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Genome‐wide identification and in silico characterisation of micro RNA s, their targets and processing pathway genes in Phaseolus vulgaris L.
Author(s) -
Sousa Cardoso T. C.,
Portilho L. G.,
Oliveira C. L.,
McKeown P. C.,
Maluf W. R.,
Gomes L. A. A.,
Teixeira T. A.,
Amaral L. R.,
Spillane C.,
Souza Gomes M.
Publication year - 2016
Publication title -
plant biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.871
H-Index - 87
eISSN - 1438-8677
pISSN - 1435-8603
DOI - 10.1111/plb.12377
Subject(s) - biology , phaseolus , microrna , in silico , genome , gene , transcriptome , genetics , non coding rna , computational biology , small rna , gene expression , botany
Common bean ( Phaseolus vulgaris L., Fabaceae) is a globally important staple crop, which is an important source of calories, protein and essential micronutrients. At the genomic level little is known regarding the small non‐coding RNA s within the common bean genome. One of the most important classes of such small non‐coding RNA s is micro RNA s (mi RNA s), which control mRNA and protein expression levels in many eukaryotes. Computational methods have been applied to identify putative mi RNA s in the genomes of different organisms. In this study, our objective was to comprehensively identify and characterise mi RNA s from the genome and transcriptome of P. vulgaris , including both mature and precursor mi RNA forms. We also sought to identify the putative proteins involved in mi RNA processing and the likely target genes of common bean mi RNA s. We identified 221 mature mi RNA s and 136 precursor mi RNA s distributed across 52 different mi RNA families in the P. vulgaris genome. Amongst these, we distinguished 129 novel mature mi RNA s and 123 mi RNA precursors belonging to 24 different mi RNA families. We also identified 31 proteins predicted to participate in the mi RNA ‐processing pathway in P. vulgaris . Finally, we also identified 483 predicted mi RNA targets, including many which corroborate results from other species, suggesting that mi RNA regulatory systems are evolutionarily conserved and important for plant development. Our results expand the study of mi RNA s and their target genes in common bean, and provide new opportunities to understand their roles in the biology of this important staple crop.