Ganie Showkat Ahmad, Debnath Ananda Bhusan, Gumi Abubakar Mohammad, Mondal Tapan Kumar
Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India.
BMC Genomics. 2017 Sep 11;18(1):711. doi: 10.1186/s12864-017-4089-4.
MicroRNAs (miRNAs) are non-coding RNAs that play versatile roles in post-transcriptional gene regulation. Although much is known about their biogenesis, and gene regulation very little is known about their evolutionary relation among the closely related species.
All the orthologous miRNA genes of Oryza sativa (japonica) from 10 different Oryza species were identified, and the evolutionary changes among these genes were analysed. Significant differences in the expansion of miRNA gene families were observed across the Oryza species. Analysis of the nucleotide substitution rates indicated that the mature sequences show the least substitution rates among the different regions of miRNA genes, and also show a very much less substitution rates as compared to that of all protein-coding genes across the Oryza species. Evolution of miRNA genes was also found to be contributed by transposons. A non-neutral selection was observed at 80 different miRNA loci across Oryza species which were estimated to have lost ~87% of the sequence diversity during the domestication. The phylogenetic analysis revealed that O. longistaminata diverged first among the AA-genomes, whereas O. brachyantha and O. punctata appeared as the eminent out-groups. The miR1861 family organised into nine distinct compact clusters in the studied Oryza species except O. brachyantha. Further, the expression analysis showed that 11 salt-responsive miRNAs were differentially regulated between O. coarctata and O. glaberrima.
Our study provides the evolutionary dynamics in the miRNA genes of 10 different Oryza species which will support more investigations about the structural and functional organization of miRNA genes of Oryza species.
微小RNA（miRNA）是非编码RNA，在转录后基因调控中发挥多种作用。尽管人们对其生物合成和基因调控了解很多，但对其在近缘物种间的进化关系却知之甚少。
鉴定了来自10个不同稻属物种的水稻（粳稻）所有直系同源miRNA基因，并分析了这些基因间的进化变化。在不同稻属物种中观察到miRNA基因家族扩张存在显著差异。核苷酸替换率分析表明，成熟序列在miRNA基因的不同区域中显示出最低的替换率，并且与整个稻属物种的所有蛋白质编码基因相比，其替换率也非常低。还发现转座子对miRNA基因的进化有贡献。在整个稻属物种的80个不同miRNA位点观察到非中性选择，据估计这些位点在驯化过程中失去了约87%的序列多样性。系统发育分析表明，长雄蕊野生稻在AA基因组中最先分化，而短药野生稻和斑点野生稻则是明显的外类群。除短药野生稻外，在研究的稻属物种中，miR1861家族组织成9个不同的紧密簇。此外，表达分析表明，11个盐响应性miRNA在窄叶野生稻和光稃稻之间存在差异调控。
我们的研究提供了10个不同稻属物种miRNA基因的进化动态，这将支持对稻属物种miRNA基因的结构和功能组织进行更多研究。
