School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China.
Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and.
Plant Physiol. 2017 May;174(1):284-300. doi: 10.1104/pp.16.01981. Epub 2017 Mar 21.
Mainly due to their economic importance, genomes of 10 legumes, including soybean (), wild peanut ( and ), and barrel medic (), have been sequenced. However, a family-level comparative genomics analysis has been unavailable. With grape () and selected legume genomes as outgroups, we managed to perform a hierarchical and event-related alignment of these genomes and deconvoluted layers of homologous regions produced by ancestral polyploidizations or speciations. Consequently, we illustrated genomic fractionation characterized by widespread gene losses after the polyploidizations. Notably, high similarity in gene retention between recently duplicated chromosomes in soybean supported the likely autopolyploidy nature of its tetraploid ancestor. Moreover, although most gene losses were nearly random, largely but not fully described by geometric distribution, we showed that polyploidization contributed divergently to the copy number variation of important gene families. Besides, we showed significantly divergent evolutionary levels among legumes and, by performing synonymous nucleotide substitutions at synonymous sites correction, redated major evolutionary events during their expansion. This effort laid a solid foundation for further genomics exploration in the legume research community and beyond. We describe only a tiny fraction of legume comparative genomics analysis that we performed; more information was stored in the newly constructed Legume Comparative Genomics Research Platform (www.legumegrp.org).
主要由于其经济重要性，包括大豆（）、野生落花生（和）和兵豆（）在内的 10 种豆科植物的基因组已经被测序。然而，一直缺乏家族水平的比较基因组学分析。以葡萄（）和选定的豆科基因组作为外群，我们成功地对这些基因组进行了分层和与事件相关的比对，并解析了由祖先多倍化或物种形成产生的同源区域的层次。因此，我们说明了基因组的分裂特征，即在多倍化后广泛发生基因丢失。值得注意的是，大豆中最近复制的染色体之间在基因保留上的高度相似性支持了其四倍体祖先可能是自倍性的。此外，尽管大多数基因丢失几乎是随机的，在很大程度上但不完全由几何分布描述，但我们表明，多倍化对重要基因家族的拷贝数变异有不同的影响。此外，我们还表明豆科植物之间存在明显不同的进化水平，并通过在同义位点校正后进行同义核苷酸替换，重新确定了它们扩张过程中的主要进化事件。这项工作为豆科植物研究界及其他领域的进一步基因组学探索奠定了坚实的基础。我们仅描述了我们进行的豆科比较基因组学分析的一小部分；更多信息存储在新构建的豆科比较基因组学研究平台（www.legumegrp.org）中。
