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

Abstract

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.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4089-4) contains supplementary material, which is available to authorized users.

Analysis of Homologous Regions of Small RNAs MIR397 and MIR408 Reveals the Conservation of Microsynteny among Rice Crop-Wild Relatives

“…Tajima’s D and Fu and Li’s F values were found to be most negative at the MIR408 locus, whereas both test values were the least negative at the MIR397B locus. Previously, negative values of one or both tests were also reported in rice and Arabidopsis [ 83 ]. Nucleotide diversity was also found to vary at different MIRNA loci.…”

Clustering pattern and evolution characteristic of microRNAs in grass carp (Ctenopharyngodon idella)

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Clustering pattern and evolution characteristic of microRNAs in grass carp (Ctenopharyngodon Idella)

“…New miRNAs, which always coincide with rapid evolution rates, are less conserved [57], have lowly expression levels [58], and appear to be species-speci c [59], have been identi ed as a component of the overall process by which speciation occurs [60]. Strikingly, the evolution ratio for the single new miRNAs was signi cantly higher than that of the clustered, suggesting purifying selection might have driven the clustered new miRNAs to develop the function.…”