Comparative genomic and transcriptomic analysis of tandemly and segmentally duplicated genes in rice.
Comparative genomic and transcriptomic analysis of tandemly and segmentally duplicated genes in rice.
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DOI：
10.1371/journal.pone.0063551
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Ramachandran S
中科院分区：
文献类型：
--
作者：
Jiang SY;González JM;Ramachandran S
串联重复和片段重复对基因家族扩展和基因组进化有重要作用。串联基因和节段基因的全基因组鉴定已经在几种植物基因组中进行了分析。然而，在功能偏好、表达差异及其在物种驯化中的作用方面的比较研究还很缺乏。我们对水稻基因组中的串联基因和节段基因进行了全基因组鉴定和比较分析。在基因组中分别鉴定了总共3，646对和3，633对串联和节段基因。它们约占所有注释的水稻基因（不包括转座子编码基因）的30%。串联和节段重复显示不同的物理位置，并表现出偏见的功能子集。这两种类型的重复基因也在不同的功能限制下，如每个位点的非同义取代（Ka）和每个位点的同义取代（Ks）分析所示。基于转录组学数据，它们也根据组织和非生物和生物胁迫而受到不同的调节。这种表达差异可能与基因启动子分化程度和DNA甲基化状态有关。串联重复和片段重复对遗传新奇的贡献不同，但有证据表明它们在物种驯化和基因组进化中发挥作用。
Tandem and segmental duplications significantly contribute to gene family expansion and genome evolution. Genome-wide identification of tandem and segmental genes has been analyzed before in several plant genomes. However, comparative studies in functional bias, expression divergence and their roles in species domestication are still lacking. We have carried out a genome-wide identification and comparative analysis of tandem and segmental genes in the rice genome. A total of 3,646 and 3,633 pairs of tandem and segmental genes, respectively, were identified in the genome. They made up around 30% of total annotated rice genes (excluding transposon-coding genes). Both tandem and segmental duplicates showed different physical locations and exhibited a biased subset of functions. These two types of duplicated genes were also under different functional constrains as shown by nonsynonymous substitutions per site (Ka) and synonymous substitutions per site (Ks) analysis. They are also differently regulated depending on the tissues and abiotic and biotic stresses based on transcriptomics data. The expression divergence might be related to promoter differentiation and DNA methylation status after tandem or segmental duplications. Both tandem and segmental duplications differ in their contribution to genetic novelty but evidence suggests that they play their role in species domestication and genome evolution.
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