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.
Highlights
MicroRNAs are non-coding RNAs that play versatile roles in post-transcriptional gene regulation
Number and distribution of miRNA genes in the 10 Oryza genomes Based on the sequence conservation of miRNA genes in plants, we identified an average number of ~326 miRNA genes by homology search in the 10 Oryza species
The number of miRNA gene families was found to be the least (28) in O. brachyantha, and the highest (184) in O. rufipogon. This number was the least in O. brachyantha and O. punctata, and the gains in the number might have taken place during the course of evolution from FF- and BB- genomes to AA- Oryza genomes as well as during the domestication. This is fairly justified from the fact that progenators of O. brachyantha and O. punctata diverged from the domesticated rice O. sativa progenitor almost ~15 and 9.11 million years ago (MYA) respectively [36, 37]
Summary
MicroRNAs (miRNAs) are non-coding RNAs that play versatile roles in post-transcriptional gene regulation. Much is known about their biogenesis, and gene regulation very little is known about their evolutionary relation among the closely related species. MicroRNAs (miRNAs) are a class of non-protein-coding small RNAs playing versatile roles in post-transcriptional gene regulation. These regulatory genetic elements are formed from long self-complementary precursor sequences which in turn originate from still much longer primary miRNA sequences [1]. There are two main categories of the genes encoding the miRNA precursors [2]. Some of the miRNA gene families in both plants and animals are highly conserved through millions of years [10, 11].
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