The monosaccharide transporter gene family in Arabidopsis and rice:: A history of duplications, adaptive evolution, and functional divergence
The monosaccharide transporter gene family in Arabidopsis and rice:: A history of duplications, adaptive evolution, and functional divergence
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DOI：
10.1093/molbev/msm184
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发表时间：
2007-11-01
影响因子：
10.7
通讯作者：
Thomas, Michael A.
中科院分区：
文献类型：
--
作者：
Johnson, Deborah A.;Thomas, Michael A.
基因重复差异的当前假设提出，基因重复对的幸存成员可能在纯化或几乎中性选择的条件下以两种方式进化：新功能在一个重复中产生，而另一个副本保留了原始功能（NF [NF [NF [NF）[NF [NF] ]）或两个旁系同源物之间的原始函数（亚功能化[SF]）。最新的研究表明，SF紧随其后的NF（次功能化[SNF]）解释了许多重复基因的差异。在此分析中，我们在拟南芥和水稻中的大型单糖转运蛋白（MST）基因家族的背景下评估了这些假设。 MSTs具有古老的起源，早于植物，并且已经在种子植物谱系中进化，包括7种亚家族。在拟南芥中，已经鉴定出53个假定的MST基因，其中1个由串联基因重复大大扩展。我们搜索了MST基因家族成员的水稻基因组，并将其与拟南芥中的MST基因家族进行了比较，以确定亚家族膨胀模式并估算基因重复分散时间。我们通过比较蛋白质序列差异率，估计密码子位点上的阳性选择并分析组织表达模式，通过比较蛋白质序列的差异率，测试了24个旁系同源物对中基因重复差异的假设。结果表明，在大米中，MST基因家族在2个亚家族的大米中显着更大（65），并通过串联重复大大扩展。基因的重复分歧时间估计表明，大多数亚家族的早期多样化发生在proteroyoic（2500-540 MYR）中，并且大型亚家族的扩张继续通过新生代（65-0 Myr）。三分之二的旁系同源对序列演化的统计对称速率，最与SF模型一致，其中一半的人在一个或两个基因中表现出阳性选择的证据。在显示不对称差异速率的8个旁学对中，最与NF模型一致，将近一半显示了阳性选择的证据。肯定的选择不会出现在与34 Myr相似的年轻的重复对中。我们的数据表明，NF，SF和SNF模型描述了复制后放松约束的初始条件引起的差异的不同结果。
Current hypotheses of gene duplicate divergence propose that surviving members of a gene duplicate pair may evolve, under conditions of purifying or nearly neutral selection, in one of two ways: with new function arising in one duplicate while the other retains original function (neofunctionalization [NF]) or partitioning of the original function between the 2 paralogs (subfunctionalization [SF]). More recent studies propose that SF followed by NF (subneofunctionalization [SNF]) explains the divergence of many duplicate genes. In this analysis, we evaluate these hypotheses in the context of the large monosaccharide transporter (MST) gene families in Arabidopsis and rice. MSTs have an ancient origin, predating plants, and have evolved in the seed plant lineage to comprise 7 subfamilies. In Arabidopsis, 53 putative MST genes have been identified, with one subfamily greatly expanded by tandem gene duplications. We searched the rice genome for members of the MST gene family and compared them with the MST gene family in Arabidopsis to determine subfamily expansion patterns and estimate gene duplicate divergence times. We tested hypotheses of gene duplicate divergence in 24 paralog pairs by comparing protein sequence divergence rates, estimating positive selection on codon sites, and analyzing tissue expression patterns. Results reveal the MST gene family to be significantly larger (65) in rice with 2 subfamilies greatly expanded by tandem duplications. Gene duplicate divergence time estimates indicate that early diversification of most subfamilies occurred in the Proterozoic (2500-540 Myr) and that expansion of large subfamilies continued through the Cenozoic (65-0 Myr). Two-thirds of paralog pairs show statistically symmetric rates of sequence evolution, most consistent with the SF model, with half of those showing evidence for positive selection in one or both genes. Among 8 paralog pairs showing asymmetric divergence rates, most consistent with the NF model, nearly half show evidence of positive selection. Positive selection does not appear in any duplicate pairs younger than similar to 34 Myr. Our data suggest that the NF, SF, and SNF models describe different outcomes along a continuum of divergence resulting from initial conditions of relaxed constraint after duplication.