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Evolution of MicroRNA Genes in Oryza sativa and Arabidopsis thaliana: An Update of the Inverted Duplication Model
Zhang, Yun1,2; Jiang, Wen-kai1; Gao, Li-zhi1
2011-12-14
发表期刊PLOS ONE
ISSN1932-6203
卷号6期号:12页码:e28073
摘要The origin and evolution of microRNA (miRNA) genes, which are of significance in tuning and buffering gene expressions in a number of critical cellular processes, have long attracted evolutionary biologists. However, genome-wide perspectives on their origins, potential mechanisms of their de novo generation and subsequent evolution remain largely unsolved in flowering plants. Here, genome-wide analyses of Oryza sativa and Arabidopsis thaliana revealed apparently divergent patterns of miRNA gene origins. A large proportion of miRNA genes in O. sativa were TE-related and MITE-related miRNAs in particular, whereas the fraction of these miRNA genes much decreased in A. thaliana. Our results show that the majority of TE-related and pseudogene-related miRNA genes have originated through inverted duplication instead of segmental or tandem duplication events. Based on the presented findings, we hypothesize and illustrate the four likely molecular mechanisms to de novo generate novel miRNA genes from TEs and pseudogenes. Our rice genome analysis demonstrates that non-MITEs and MITEs mediated inverted duplications have played different roles in de novo generating miRNA genes. It is confirmed that the previously proposed inverted duplication model may give explanations for non-MITEs mediated duplication events. However, many other miRNA genes, known from the earlier proposed model, were rather arisen from MITE transpositions into target genes to yield binding sites. We further investigated evolutionary processes spawned from de novo generated to maturely-formed miRNA genes and their regulatory systems. We found that miRNAs increase the tunability of some gene regulatory systems with low gene copy numbers. The results also suggest that gene balance effects may have largely contributed to the evolution of miRNA regulatory systems.
关键词Small Rnas Processed Pseudogenes Transposable Elements Plant Micrornas Genome Rice Expression Mirna Diversification Canalization
资助信息Chinese Academy of Sciences (CAS)[KSCX2-YW-N-029]; Talents Program of Yunnan Province[20080A009]; Chinese Department of Science and Technology[2007CB815703]; Kunming Institute of Botany, CAS
收录类别SCI
语种英语
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文献类型期刊论文
条目标识符http://ir.kib.ac.cn/handle/151853/5193
专题中国西南野生生物种质资源库
作者单位1.Chinese Acad Sci, Plant Germplasm & Genom Ctr, Kunming Inst Bot, Kunming, Peoples R China
2.Chinese Acad Sci, Grad Sch, Beijing, Peoples R China
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Zhang, Yun,Jiang, Wen-kai,Gao, Li-zhi. Evolution of MicroRNA Genes in Oryza sativa and Arabidopsis thaliana: An Update of the Inverted Duplication Model[J]. PLOS ONE,2011,6(12):e28073.
APA Zhang, Yun,Jiang, Wen-kai,&Gao, Li-zhi.(2011).Evolution of MicroRNA Genes in Oryza sativa and Arabidopsis thaliana: An Update of the Inverted Duplication Model.PLOS ONE,6(12),e28073.
MLA Zhang, Yun,et al."Evolution of MicroRNA Genes in Oryza sativa and Arabidopsis thaliana: An Update of the Inverted Duplication Model".PLOS ONE 6.12(2011):e28073.
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