Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform
Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform
复制标题
分层比对10个豆类基因组，建立科级基因组平台
DOI：
10.1104/pp.16.01981
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发表时间：
2017-05-01
期刊：
影响因子：
7.4
通讯作者：
Wang, Xiyin
中科院分区：
文献类型：
--
作者：
Wang, Jinpeng;Sun, Pengchuan;Wang, Xiyin
主要是由于它们的经济重要性，10个豆科植物，包括大豆（Glycine max），野生花生（Arachis duranensis和Arachis ipaensis），和桶苜蓿（Medicago truncatula）的基因组已被测序。然而，还没有家庭一级的比较基因组学分析。与葡萄（葡萄属酿酒）和选定的豆类基因组作为外群，我们设法执行这些基因组和祖先多倍体化或物种形成产生的同源区域的去卷积层的层次和事件相关的对齐。因此，我们说明了基因组分馏的特点是广泛的基因损失后，多倍化。值得注意的是，大豆中最近复制的染色体之间的基因保留的高度相似性支持其四倍体祖先的可能同源多倍体性质。此外，虽然大多数基因损失几乎是随机的，很大程度上，但不完全描述的几何分布，我们表明，多倍化贡献分歧的重要基因家族的拷贝数变异。此外，我们表现出显着不同的豆科植物之间的进化水平，并通过执行同义核苷酸替换在同义位点校正，redated其扩展过程中的主要进化事件。这一努力为豆类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。我们只描述了我们进行的豆类比较基因组学分析的一小部分;更多的信息存储在新构建的豆类比较基因组学研究平台（www.legumegrp.org）中。
Mainly due to their economic importance, genomes of 10 legumes, including soybean (Glycine max), wild peanut (Arachis duranensis and Arachis ipaensis), and barrel medic (Medicago truncatula), have been sequenced. However, a family-level comparative genomics analysis has been unavailable. With grape (Vitis vinifera) 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).