Articles Bioinformatics

Chinese Science Bulletin

, Volume 55, Issue 13, pp 1263-1270

Prediction of sorghum miRNAs and their targets with computational methods

  • JiangFeng DuAffiliated withBioinformatics Center, Northwest Agricultural & Forestry UniversityCollege of Life Sciences, Northwest Agricultural & Forestry University
  • , YongJun WuAffiliated withCollege of Life Sciences, Northwest Agricultural & Forestry University
  • , XiaoFeng FangAffiliated withCollege of Life Sciences, Northwest Agricultural & Forestry University
  • , JunXia CaoAffiliated withBioinformatics Center, Northwest Agricultural & Forestry UniversityCollege of Life Sciences, Northwest Agricultural & Forestry University
  • , Liang ZhaoAffiliated withCollege of Life Sciences, Northwest Agricultural & Forestry University
  • , ShiHeng TaoAffiliated withBioinformatics Center, Northwest Agricultural & Forestry UniversityCollege of Life Sciences, Northwest Agricultural & Forestry University Email author 

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Abstract

microRNAs are a class of ∼21-nt long, non-coding and newly-identified RNAs that play critical roles in post-transcriptional gene regulation. Their targets are involved in various biological processes, including development, metabolism, and stress response. Though a large number of miRNAs have been reported in many species, reports of miRNAs in sorghum are limited. Using a homology search based on the genomic survey sequence (GSS) and the microRNA (miRNA) secondary structure, a total of 17 new miRNAs were identified in this work. They were found to be distributed unevenly among 11 miRNA families. Some miRNA genes were found at multiple locations and in more than one genomic context. Most miRNAs are conserved within the same kingdom, but we found in sorghum that sbi-miR127 and sbi-miR466 showed conservation with H. sapiens and M. musculus, respectively. Analysis of those 17 new miRNAs via online software miRU showed that they might regulate 64 target genes, most of which are involved in RNA processing, metabolism, cell cycle, protein degradation, stress response and transportation. At least 7 of 11 miRNA families target proteins that are necessary in metabolism and stress response, including NADPH-cytochrome P450 reductase, nucleoside diphosphate kinase and superoxide dismutase, suggesting that miRNAs play an essential role in biological processes.

Keywords

microRNA sorghum precursor genome survey sequence (GSS) prediction targets function