远缘植物同源/异源基因的系统发育推断

Zilong Xu, Wenyan Sun, Ziqiang Zhu, Bojian Zhong, Zhenhua Zhang
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摘要

近年来,植物基因组学和转录组学数据的激增为重建植物进化情景和推断与植物发育和逆境反应相关的关键基因的潜在功能奠定了基础。识别同源基因的经典方案是基于序列相似性的搜索,其关键假设是同源序列之间的相似性大于任何其他非同源序列。植物系统基因组学和计算算法的进步使我们能够系统地识别同源/同源物,并在远亲谱系中重建它们的进化历史。在这里,我们提出了一个全面的管道同源序列鉴定,系统发育关系推断和潜在的功能分析的基因在植物中。使用大规模基因组学和转录组学数据鉴定同源物。•该协议适用于分析植物基因的进化。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Phylogenetic Inference of Homologous/Orthologous Genes Among Distantly Related Plants
The recent surge in plant genomic and transcriptomic data has laid a foundation for reconstructing evolutionary scenarios and inferring potential functions of key genes related to plants’ development and stress responses. The classical scheme for identifying homologous genes is sequence similarity–based searching, under the crucial assumption that homologous sequences are more similar to each other than they are to any other non-homologous sequences. Advances in plant phylogenomics and computational algorithms have enabled us to systemically identify homologs/orthologs and reconstruct their evolutionary histories among distantly related lineages. Here, we present a comprehensive pipeline for homologous sequences identification, phylogenetic relationship inference, and potential functional profiling of genes in plants. Key features • Identification of orthologs using large-scale genomic and transcriptomic data. • This protocol is generalized for analyzing the evolution of plant genes.
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