Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton.
Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton.
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DOI：
10.1186/1471-2164-13-302
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发表时间：
2012-07-06
期刊：
影响因子：
4.4
通讯作者：
Udall JA
中科院分区：
文献类型：
--
作者：
Flagel LE;Wendel JF;Udall JA
现代异源四倍体棉花含有来自大约1-2百万年前发生的祖先多倍体事件的“A”和“D”基因组。二倍体A和D基因组物种可以与这些异源四倍体中发现的A和D基因组进行比较，以得出关于多倍体的进化推论。在本文中，我们提出了一个全面的EST大会来自二倍体和模型异源四倍体棉花，并展示了几个进化推论，基因进化，可以从这些数据。我们生成了一组棉花表达序列标签（EST），包括约440万个桑格和下一代（454）转录物，补充有来自二倍体和异源四倍体棉花的约1.52亿个Illumina读段。从EST比对中，我们推断出259，192个基因组特异性单核苷酸多态性（SNP）。蛋白质编码区的分子进化分析表明，核苷酸取代的速率增加了两个异源四倍体基因组相对于二倍体，和非同义的同义取代的比例增加了我们采样的两个多倍体谱系之一。我们还使用这些SNP来表明，在经历了一次或多次非相互同源重组（NRHR）的异源四倍体细胞核中，重复基因的百分比（约7%）令人惊讶地高，显示出非独立进化的特征。在这项研究中，我们的棉花转录组的功能和突变特性的特点，产生一个大的基因组特异性SNP数据库，并检测共享一个共同的异源四倍体细胞核的重复基因组之间的非法遗传交换。我们的发现对我们理解多倍性和重复基因进化的后果具有重要意义。我们证明，棉花基因经历了一个增加的分子进化率重复多倍体，和多倍体使相当程度的同源异源基因之间的非互惠交换。
Modern allotetraploid cotton contains an “A” and “D” genome from an ancestral polyploidy event that occurred approximately 1–2 million years ago. Diploid A- and D-genome species can be compared to the A- and D-genomes found within these allotetraploids to make evolutionary inferences about polyploidy. In this paper we present a comprehensive EST assembly derived from diploid and model allotetraploid cottons and demonstrate several evolutionary inferences regarding genic evolution that can be drawn from these data. We generated a set of cotton expressed sequence tags (ESTs), comprising approximately 4.4 million Sanger and next-generation (454) transcripts supplemented by approximately 152 million Illumina reads from diploid and allotetraploid cottons. From the EST alignments we inferred 259,192 genome-specific single nucleotide polymorphisms (SNPs). Molecular evolutionary analyses of protein-coding regions demonstrate that the rate of nucleotide substitution has increased among both allotetraploid genomes relative to the diploids, and that the ratio of nonsynonymous to synonymous substitutions has increased in one of the two polyploid lineages we sampled. We also use these SNPs to show that a surprisingly high percentage of duplicate genes (~7 %) show a signature of non-independent evolution in the allotetraploid nucleus, having experienced one or more episodes of nonreciprocal homoeologous recombination (NRHR). In this study we characterize the functional and mutational properties of the cotton transcriptome, produce a large genome-specific SNP database, and detect illegitimate genetic exchanges between duplicate genomes sharing a common allotetraploid nucleus. Our findings have important implications for our understanding of the consequences of polyploidy and duplicate gene evolution. We demonstrate that cotton genes have experienced an increased rate of molecular evolution following duplication by polyploidy, and that polyploidy has enabled considerable levels of nonreciprocal exchange between homoeologous genes.
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影响因子：
4.4
作者：
Chaudhary B;Hovav R;Flagel L;Mittler R;Wendel JF
通讯作者：
Wendel JF
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7
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影响因子：
3.1
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影响因子：
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