Takeuchi Takeshi, Suzuki Yoshihiko, Shoguchi Eiichi, Fujie Manabu, Kawamitsu Mayumi, Shinzato Chuya, Satoh Noriyuki, Myers Eugene W
Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
Algorithms for Eco and Evo Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
DNA Res. 2025 Jul 4;32(4). doi: 10.1093/dnares/dsaf017.
Gene family expansion illustrates a critical aspect of evolutionary adaptation. However, the mechanisms by which gene family expansions emerge and are maintained in the genome remain unclear. Here, we report de novo, nearly telomere-to-telomere (T2T), haplotype-phased genome assemblies of 2 coral species, Acropora tenuis and Acropora digitifera. By comparing haplotypes within a single individual and across species, we identified genomic regions spanning several megabases with highly disordered gene arrangements, termed non-syntenic regions (nSRs). In these nSRs, there are clusters of genes that emerged by lineage-specific gene family expansion. The gene repertoire within nSRs exhibits significant sequence diversity and distinct expression patterns, suggesting functional diversification. We propose that lineage-specific gene family expansion in nSRs occurs through recurrent tandem duplications mediated by non-allelic homologous recombination (NAHR) events, with nSRs serving as reservoirs for a diverse gene repertoire advantageous for survival. The nearly T2T-phased genomes provide new insights into the remarkable flexibility of genome organization and the evolution of gene family expansions.
基因家族扩张体现了进化适应的一个关键方面。然而，基因家族扩张在基因组中出现并得以维持的机制仍不清楚。在此，我们报告了两种珊瑚物种——细枝鹿角珊瑚（Acropora tenuis）和指状鹿角珊瑚（Acropora digitifera）从头开始的、近乎端粒到端粒（T2T）的、单倍型定相的基因组组装。通过比较单个个体内以及跨物种的单倍型，我们鉴定出了跨越几个兆碱基的基因组区域，这些区域的基因排列高度紊乱，称为非共线性区域（nSRs）。在这些nSRs中，存在通过谱系特异性基因家族扩张而出现的基因簇。nSRs内的基因库表现出显著的序列多样性和独特的表达模式，表明其功能具有多样性。我们提出，nSRs中谱系特异性基因家族扩张是通过由非等位基因同源重组（NAHR）事件介导的反复串联重复发生的，nSRs作为一个多样化基因库的储存库，有利于生存。近乎T2T定相的基因组为基因组组织的显著灵活性和基因家族扩张的进化提供了新的见解。
