Revealing Deep Phylogeny of Brassicaceae Using Composition Analysis of Low-copy Nuclear Genes

Abstract

Abstract: Brassicaceae，as many vegetable crops and important model plants，is one of the most successful and economically valuable angiosperm families. Recent phylogenetic studies revealed that plants of Brassicaceae were classified into 3 major lineages（I，II，and III），however，detailed evolutionary relationships among them and intra-lineage still remain unknown. In order to quickly and accurately understand the phylogeny of Brassicaceae species，39 Brassicaceae species and two species of other family were chosen as research materials，and a set of low copy orthologous genes covering all the selected species was acquired via phylogenetic genomics. Further，the composition characteristics of low copy nuclear genes were analyzed by CVTree，the phylogeny of Brassicaceae in highly supported and stable relationship was obtained. The results revealed that Brassicaceae could be classified into 6 major lineages，and 3 of which agreed well with the classification by the priors，and 2 new major lineages were defined. Moreover，lineage II that was in dispute in previous studies was confirmed as the single lineage with stable supports. This indicated that a large number of low copy orthologous genes set combined with the analysis of composition vector may more accurately reflect phylogeny of Brassicaceae species. Therefore，CVTree not only is suitable for studying the phylogeny of microorganisms such as prokaryotic organisms and fungi，but also for exploring the genetic relationship of higher organisms such as Brassicaceae plants

Key words: Brassicaceae, phylogeny, composition vector, low-copy nuclear gene

CLC Number:

10.13560/j.cnki.biotech.bull.1985.2016.12.015

ZHANG Zhe,HUANG Chien-hsun,QI Ji. Revealing Deep Phylogeny of Brassicaceae Using Composition Analysis of Low-copy Nuclear Genes[J]. Biotechnology Bulletin, 2016, 32(12): 86-95.

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