title: Genome-wide identification and in silico characterisation of microRNAs, their targets and processing pathway genes in Phaseolus vulgaris L.
abstract: 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 RNAs within the common bean genome. One of the most important classes of such small non-coding RNAs is microRNAs (miRNAs), which control mRNA and protein expression levels in many eukaryotes. Computational methods have been applied to identify putative miRNAs in the genomes of different organisms. In this study, our objective was to comprehensively identify and characterise miRNAs from the genome and transcriptome of P. vulgaris, including both mature and precursor miRNA forms. We also sought to identify the putative proteins involved in miRNA processing and the likely target genes of common bean miRNAs. We identified 221 mature miRNAs and 136 precursor miRNAs distributed across 52 different miRNA families in the P. vulgaris genome. Amongst these, we distinguished 129 novel mature miRNAs and 123 miRNA precursors belonging to 24 different miRNA families. We also identified 31 proteins predicted to participate in the miRNA-processing pathway in P. vulgaris. Finally, we also identified 483 predicted miRNA targets, including many which corroborate results from other species, suggesting that miRNA regulatory systems are evolutionarily conserved and important for plant development. Our results expand the study of miRNAs and their target genes in common bean, and provide new opportunities to understand their roles in the biology of this important staple crop.
authors.affiliation: Laboratory of Bioinformatics and Molecular Analysis - INGEB/FACOM, Federal University of Uberlandia, Patos de Minas, Brazil.
authors.forename: T C
authors.initials: TC
authors.lastname: de Sousa Cardoso
authors.affiliation: Laboratory of Bioinformatics and Molecular Analysis - INGEB/FACOM, Federal University of Uberlandia, Patos de Minas, Brazil.
authors.forename: L G
authors.initials: LG
authors.lastname: Portilho
authors.affiliation: Department of Agriculture, Federal University of Lavras, Lavras, Brazil.
authors.forename: C L
authors.initials: CL
authors.lastname: de Oliveira
authors.affiliation: Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, Áras de Brún, National University of Ireland, Galway, Ireland.
authors.forename: P C
authors.initials: PC
authors.lastname: McKeown
authors.affiliation: Department of Agriculture, Federal University of Lavras, Lavras, Brazil.
authors.forename: W R
authors.initials: WR
authors.lastname: Maluf
authors.affiliation: Department of Agriculture, Federal University of Lavras, Lavras, Brazil.
authors.forename: L A A
authors.initials: LA
authors.lastname: Gomes
authors.affiliation: Laboratory of Bioinformatics and Molecular Analysis - INGEB/FACOM, Federal University of Uberlandia, Patos de Minas, Brazil.
authors.forename: T A
authors.initials: TA
authors.lastname: Teixeira
authors.affiliation: Laboratory of Bioinformatics and Molecular Analysis - INGEB/FACOM, Federal University of Uberlandia, Patos de Minas, Brazil.
authors.forename: L R
authors.initials: LR
authors.lastname: do Amaral
authors.affiliation: Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, Áras de Brún, National University of Ireland, Galway, Ireland.
authors.forename: C
authors.initials: C
authors.lastname: Spillane
authors.affiliation: Laboratory of Bioinformatics and Molecular Analysis - INGEB/FACOM, Federal University of Uberlandia, Patos de Minas, Brazil.
authors.forename: M
authors.identifier: http://orcid.org/0000-0002-6163-810X
authors.initials: M
authors.lastname: de Souza Gomes
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D020134:Catalytic Domain; D003198:Computer Simulation; D017124:Conserved Sequence; D017343:Genes, Plant; D018745:Genome, Plant; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D027805:Phaseolus / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017434:Protein Structure, Tertiary; D012323:RNA Processing, Post-Transcriptional / Q000235:genetics*; D016415:Sequence Alignment
chemical_list: D035683:MicroRNAs; D010940:Plant Proteins
keywords: Argonaute (AGO); Phaseolus vulgaris L.; computational analysis; dicer-like (DCL); microRNAs