Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species

BMC Genomics

Research Article

Ananda Bhusan Debnath¹  Abubakar Mohammad Gumi¹  Tapan Kumar Mondal¹  Showkat Ahmad Ganie¹ 

[1] Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, 110012, New Delhi, India;

关键词: Cluster;    Evolutionary rate;    miRNA;    Oryza;    Selection;    Transposons;   

DOI  :  10.1186/s12864-017-4089-4

 received in 2016-07-28, accepted in 2017-08-25,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundMicroRNAs (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.ResultAll 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.ConclusionOur 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.

【 授权许可】

CC BY   
© The Author(s). 2017