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首页> 美国卫生研究院文献>Genetics >Combining Bioinformatics and Phylogenetics to Identify Large Sets of Single-Copy Orthologous Genes (COSII) for Comparative Evolutionary and Systematic Studies: A Test Case in the Euasterid Plant Clade
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Combining Bioinformatics and Phylogenetics to Identify Large Sets of Single-Copy Orthologous Genes (COSII) for Comparative Evolutionary and Systematic Studies: A Test Case in the Euasterid Plant Clade

机译：结合生物信息学和系统发育学来识别大套单拷贝直系同源基因（COSII）以进行比较进化和系统研究：优等生植物进化枝中的一个测试案例

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We report herein the application of a set of algorithms to identify a large number (2869) of single-copy orthologs (COSII), which are shared by most, if not all, euasterid plant species as well as the model species Arabidopsis. Alignments of the orthologous sequences across multiple species enabled the design of “universal PCR primers,” which can be used to amplify the corresponding orthologs from a broad range of taxa, including those lacking any sequence databases. Functional annotation revealed that these conserved, single-copy orthologs encode a higher-than-expected frequency of proteins transported and utilized in organelles and a paucity of proteins associated with cell walls, protein kinases, transcription factors, and signal transduction. The enabling power of this new ortholog resource was demonstrated in phylogenetic studies, as well as in comparative mapping across the plant families tomato (family Solanaceae) and coffee (family Rubiaceae). The combined results of these studies provide compelling evidence that (1) the ancestral species that gave rise to the core euasterid families Solanaceae and Rubiaceae had a basic chromosome number of x = 11 or 12.2) No whole-genome duplication event (i.e., polyploidization) occurred immediately prior to or after the radiation of either Solanaceae or Rubiaceae as has been recently suggested.
机译：我们在此报告了一组算法的应用，以识别大量（2869）单拷贝直系同源物（COSII），大多数（如果不是全部）非甾体植物物种以及模型物种拟南芥共有这些。跨物种的直系同源序列的比对使得“通用PCR引物”的设计成为可能，该引物可用于从广泛的分类单元（包括缺乏任何序列数据库的那些）中扩增相应的直系同源序列。功能注释显示，这些保守的单拷贝直向同源物编码在细胞器中运输和利用的蛋白质的频率高于预期，并且与细胞壁，蛋白质激酶，转录因子和信号转导相关的蛋白质也很少。这种新的直向同源物资源的促成能力在系统发育研究中以及在番茄（茄科）和咖啡（茜草科）的植物科系作图比较中得到了证明。这些研究的综合结果提供了令人信服的证据，（1）导致核心古猿科（茄科和茜草科）的祖先物种的基本染色体数为x = 11或12.2）没有全基因组复制事件（即多倍体化）如最近所建议的那样，发生在茄科或茜草科辐射之前或之后。

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