Table_2_Cercis: A Non-polyploid Genomic Relic Within the Generally Polyploid Legume Family.xlsx

Based on evolutionary, phylogenomic, and synteny analyses of genome sequences for more than a dozen diverse legume species as well as analysis of chromosome counts across the legume family, we conclude that the genus Cercis provides a plausible model for an early evolutionary form of the legume genome. The small Cercis genus is in the earliest-diverging clade in the earliest-diverging legume subfamily (Cercidoideae). The Cercis genome is physically small, and has accumulated mutations at an unusually slow rate compared to other legumes. Chromosome counts across 477 legume genera, combined with phylogenetic reconstructions and histories of whole-genome duplications, suggest that the legume progenitor had 7 chromosomes – as does Cercis. We propose a model in which a legume progenitor, with 7 chromosomes, diversified into species that would become the Cercidoideae and the remaining legume subfamilies; then speciation in the Cercidoideae gave rise to the progenitor of the Cercis genus. There is evidence for a genome duplication in the remaining Cercidoideae, which is likely due to allotetraploidy involving hybridization between a Cercis progenitor and a second diploid species that existed at the time of the polyploidy event. Outside the Cercidoideae, a set of probably independent whole-genome duplications gave rise to the five other legume subfamilies, at least four of which have predominant counts of 12–14 chromosomes among their early-diverging taxa. An earlier study concluded that independent duplications occurred in the Caesalpinioideae, Detarioideae, and Papilionoideae. We conclude that Cercis may be unique among legumes in lacking evidence of polyploidy, a process that has shaped the genomes of all other legumes thus far investigated.

本研究基于对十余种多样化豆科植物（legume）基因组序列开展的演化分析、系统发育基因组学分析与共线性（synteny）分析，结合跨豆科类群的染色体数目统计结果，得出结论：紫荆属（Cercis）可为豆科基因组早期演化形式提供合理的研究模型。紫荆属这一小属隶属于最早分化的豆科亚科（subfamily）——紫荆亚科（Cercidoideae）的最早演化支（clade）。紫荆属基因组体量小巧，且相较于其他豆科植物，其突变累积速率异乎寻常地缓慢。对477个豆科属的染色体数目统计，结合系统发育重建与全基因组复制（whole-genome duplications）历史分析，结果显示豆科祖先类群具有7条染色体，紫荆属亦保持这一染色体数目。我们提出如下演化模型：具有7条染色体的豆科祖先分化为紫荆亚科类群与其余豆科亚科类群；随后紫荆亚科内的物种形成事件催生了紫荆属的祖先类群。现有证据表明，紫荆亚科其余类群曾发生基因组复制事件，该事件大概率源于多倍化（polyploidy）发生时，紫荆属祖先与同期存在的另一二倍体物种间的杂交所导致的异源四倍体化（allotetraploidy）。在紫荆亚科之外，多组独立的全基因组复制事件催生了其余五个豆科亚科，其中至少四个亚科的早期分化类群的染色体数目以12~14条为主。此前一项研究已证实，云实亚科（Caesalpinioideae）、决明亚科（Detarioideae）与蝶形花亚科（Papilionoideae）中均发生过独立的基因组复制事件。我们最终得出结论：紫荆属可能是豆科中唯一未发现多倍化证据的类群，而多倍化过程已塑造了迄今所有被研究过的其他豆科物种的基因组。