| 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
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| 通讯作者 | Zhang, Y (reprint author), Chinese Acad Sci, Plant Germplasm & Genom Ctr, Kunming Inst Bot, Kunming, Peoples R China |
| 2011-12-14 | |
| 发表期刊 | PLOS ONE
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| ISSN | 1932-6203 |
| 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 |
| 学科领域 | Life Sciences & Biomedicine - Other Topics |
| DOI | 10.1371/journal.pone.0028073 |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000298369100020 |
| 引用统计 | |
| 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 |
| 推荐引用方式 GB/T 7714 | 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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