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
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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DOI：
10.1534/genetics.106.062455
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发表时间：
2006-11-01
期刊：
影响因子：
3.3
通讯作者：
Tanksley, Steven D.
中科院分区：
文献类型：
--
作者：
Wu, Feinan;Mueller, Lukas A.;Tanksley, Steven D.
我们在此报告了应用一组算法来识别大量（2869）个单拷贝直向同源物（COSII），这些单拷贝直向同源物（COSII）是大多数（如果不是全部）真菊科植物物种以及模式物种拟南芥所共有的。跨多个物种的直向同源序列的比对使得能够设计“通用PCR引物”，该引物可用于从广泛的分类单元中扩增相应的直向同源物，包括那些缺乏任何序列数据库的类群。功能注释显示，这些保守的、单cop）直向同源物编码的蛋白质在细胞器中运输和利用的频率高于预期，并且与细胞壁、蛋白激酶、转录因子和细胞相关的蛋白质很少。这种新的直系同源资源的支持能力在系统发育研究以及番茄（茄科）和咖啡（茜草科）植物科的比较图谱中得到了证明。这些研究的综合结果提供了令人信服的证据，表明（1）产生核心 euasterid 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）没有全基因组重复事件。正如最近所建议的，茄科或茜草科的辐射（即多倍化）发生在辐射之前或之后。
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-cop), 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.