \u003cem\u003eA. hyacinthus\u003c/em\u003e reference genome (Shinzato et al., 2021) followed by a custom filtering script. We evaluated the final primary assembly metrics (genome size, contig number, N50, GC content) using QUAST. We assessed genome completeness using BUSCO (v5) against the metazoa_odb10 lineage dataset. To prepare for annotation, we identified tandem repeats on the primary assembly using Tandem Repeat Finder (TRF) with parameters \u0026quot;2 5 7 80 10 50 2000 -d -h\u0026quot; and generated a repeat-masked version of the genome. We then predicted protein-coding genes using MAKER (v3.01.04) in two iterations (Rnd1, Rnd2). Input evidence included transcript alignments from \u003cem\u003eAcropora\u003c/em\u003e ESTs (Moya et al., 2012), protein alignments from existing \u003cem\u003eAcropora\u003c/em\u003e annotations (Shinzato et al., 2021), and ab initio predictions. We trained SNAP and AUGUSTUS on high-confidence gene models identified within the MAKER pipeline. We retained gene models meeting stringent criteria (Annotation Edit Distance [AED] \u0026lt; 0.5, transcript or protein support). We generated a final consensus gene set using EVidenceModeler (EVM) by merging ab initio predictions with transcript and protein alignments. We assessed the quality of the final predicted proteome using BUSCO (metazoa_odb10). We identified and consolidated redundant protein isoforms using Clusterize (Wright, 2024) and updated the final GFF annotation file using agat_sp_filter_feature_from_keep_list.pl to retain only primary, non-redundant gene models. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JBMUIC000000000. The version described in this paper is version JBMUIC010000000.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eComparative and Phylogenetic Analyses\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe performed pairwise genome alignments using NUCMER (MUMmer suite) to compare the Kochi genome structure and determine alignment rates against other \u003cem\u003eAcropora\u003c/em\u003e assemblies. We conducted protein-level homology and similarity searches using BLASTp. To investigate gene family evolution, we detected orthologous gene clusters (orthogroups) among 21 initial cnidarian species using OrthoFinder (v2.5.5). We inferred a species phylogeny using the STAG algorithm (unrooted) and STRIDE (rooting) within OrthoFinder. In a focused secondary analysis of 16 \u003cem\u003eAcropora\u003c/em\u003e species, we identified significantly expanded or contracted orthogroups based on gene count variation Z-scores (|Z| \u0026gt; 2). We selected significantly expanded families for detailed characterization, inspecting gene trees (FigTree), aligning sequences (Clustal Omega via EMBL-EBI MSA), and visualizing alignments (Jalview). We functionally annotated selected orthogroups using BLASTp against UniProt (Jan 2025 release) and domain identification with InterProScan, retaining only those with clear phylogenetic patterns and functional annotation. Specifically for the FOX gene family, we performed two separate Maximum Likelihood (ML) phylogenetic analyses using MEGA12. The first analysis aligned 28 representative FOX sequences and inferred phylogeny using the LG+G+I (5 categories) model. The second re-analyzed the target FOX orthogroup (19 sequences, 295 positions) using the JTT+I model. Both analyses used Nearest-Neighbor-Interchange (NNI) search, automatic initial tree generation (NJ/MP), and fast adaptive bootstrap (1000 replicates, threshold 5.0) with no branch swap filter, including gaps/missing data and utilizing 18 threads. We visualized gene locations and structures using IGV and examined specific protein domain features (e.g., FOXA2-DBD residues 157\u0026ndash;258) using sequence alignments in Jalview. This integrated workflow allowed us to characterize comparative genomics, orthogroup evolution, and specific gene family phylogenetics.\u003c/p\u003e"},{"header":"Results","content":"\u003cp\u003e\u003cstrong\u003eGenome Assembly and Quality Assessment\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cem\u003eDe novo\u0026nbsp;\u003c/em\u003eassembly of the \u003cem\u003eAcropora hyacinthus\u003c/em\u003e Kochi population yielded a 480.16 Mb genome partitioned into 189 contigs (Table 1), with a GC content of 39.03%. Contiguity was high (N50 = 6.99 Mb, L50 = 22). BUSCO analysis showed 94.0% genome completeness against the metazoa_odb10 dataset (Table 2), with 93.1% identified as complete and single-copy, 0.9% duplicated, 3.2% fragmented, and 2.8% missing.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eGene Prediction and Proteome Completeness\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eGene prediction identified 35,721 protein-coding genes in the \u003cem\u003eA. hyacinthus\u003c/em\u003e (Kochi) genome compared to what was predicted by Shinzato et al. (2021) at 27,215 in the \u003cem\u003eA. hyacinthus\u003c/em\u003e (Okinawa) genome. Protein-level BUSCO assessment for \u003cem\u003eA. hyacinthus\u003c/em\u003e (Kochi) showed 86.8% of BUSCOs were complete within the predicted proteome (Table 3), with 4.5% fragmented and 8.7% missing. For comparison, the \u003cem\u003eA. hyacinthus\u003c/em\u003e (Okinawa) proteome showed 83.5% complete BUSCOs, 7.8% fragmented and 8.7% missing.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eComparative Genomic Divergence within \u003cem\u003eAcropora\u003c/em\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eGenome-wide alignment analysis of the \u003cem\u003eA. hyacinthus\u003c/em\u003e (Kochi) genome against other \u003cem\u003eAcropora\u003c/em\u003e species revealed varying alignment rates. The alignment rate against \u003cem\u003eA. hyacinthus\u003c/em\u003e (Okinawa) was 51.18%. Alignment rates against other \u003cem\u003eAcropora\u003c/em\u003e species were: \u003cem\u003eA. tenuis\u003c/em\u003e (Clade I): 1.03%, \u003cem\u003eA. gemmifera\u003c/em\u003e (II): 6.67%, \u003cem\u003eA. acuminata\u003c/em\u003e (III): 13.52%, \u003cem\u003eA. digitifera\u003c/em\u003e (III): 23.36%, and \u003cem\u003eA. echinata\u003c/em\u003e (IV): 3.87%. These alignment patterns are consistent with previously established clade divisions within \u003cem\u003eAcropora\u003c/em\u003e. Additionally, protein similarity analysis showed high sequence identity between \u003cem\u003eA. hyacinthus\u003c/em\u003e (Kochi and Okinawa) and \u003cem\u003eA. acuminata\u003c/em\u003e, with median identities of 66.4%, 66.4%, and 65.9% respectively.\u003c/p\u003e\n\u003ctable border=\"0\" cellspacing=\"0\" cellpadding=\"0\" width=\"606\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"7\" valign=\"top\" style=\"width: 606px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eTable 1.\u0026nbsp;\u003c/strong\u003eGenome assembly metrics for Acropora species. The Acropora hyacinthus assembly from Kochi is from this study, while all other assemblies, including the Acropora hyacinthus assembly from Okinawa, are sourced from Shinzato et al. (2021).\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 182px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eSpecies\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 59px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eContigs\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 101px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eTotal Length\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 61px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMBP\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 71px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eGC (%)\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eN50\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 44px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eL50\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 182px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora hyacinthus\u003c/em\u003e (Kochi, This study)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 59px;\"\u003e\n \u003cp\u003e189\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 101px;\"\u003e\n \u003cp\u003e480,158,887\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 61px;\"\u003e\n \u003cp\u003e480.16\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 71px;\"\u003e\n \u003cp\u003e39.03\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e6,994,003.00\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 44px;\"\u003e\n \u003cp\u003e22\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 182px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora digitifera\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 59px;\"\u003e\n \u003cp\u003e943\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 101px;\"\u003e\n \u003cp\u003e415,831,903\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 61px;\"\u003e\n \u003cp\u003e415.83\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 71px;\"\u003e\n \u003cp\u003e39.04\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e1,856,312.00\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 44px;\"\u003e\n \u003cp\u003e69\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 182px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora tenuis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 59px;\"\u003e\n \u003cp\u003e1825\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 101px;\"\u003e\n \u003cp\u003e406,855,084\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 61px;\"\u003e\n \u003cp\u003e406.86\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 71px;\"\u003e\n \u003cp\u003e38.93\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e1,160,220.00\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 44px;\"\u003e\n \u003cp\u003e103\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 182px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora echinata\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 59px;\"\u003e\n \u003cp\u003e2229\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 101px;\"\u003e\n \u003cp\u003e409,633,553\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 61px;\"\u003e\n \u003cp\u003e409.63\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 71px;\"\u003e\n \u003cp\u003e38.94\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e1,812,701.00\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 44px;\"\u003e\n \u003cp\u003e63\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 182px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora gemmifera\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 59px;\"\u003e\n \u003cp\u003e2309\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 101px;\"\u003e\n \u003cp\u003e405,175,433\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 61px;\"\u003e\n \u003cp\u003e405.18\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 71px;\"\u003e\n \u003cp\u003e38.93\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e1,134,581.00\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 44px;\"\u003e\n \u003cp\u003e103\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 182px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora hyacinthus\u0026nbsp;\u003c/em\u003e(Okinawa)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 59px;\"\u003e\n \u003cp\u003e2837\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 101px;\"\u003e\n \u003cp\u003e452,664,370\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 61px;\"\u003e\n \u003cp\u003e452.66\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 71px;\"\u003e\n \u003cp\u003e39\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e1,562,592.00\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 44px;\"\u003e\n \u003cp\u003e88\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 182px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora nasuta\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 59px;\"\u003e\n \u003cp\u003e4645\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 101px;\"\u003e\n \u003cp\u003e419,336,012\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 61px;\"\u003e\n \u003cp\u003e419.34\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 71px;\"\u003e\n \u003cp\u003e38.97\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e1,045,289.00\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 44px;\"\u003e\n \u003cp\u003e111\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 182px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora microphthalma\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 59px;\"\u003e\n \u003cp\u003e4855\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 101px;\"\u003e\n \u003cp\u003e387,847,894\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 61px;\"\u003e\n \u003cp\u003e387.85\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 71px;\"\u003e\n \u003cp\u003e38.95\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e1,050,196.00\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 44px;\"\u003e\n \u003cp\u003e117\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 182px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora selago\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 59px;\"\u003e\n \u003cp\u003e5691\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 101px;\"\u003e\n \u003cp\u003e393,033,298\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 61px;\"\u003e\n \u003cp\u003e393.03\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 71px;\"\u003e\n \u003cp\u003e38.96\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e657,172.00\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 44px;\"\u003e\n \u003cp\u003e173\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 182px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora intermedia\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 59px;\"\u003e\n \u003cp\u003e6073\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 101px;\"\u003e\n \u003cp\u003e416,762,810\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 61px;\"\u003e\n \u003cp\u003e416.76\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 71px;\"\u003e\n \u003cp\u003e38.94\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e577,312.00\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 44px;\"\u003e\n \u003cp\u003e216\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 182px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora muricata\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 59px;\"\u003e\n \u003cp\u003e6680\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 101px;\"\u003e\n \u003cp\u003e420,608,036\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 61px;\"\u003e\n \u003cp\u003e420.61\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 71px;\"\u003e\n \u003cp\u003e39.03\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e574,627.00\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 44px;\"\u003e\n \u003cp\u003e217\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 182px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora florida\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 59px;\"\u003e\n \u003cp\u003e6816\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 101px;\"\u003e\n \u003cp\u003e442,722,093\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 61px;\"\u003e\n \u003cp\u003e442.72\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 71px;\"\u003e\n \u003cp\u003e38.96\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e751,376.00\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 44px;\"\u003e\n \u003cp\u003e174\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003e\u0026nbsp;\u003c/p\u003e\n\u003ctable border=\"1\" cellspacing=\"0\" cellpadding=\"0\" width=\"608\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"7\" valign=\"top\" style=\"width: 598px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eTable 2.\u0026nbsp;\u003c/strong\u003eBUSCO assessment of genome completeness for \u003cem\u003eAcropora\u003c/em\u003e species using the metazoa_odb10 lineage dataset.\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eSpecies\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 76px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eComplete (C)\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 84px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eSingle-Copy (S)\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 72px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eDuplicated (D)\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 77px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eFragmented (F)\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 67px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMissing (M)\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 78px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eTotal BUSCOs\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 76px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 84px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 72px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 77px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 67px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 78px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora hyacinthus\u0026nbsp;\u003c/em\u003e(Kochi)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 76px;\"\u003e\n \u003cp\u003e94.00%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 84px;\"\u003e\n \u003cp\u003e93.10%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 72px;\"\u003e\n \u003cp\u003e0.90%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 77px;\"\u003e\n \u003cp\u003e3.20%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 67px;\"\u003e\n \u003cp\u003e2.80%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 78px;\"\u003e\n \u003cp\u003e954\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora digitifera\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 76px;\"\u003e\n \u003cp\u003e92.60%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 84px;\"\u003e\n \u003cp\u003e92.20%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 72px;\"\u003e\n \u003cp\u003e0.40%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 77px;\"\u003e\n \u003cp\u003e3.90%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 67px;\"\u003e\n \u003cp\u003e3.50%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 78px;\"\u003e\n \u003cp\u003e954\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora echinata\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 76px;\"\u003e\n \u003cp\u003e87.50%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 84px;\"\u003e\n \u003cp\u003e87.30%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 72px;\"\u003e\n \u003cp\u003e0.20%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 77px;\"\u003e\n \u003cp\u003e7.50%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 67px;\"\u003e\n \u003cp\u003e5.00%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 78px;\"\u003e\n \u003cp\u003e954\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora acuminata\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 76px;\"\u003e\n \u003cp\u003e91.90%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 84px;\"\u003e\n \u003cp\u003e91.00%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 72px;\"\u003e\n \u003cp\u003e0.90%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 77px;\"\u003e\n \u003cp\u003e5.20%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 67px;\"\u003e\n \u003cp\u003e2.90%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 78px;\"\u003e\n \u003cp\u003e954\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora gemmifera\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 76px;\"\u003e\n \u003cp\u003e87.50%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 84px;\"\u003e\n \u003cp\u003e86.70%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 72px;\"\u003e\n \u003cp\u003e0.80%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 77px;\"\u003e\n \u003cp\u003e7.20%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 67px;\"\u003e\n \u003cp\u003e5.30%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 78px;\"\u003e\n \u003cp\u003e954\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora tenuis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 76px;\"\u003e\n \u003cp\u003e92.00%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 84px;\"\u003e\n \u003cp\u003e91.30%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 72px;\"\u003e\n \u003cp\u003e0.70%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 77px;\"\u003e\n \u003cp\u003e4.50%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 67px;\"\u003e\n \u003cp\u003e3.50%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 78px;\"\u003e\n \u003cp\u003e954\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora hyacinthus\u003c/em\u003e\u003cem\u003e\u0026nbsp;\u003c/em\u003e(Okinawa)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 76px;\"\u003e\n \u003cp\u003e92.40%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 84px;\"\u003e\n \u003cp\u003e90.00%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 72px;\"\u003e\n \u003cp\u003e2.40%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 77px;\"\u003e\n \u003cp\u003e3.90%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 67px;\"\u003e\n \u003cp\u003e3.70%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 78px;\"\u003e\n \u003cp\u003e954\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003e\u0026nbsp;\u003c/p\u003e\n\u003ctable border=\"1\" cellspacing=\"0\" cellpadding=\"0\" width=\"608\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"7\" valign=\"top\" style=\"width: 608px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eTable 3.\u003c/strong\u003e BUSCO assessment of protein completeness for \u003cem\u003eAcropora hyacinthus\u003c/em\u003e (Okinawa) and \u003cem\u003eAcropora hyacinthus\u003c/em\u003e (Kochi) using the metazoa_odb10 lineage dataset.\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003eSpecies\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 63px;\"\u003e\n \u003cp\u003eComplete (C)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 83px;\"\u003e\n \u003cp\u003eSingle-Copy (S)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 84px;\"\u003e\n \u003cp\u003eDuplicated (D)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003eFragmented (F)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 74px;\"\u003e\n \u003cp\u003eMissing (M)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 76px;\"\u003e\n \u003cp\u003eTotal BUSCOs\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora hyacinthus\u0026nbsp;\u003c/em\u003e(Okinawa)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 63px;\"\u003e\n \u003cp\u003e83.50%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 83px;\"\u003e\n \u003cp\u003e71.20%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 84px;\"\u003e\n \u003cp\u003e12.30%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e7.80%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 74px;\"\u003e\n \u003cp\u003e8.70%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 76px;\"\u003e\n \u003cp\u003e954\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e\u003cem\u003eAcropora hyacinthus\u003c/em\u003e (Kochi)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 63px;\"\u003e\n \u003cp\u003e86.80%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 83px;\"\u003e\n \u003cp\u003e86.40%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 84px;\"\u003e\n \u003cp\u003e0.40%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 88px;\"\u003e\n \u003cp\u003e4.50%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 74px;\"\u003e\n \u003cp\u003e8.70%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 76px;\"\u003e\n \u003cp\u003e954\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003e\u003cstrong\u003eRegional Phylogeny of \u003cem\u003eAcropora hyacinthus\u003c/em\u003e\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003ePhylogenomic analysis (588 single-copy orthologs) clearly separated the Kochi and Okinawa \u003cem\u003eA. hyacinthus\u003c/em\u003e populations (Figure 2). The longer Kochi branch length suggests an accelerated evolutionary rate relative to the Okinawa population. Proteome-based phylogeny also placed both \u003cem\u003eA. hyacinthus\u003c/em\u003e populations within \u003cem\u003eAcropora\u003c/em\u003e Clade IV (Figure 2, inset), consistent with taxonomic classifications. These congruent signals underscore the evolutionary distinctiveness of the Kochi population.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eOrthogroup Analysis and FOX Gene Expansion\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eOrthogroup analysis across 16 \u003cem\u003eAcropora\u003c/em\u003e species and an outgroup identified 24,959 orthogroups, encompassing 455,187 genes (97.7%). We found 2,151 species-specific orthogroups, 8,425 orthogroups present across all 17 species, and 1,489 single-copy orthologs. Comparative analysis based on Z-scores (|Z| \u0026gt; 2) revealed significant orthogroup expansions in Kochi \u003cem\u003eA. hyacinthus\u003c/em\u003e compared to the other 15 \u003cem\u003eAcropora\u003c/em\u003e species. Notably, the mean gene count in expanded orthogroups was substantially higher in Kochi (mean = 21.89, SD = 24.83) than in Okinawa (mean = 2.445, SD = 2.099). For example, orthogroup OG0000015 contains 323 genes in Kochi \u003cem\u003eA. hyacinthus\u003c/em\u003e compared to an average of approximately 20 genes in other species. Nine of the top 20 expanded orthogroups in Kochi were functionally annotated (Table 4).\u003c/p\u003e\n\u003cp\u003eWe selected orthogroup OG0009671 (Forkhead domain-related) for detailed analysis due to its species tree-approximating gene tree, clear annotation, and significant expansion in Kochi (Z=3.881; Kochi count=2 vs. mean=1.059). Within this group, we characterized two \u003cem\u003eA. hyacinthus\u003c/em\u003e isoforms: AhyaKCZ.442 and AhyaKCZ.437. Both isoforms are located on contig ptg000050l (~6,994 kb), separated by 44,945 bp containing intervening genes (Exocyst complex component 8-like, Exosome complex component 10-like). This indicates the isoforms are distinct gene copies, not tandem duplicates.\u003c/p\u003e\n\u003cp\u003ePhylogenetic analysis (Figure 3) showed AhyaKCZ.442 clusters robustly within the main \u003cem\u003eAcropora\u003c/em\u003e FOX clade, while AhyaKCZ.437 occupies a basal position with a long branch (0.38623), suggesting greater divergence and a potential paralogous/specialized role. Cnidarian FOX sequences formed an intermediate clade between vertebrate FOXJ and FOXF subfamilies.\u003c/p\u003e\n\u003ctable border=\"1\" cellspacing=\"0\" cellpadding=\"0\" width=\"604\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"6\" valign=\"top\" style=\"width: 604px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eTable 4.\u003c/strong\u003e Top expanded orthogroups in Acropora hyacinthus (Kochi) compared to 15 other Acropora species, identified through OrthoFinder analysis. The table displays orthogroups with high Z-scores indicating significant expansion, along with the mean gene count across other species, standard deviation, gene count in the Kochi assembly, and the top UniProt BLAST match for functional annotation.\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOrthogroup\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003eZ-score\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003eMean_Count\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003eStandard_Deviation\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003eKochi Gene_Count\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003euniprot BLAST Match (Top %id, E-value)\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOG0001291\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e3.881\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003e2.529\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003e10.429\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003e43\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003enot curated\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOG0001548\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e3.881\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003e2.353\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003e9.701\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003e40\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003enot curated\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOG0006919\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e3.881\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003e1.176\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003e4.851\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003e20\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003enot curated\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOG0007423\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e3.881\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003e1.176\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003e0.728\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003e4\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003esp|A2A9A2|DMTA2_MOUSE\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOG0008061\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e3.881\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003e1.118\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003e0.485\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003e3\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003esp|O73823|TAL1_XENLA\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOG0009241\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e3.881\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003e1.059\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003e4.366\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003e18\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003enot curated\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOG0009671\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e3.881\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003e1.059\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003e0.243\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003e2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003esp|Q63245|FOXD3_RAT\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOG0009784\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e3.881\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003e1.059\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003e0.243\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003e2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003eNO MATCH\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOG0010077\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e3.881\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003e1.059\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003e0.243\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003e2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003esp|Q9D411|TSSK4_MOUSE\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOG0010119\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e3.881\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003e1.059\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003e0.243\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003e2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003esp|Q6DBY9|CHST1_DANRE\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOG0010189\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e3.881\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003e1.059\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003e0.243\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003e2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003esp|Q3SZ21|RPP30_BOVIN\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOG0010327\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e3.881\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003e1.059\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003e0.243\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003e2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003esp|F4K2M8|JMJ31_ARATH\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOG0000015\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e3.88\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003e19.941\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003e78.099\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003e323\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003enot curated\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOG0000021\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e3.88\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003e17.412\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003e58.145\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003e243\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003enot curated\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOG0000048\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e3.88\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003e10.824\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003e43.087\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003e178\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003enot curated\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOG0000107\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e3.88\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003e7.706\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003e29.459\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003e122\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003esp|Q86TV6|TTC7B_HUMAN\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOG0000201\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e3.88\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003e5.706\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003e22.756\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003e94\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003enot curated\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOG0000018\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e3.878\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003e18.588\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003e51.163\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003e217\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003enot curated\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOG0000026\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e3.878\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003e15.529\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003e47.309\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003e199\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003enot curated\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 80px;\"\u003e\n \u003cp\u003eOG0000052\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e3.878\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 86px;\"\u003e\n \u003cp\u003e10.294\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 121px;\"\u003e\n \u003cp\u003e38.6\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 90px;\"\u003e\n \u003cp\u003e160\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 180px;\"\u003e\n \u003cp\u003enot curated\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003ePreliminary analysis of domain architecture using InterProScan revealed that both isoforms contain the Forkhead domain (IPR001766; PF00250). However, AhyaKCZ.442 exhibits a more conserved domain structure, featuring multiple ProSitePatterns\u0026mdash;indicative of potential phosphorylation and myristoylation sites\u0026mdash;and predicted intrinsically disordered regions (IDRs). In contrast, while AhyaKCZ.437 retains the Forkhead domain, it lacks several of these conserved motifs and displays a notable substitution in helix 3 (a glutamic acid replacing the conserved glycine), as determined by alignment with the human FOXA2 DNA-binding domain (Li et al., 2017). Complementary analysis using the NCBI Conserved Domain Database confirmed that both proteins are classified as forkhead box transcription factors (CDD ID 15331620), with significant hits for FH_FOXQ2-like, Forkhead, FH, and COG5025. These domains, localized in the N-terminal region, are associated with DNA binding (GO:0003677) and transcription factor activity (GO:0003700).\u003c/p\u003e\n\u003cp\u003eFIMO motif scanning (Table 5) further identified high-confidence occurrences of the FORK_HEAD_2 motif (PS00658) in both isoforms. The motif \u0026ldquo;WRNSIRH\u0026rdquo; was detected at positions 139\u0026ndash;145 in AhyaKCZ.442 and 140\u0026ndash;146 in AhyaKCZ.437, each with a p-value of 1.4\u0026times;10^\u0026ndash;9 and a q-value of 3\u0026times;10^\u0026ndash;7. In addition, AhyaKCZ.442 harbors several motifs related to metabolic and transport functions (including motifs for MIP, CPSASE_2, COA_TRANSF_2, and AIPM_HOMOCIT_SYNTH_2), as well as motifs corresponding to REACTION_CENTER, CYTOCHROME_B559, HEMOCYANIN_1, TYROSINASE_2, SULFATASE_1, MACPF_1, GLYCO_HORMONE_BETA_1, BTG_1, and RIBOSOMAL_L16_2. Conversely, AhyaKCZ.437 uniquely exhibits an ammonium transport motif (PS01219) and additional motifs linked to enzyme-related domains such as CARBOXYPEPT_SER_SER, PEROXIDASE_2, and HSP70_3. Sequence analysis confirmed that both isoforms conserve critical DNA-binding residues (Arg140, Asn141, and Ser142) within the FORK_HEAD_2 motif, although the \u0026ldquo;WRNSIRH\u0026rdquo; sequence deviates from the canonical motifs observed in vertebrate FOXJ and FOXF subfamilies.\u003c/p\u003e\n\u003ctable border=\"1\" cellspacing=\"0\" cellpadding=\"0\" width=\"606\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"9\" valign=\"top\" style=\"width: 606px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eTable 5.\u003c/strong\u003e Motif analysis of the FOX paralogs AhyaKCZ.442 and AhyaKCZ.437 from \u003cem\u003eAcropora hyacinthus\u003c/em\u003e (Kochi) using FIMO motif scanning. The table lists identified motifs, their IDs, matched sequences, start and end positions, strand, p-values, and q-values. Both paralogs contain the FORK HEAD_2 motif, while AhyaKCZ.437 uniquely possesses an ammonium transport motif.\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMotif ID\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eAlt ID\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eSequence Name\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eStrand\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eStart\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eEnd\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e\u003cstrong\u003ep-value\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eq-value\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMatched Sequence\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00658\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eFORK_HEAD_2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.442\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e139\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e145\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e1.4e-09\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e3e-07\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eWRNSIRH\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00658\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eFORK_HEAD_2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e140\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e146\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e1.4e-09\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e3e-07\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eWRNSIRH\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS01219\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eAMMONIUM_TRANSP\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e41\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e64\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e2.71e-06\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.00101\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eDPAVSPCVPYWGASYASPNMFPLR\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00221\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eMIP\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.442\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e37\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e45\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e1.09e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.00472\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eNSVPAFSFA\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00537\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eCYTOCHROME_B559\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.442\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e26\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e40\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e1.32e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.00586\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eLTSGRFYLPGTNSVP\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00117\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eGAL_P_UDP_TRANSF_I\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.442\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e132\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e149\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e1.38e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.00516\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eFRNRGPGWRNSIRHNLSL\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00353\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eHMG_BOX_1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e178\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e189\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e1.73e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.00754\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eFSRGEYKRKRRV\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00867\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eCPSASE_2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.442\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e217\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e224\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e1.88e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0087\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eVIPLNTRC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00131\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eCARBOXYPEPT_SER_SER\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e50\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e57\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e1.96e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.00839\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eYWGASYAS\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00197\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003e2FE2S_FER_1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.442\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e72\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e80\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e2.55e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0116\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eCHTGHCYQP\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00244\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eREACTION_CENTER\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.442\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e65\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e91\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e3.18e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0115\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eDMRGLPACHTGHCYQPPFQGVMSYHGN\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00229\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eTAU_MAP_1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e189\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e201\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e3.26e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0129\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eVSRRNHGFFAAGI\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00496\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003ePII_GLNB_UMP\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e50\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e55\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n 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style=\"width: 38px;\"\u003e\n \u003cp\u003e4.15e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0187\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eISIEGGSGQVDEMKR\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00209\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eHEMOCYANIN_1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.442\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e61\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e80\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e4.72e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0178\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eHRDKDMRGLPACHTGHCYQP\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00701\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eRIBOSOMAL_L16_2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.442\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e158\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e169\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e4.76e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.00982\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eRSPNGKGHFWAI\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00701\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eRIBOSOMAL_L16_2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e159\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e170\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e4.76e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.00982\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eRSPNGKGHFWAI\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS01152\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eHESB\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.442\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e217\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e234\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e5.32e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0174\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eVIPLNTRCSNKGAENRSF\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00504\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eFRD_SDH_FAD_BINDING\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e192\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e201\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e5.4e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.021\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eRNHGFFAAGI\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00876\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eIDO_1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.442\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e104\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e114\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e5.84e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0154\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eIGKAILSSPQQ\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00498\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eTYROSINASE_2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.442\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e54\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e65\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e5.92e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0247\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eSPQMYSPHRDKD\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00279\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eMACPF_1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.442\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e41\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e52\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e6.03e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0207\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eAFSFAPYFGTGY\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00436\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003ePEROXIDASE_2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e65\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e76\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e6.26e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0266\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eSDADIRVFSHGS\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00816\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eAIPM_HOMOCIT_SYNTH_2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.442\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e86\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e99\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e6.82e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0268\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eMSYHGNNDDKPTQS\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00261\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eGLYCO_HORMONE_BETA_1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.442\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e73\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e79\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e7.02e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0299\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eHTGHCYQ\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n 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valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00187\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eTPP_ENZYMES\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e189\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e208\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e7.47e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.031\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eVSRRNHGFFAAGISIEGGSG\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00960\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eBTG_1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.442\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e37\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e57\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e7.48e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0283\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eNSVPAFSFAPYFGTGYISPQM\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00873\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eNA_ALANINE_SYMP\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e205\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e220\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e7.56e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0339\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eGGSGQVDEMKRQTYDG\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00876\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eIDO_1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e105\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e115\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e7.71e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0154\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eIGNAILSSPRQ\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00607\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003ePDEASE_II\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e99\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e113\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e8.01e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0358\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eQPYIDLIGNAILSSP\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00448\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eCLOS_CELLULOSOME_RPT\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e103\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e122\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e8.23e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0332\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eDLIGNAILSSPRQKLVLSDI\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00523\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eSULFATASE_1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.442\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e56\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e68\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e8.27e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0347\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eQMYSPHRDKDMRG\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00997\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eG10_1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e27\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e49\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e8.77e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0356\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eLPCSGRFYLLQPNADPAVSPCVP\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00647\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eTHYMID_PHOSPHORYLASE\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e9\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e24\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e9.56e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0414\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eSSRFAHTESLTTRFLS\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS01288\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eUPF0027\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.442\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e52\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e81\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e9.57e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0371\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eYISPQMYSPHRDKDMRGLPACHTGHCYQPP\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00675\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eSIGMA54_INTERACT_1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.442\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e153\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e166\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e9.99e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0224\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eFVKVGRSPNGKGHF\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 48px;\"\u003e\n \u003cp\u003ePS00675\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 135px;\"\u003e\n \u003cp\u003eSIGMA54_INTERACT_1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 117px;\"\u003e\n \u003cp\u003eevm.model.ptg000050l.437\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 42px;\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 35px;\"\u003e\n \u003cp\u003e154\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 31px;\"\u003e\n \u003cp\u003e167\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 38px;\"\u003e\n \u003cp\u003e9.99e-05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 45px;\"\u003e\n \u003cp\u003e0.0224\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eFVKVGRSPNGKGHF\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003e\u0026nbsp;\u003c/p\u003e"},{"header":"Discussion","content":"\u003cp\u003e\u003cstrong\u003eKochi \u003cem\u003eA. hyacinthus\u003c/em\u003e Genome Assembly and Annotation\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis study presents the first high-quality genome assembly of \u003cem\u003eAcropora hyacinthus\u003c/em\u003e from a temperate region (Kochi, Japan). Using PacBio HiFi sequencing, we generated an assembly that spans 480.16 Mb across 189 contigs, with a contig N50 of 6.99 Mb and a BUSCO completeness of 94.0% (Table 1; Table 2). In contrast, previous assemblies\u0026mdash;including a draft genome from Okinawa assembled with short reads (Shinzato et al., 2021) and a chromosome-level assembly from Palau (NCBI GCA_020536085.1)\u0026mdash;offer complementary perspectives from tropical populations. Although the Palau genome exhibits even higher continuity, our Kochi assembly is the first for a temperate \u003cem\u003eA. hyacinthus\u003c/em\u003e and provides an essential resource for evaluating genomic differences at the species\u0026rsquo; range edge. The high contiguity and completeness achieved here address the fragmentation issues typical of short-read assemblies (Shinzato et al., 2011) and establish a robust foundation for comparative analyses across latitudes.\u003c/p\u003e\n\u003cp\u003eGene content in the Kochi genome is in line with observations in other acroporids, with improvements arising from enhanced assembly continuity and updated annotation methods. We predicted 35,721 protein-coding genes, which is higher than the ~27,200 reported for the Okinawa genome (Shinzato et al., 2021). This difference is likely due to improved resolution of gene fragments and duplicated regions in the Kochi assembly rather than a true biological expansion of gene number. The overall genome BUSCO score of ~94% (Table 2) confirms the presence of the expected metazoan gene repertoire (Manni et al., 2021), while the proteome BUSCO score of 86.8% (Table 3) supports the effectiveness of our MAKER-based annotation. Furthermore, cross-species comparisons show that over 90% of Kochi proteins align with orthologs in other \u003cem\u003eAcropora\u003c/em\u003e species, reinforcing the accuracy of our predictions. Notably, the enhanced continuity of the Kochi assembly has allowed for the recovery of complete gene sequences for loci that were previously partial or absent in shorter assemblies. Overall, the Kochi genome\u0026rsquo;s assembly and annotation provide a reliable temperate reference that complements existing tropical datasets, enabling detailed comparative analyses of local adaptation and evolutionary divergence.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eInvestigating Genomic Differences in Variable Regions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe Kochi genome\u0026rsquo;s enhanced contiguity enabled us to resolve subtle differences in gene family structure, exemplified by the analysis of orthogroup OG0009671, associated with FOX (Forkhead) domain proteins. While most \u003cem\u003eAcropora\u003c/em\u003e species typically present a single copy in this group, our Kochi assembly revealed two distinct copies\u0026mdash;namely, AhyaKCZ.442 and AhyaKCZ.437\u0026mdash;resulting in a significant copy-number expansion (Z = 3.881; mean \u0026asymp; 1.06 in other species). Notably, these two isoforms are co-localized on contig \u003cem\u003eptg000050l\u003c/em\u003e, separated by approximately 45 kb.\u003c/p\u003e\n\u003cp\u003ePhylogenetic analysis indicates that AhyaKCZ.442 clusters with the conventional FOX homologs of other Acropora species, while AhyaKCZ.437 occupies a basal position with a long branch. This divergence suggests that AhyaKCZ.437 has followed a distinct evolutionary trajectory, potentially reflecting neofunctionalization or subfunctionalization. Furthermore, domain analyses reveal that AhyaKCZ.437 uniquely harbors an ammonium transporter motif (PS01219) alongside the canonical forkhead domain, a feature absent in AhyaKCZ.442. Such a domain configuration is unusual among FOX proteins and may indicate a modified regulatory role or an integration of additional cellular functions.\u003c/p\u003e\n\u003cp\u003eThe discovery of the divergent paralog AhyaKCZ.437 is significant for several reasons. First, it underscores the ability of HiFi sequencing to differentiate highly similar, co-localized genes that might otherwise be collapsed in short-read assemblies. Second, the presence of a uniquely modified FOX isoform in the temperate Kochi genome may signal subtle adaptations in gene regulation that are specific to the temperate environment. While further functional studies are necessary to elucidate the biological role of AhyaKCZ.437, its distinct structural features and phylogenetic placement suggest that even conserved gene families can harbor hidden diversity with potential adaptive implications.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eChallenges in Quantifying Differences (Gene Count Disparity)\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eA notable observation from our comparative orthogroup analysis is the marked disparity in gene count for expanded orthogroups between the Kochi HiFi assembly and the Okinawa short-read assembly. On average, expanded orthogroups in the Kochi genome contain approximately 21.89 genes, whereas the corresponding groups in the Okinawa genome average only about 2.445 genes. This roughly 9-fold difference is unlikely to represent a true biological expansion in the temperate population but rather reflects methodological differences in sequencing and assembly. The long-read HiFi technology provides superior resolution of repetitive regions and duplicated gene copies that short-read assemblies tend to collapse (Shinzato et al., 2021). In addition, the gene prediction and filtering pipelines used for the Kochi and Okinawa datasets differ, further contributing to these quantitative discrepancies.\u003c/p\u003e\n\u003cp\u003eThese technical factors complicate direct comparisons of gene family size and highlight the need for caution when interpreting such differences as biologically meaningful. Standardizing assembly and annotation approaches across samples would be necessary to disentangle technical bias from true genetic variation. Future work employing comparable HiFi-based sequencing for multiple individuals from different regions could resolve whether the observed gene count differences are consistent features or artifacts of differing methodologies. This challenge underscores the importance of using high-quality, uniformly generated genomic data when quantifying gene family variation across populations.\u003c/p\u003e\n\u003cp\u003e\u0026nbsp;\u003cstrong\u003eLimitations and Future Perspectives\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWhile our Kochi \u003cem\u003eAcropora hyacinthus\u003c/em\u003e genome assembly offers a valuable temperate reference, several limitations must be acknowledged. First, this study is based on a single individual from Kochi (with one Okinawan genome for comparison), which restricts our ability to capture the full range of population-level genetic variation. Some observed differences may reflect individual variation or technical artifacts rather than fixed regional traits (Ladner \u0026amp; Palumbi, 2012). Future studies involving population-scale sequencing across the Northwest Pacific are needed to validate and extend our findings.\u003c/p\u003e\n\u003cp\u003eOur automated gene annotation, although robust, may still contain errors common to draft annotations. Manual curation of key genes\u0026mdash;especially those involved in stress response or symbiosis\u0026mdash;will further refine the dataset. Additionally, this study focused solely on the coral host genome; comprehensive insights into coral adaptation would also require analysis of the symbiotic algae and associated microbial communities.\u003c/p\u003e\n\u003cp\u003eLooking forward, the Kochi genome opens avenues for functional and comparative genomic studies. Future work should examine genetic variants and expression differences that correlate with tolerance to cooler, more variable environments. Functional assays, such as common garden experiments and transcriptome profiling, can help determine whether temperate populations possess unique adaptations. Expanding high-quality, HiFi-based genomic resources to multiple populations and coral species will be essential to distinguish true adaptive variation from technical artifacts, ultimately enhancing our understanding of coral evolution and resilience in a changing ocean.\u003c/p\u003e"},{"header":"Conclusion","content":"\u003cp\u003eThis work provides the first high-fidelity genome assembly for the reef-building coral \u003cem\u003eAcropora hyacinthus\u003c/em\u003e from a temperate environment (Kochi, Japan). Leveraging this high-quality resource, our analysis of conserved single-copy orthologs confirmed substantial phylogenetic divergence relative to the subtropical Okinawa population, providing a clear genomic basis for regional differentiation. The enhanced contiguity inherent to the HiFi assembly proved critical for investigating complex genomic loci; specifically, it enabled the resolution and characterization of two distinct, co-localized FOX gene paralogs (AhyaKCZ.442 and the divergent AhyaKCZ.437) within an expanded orthogroup, revealing potential functional novelty missed in previous assemblies. While this demonstrates the value of long-read data for untangling genomic complexity, our findings also underscore the limitations of quantitatively comparing gene content (e.g., gene family sizes in expanded orthogroups) when datasets derive from different sequencing technologies and assembly methods. Future progress in comparative coral genomics, particularly for quantifying structural and gene content variation, necessitates the generation of comparable high-quality, long-read genome assemblies across diverse populations. Expanding the generation and analysis of HiFi genomes will enable deeper investigations into functionally relevant genomic divergences, such as the intriguing FOX paralog system identified here, across environmental gradients in these critical foundation species.\u003c/p\u003e"},{"header":"Declarations","content":"\u003ch2\u003eEthical Approval\u003c/h2\u003e\n\u003cp\u003ePermits for the collection of \u003cem\u003eA. hyacinthus\u003c/em\u003e samples were obtained from the local government of Kochi Prefecture (5高漁管第123号).\u003c/p\u003e\n\u003ch2\u003eFunding Declaration\u003c/h2\u003e\n\u003cp\u003eThis research was funded by the Japan Society for the Promotion of Science KAKENHI Grants-in-Aid for Scientific Research Project NOs. 21K05734, and 22K05820\u003c/p\u003e\n\u003ch2\u003eAuthor Contribution\u003c/h2\u003e\n\u003cp\u003eS.E.M., T.T., and S.K. led the conceptualization. S.E.M. led the formal analysis and writing of the original draft. T.M. led the identification of the target sample. T.T. and S.K. led the project administration, with T.M. providing support. All authors reviewed the manuscript.\u003c/p\u003e\n\u003ch2\u003eAcknowledgement\u003c/h2\u003e\n\u003cp\u003eWe extend our gratitude to the Division of Biological Research at the Science Research Center, Kochi University Oko Campus, for providing the essential resources for this study. Additionally, we acknowledge Bioengineering Lab. Co., Ltd. (株式会社生物技研) for performing the sequencing.\u003c/p\u003e\n\u003ch2\u003eData Availability\u003c/h2\u003e\n\u003cp\u003eThe whole genome assembly in this study has been deposited at GenBank under the accession JBMUIC000000000.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eBaird, A. H., Cumbo, V. R., \u0026amp; Leggat, W. (2012). 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Coral calcification and carbonate production in the eastern tropical Pacific: The role of branching and massive corals in the reef maintenance. \u003cem\u003eGeobiology\u003c/em\u003e, \u003cem\u003e20\u003c/em\u003e(4), 533\u0026ndash;545. https://doi.org/10.1111/gbi.12491\u003c/li\u003e\n\u003cli\u003eWright, E. (2024). Accurately clustering biological sequences in linear time by relatedness sorting. \u003cem\u003eNature Communications\u003c/em\u003e, \u003cem\u003e15\u003c/em\u003e(1), 3047. https://doi.org/10.1038/s41467-024-47371-9\u003c/li\u003e\n\u003cli\u003eYamano, H., Sugihara, K., \u0026amp; Nomura, K. (2011). Rapid poleward range expansion of tropical reef corals in response to rising sea surface temperatures. \u003cem\u003eGeophysical Research Letters\u003c/em\u003e, \u003cem\u003e38\u003c/em\u003e, L04601.\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":true,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"conservation-genetics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"coge","sideBox":"Learn more about [Conservation Genetics](https://www.springer.com/journal/10592)","snPcode":"10592","submissionUrl":"https://submission.nature.com/new-submission/10592/3","title":"Conservation Genetics","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"Temperate Coral, Comparative Genomics, Long-read Sequencing, Kuroshio Current, Gene Paralog","lastPublishedDoi":"10.21203/rs.3.rs-6428194/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6428194/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eReef-building \u003cem\u003eAcropora\u003c/em\u003e corals face climate change threats, necessitating genomic resources to understand adaptation, particularly at range edges. Temperate populations of \u003cem\u003eAcropora hyacinthus\u003c/em\u003e, like those in Kochi, Japan, are genetically distinct but lack a high-quality reference genome, hindering comparative studies. We generated a 480.16 Mb, highly contiguous (N50 6.99 Mb) PacBio HiFi genome assembly for Kochi \u003cem\u003eA. hyacinthus\u003c/em\u003e, achieving 94.0% BUSCO completeness. Phylogenomic analysis using 588 single-copy orthologs confirmed significant divergence between the Kochi and subtropical Okinawa populations, placing Kochi within \u003cem\u003eAcropora\u003c/em\u003e Clade IV but on a distinct, longer branch. The enhanced contiguity resolved complex genomic regions; notably, we identified and characterized two distinct, co-localized FOX gene paralogs (AhyaKCZ.442 and the divergent AhyaKCZ.437) within an orthogroup (OG0009671) significantly expanded in Kochi (Z\u0026thinsp;=\u0026thinsp;3.881) and typically containing a single copy in other \u003cem\u003eAcropora\u003c/em\u003e. The divergent paralog (AhyaKCZ.437) exhibits unique structural features, including an ammonium transporter motif, and a basal phylogenetic position, suggesting potential functional novelty relevant to temperate adaptation. While comparative analysis revealed substantial gene count differences in expanded orthogroups relative to a short-read reference (e.g., 21.89 vs 2.445 mean genes), methodological differences in sequencing and assembly likely contribute significantly to this disparity. This first high-quality temperate \u003cem\u003eA. hyacinthus\u003c/em\u003e genome provides a critical resource for investigating regional adaptation, demonstrates the power of long-read sequencing for resolving paralogs, and underscores the need for comparable datasets in comparative genomics.\u003c/p\u003e","manuscriptTitle":"High-Resolution Genome of Temperate Acropora hyacinthus Reveals Regional Divergence and Resolves Co- localized Gene Paralogs","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-07-02 07:11:29","doi":"10.21203/rs.3.rs-6428194/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-07-28T22:41:34+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-07-16T02:29:23+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"247486520356935049355848011062854130608","date":"2025-06-18T00:44:50+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-06-16T06:27:00+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"252404442261545550470904814591411873","date":"2025-06-11T02:42:52+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-04-15T20:21:45+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-04-12T07:10:30+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-04-12T07:09:25+00:00","index":"","fulltext":""},{"type":"submitted","content":"Conservation Genetics","date":"2025-04-11T11:58:34+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"conservation-genetics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"coge","sideBox":"Learn more about [Conservation Genetics](https://www.springer.com/journal/10592)","snPcode":"10592","submissionUrl":"https://submission.nature.com/new-submission/10592/3","title":"Conservation Genetics","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"af96e304-a2d9-4aea-b51d-a6aa5b48ae6f","owner":[],"postedDate":"July 2nd, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2026-02-16T16:01:54+00:00","versionOfRecord":{"articleIdentity":"rs-6428194","link":"https://doi.org/10.1007/s10592-026-01760-3","journal":{"identity":"conservation-genetics","isVorOnly":false,"title":"Conservation Genetics"},"publishedOn":"2026-02-12 15:58:08","publishedOnDateReadable":"February 12th, 2026"},"versionCreatedAt":"2025-07-02 07:11:29","video":"","vorDoi":"10.1007/s10592-026-01760-3","vorDoiUrl":"https://doi.org/10.1007/s10592-026-01760-3","workflowStages":[]},"version":"v1","identity":"rs-6428194","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6428194","identity":"rs-6428194","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}