Shifts in the evolutionary rate and intensity of purifying selection between two Brassica genomes revealed by analyses of orthologous transposons and relics of a whole genome triplication

文献类型： 外文期刊

第一作者： Zhao, Meixia

作者： Zhao, Meixia;Tong, Chaobo;Yu, Jingyin;Huang, Shunmou;Liu, Shengyi;Zhao, Meixia;Du, Jianchang;Lin, Feng;Ma, Jianxin;Wang, Xiaowu

作者机构：

关键词： asymmetric evolution;purifying selection;nucleotide substitution;transposable elements;genetic recombination;transcriptional alteration;Brassica

期刊名称：PLANT JOURNAL （ 影响因子：6.417； 五年影响因子：7.627 ）

ISSN： 0960-7412

年卷期： 2013 年 76 卷 2 期

页码：

收录情况： SCI

摘要： Recent sequencing of the Brassica rapa and Brassica oleracea genomes revealed extremely contrasting genomic features such as the abundance and distribution of transposable elements between the two genomes. However, whether and how these structural differentiations may have influenced the evolutionary rates of the two genomes since their split from a common ancestor are unknown. Here, we investigated and compared the rates of nucleotide substitution between two long terminal repeats (LTRs) of individual orthologous LTR-retrotransposons, the rates of synonymous and non-synonymous substitution among triplicated genes retained in both genomes from a shared whole genome triplication event, and the rates of genetic recombination estimated/deduced by the comparison of physical and genetic distances along chromosomes and ratios of solo LTRs to intact elements. Overall, LTR sequences and genic sequences showed more rapid nucleotide substitution in B.rapa than in B.oleracea. Synonymous substitution of triplicated genes retained from a shared whole genome triplication was detected at higher rates in B.rapa than in B.oleracea. Interestingly, non-synonymous substitution was observed at lower rates in the former than in the latter, indicating shifted densities of purifying selection between the two genomes. In addition to evolutionary asymmetry, orthologous genes differentially regulated and/or disrupted by transposable elements between the two genomes were also characterized. Our analyses suggest that local genomic and epigenomic features, such as recombination rates and chromatin dynamics reshaped by independent proliferation of transposable elements and elimination between the two genomes, are perhaps partially the causes and partially the outcomes of the observed inter-specific asymmetric evolution.

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