Genome-wide identification andin silicocharacterisation of microRNAs, their targets and processing pathway genes inPhaseolus vulgarisL
| Autor: | Terezinha Aparecida Teixeira, L. R. do Amaral, M. de Souza Gomes, Charles Spillane, Laysa Gomes Portilho, Wilson Roberto Maluf, L. A. A. Gomes, C. L. de Oliveira, T. C. de Sousa Cardoso, Peter C. McKeown |
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| Rok vydání: | 2015 |
| Předmět: |
0301 basic medicine
In silico Molecular Sequence Data Plant Science Computational biology Genes Plant Bioinformatics Genome Transcriptome 03 medical and health sciences Catalytic Domain microRNA Computer Simulation Amino Acid Sequence RNA Processing Post-Transcriptional Gene Conserved Sequence Phylogeny Ecology Evolution Behavior and Systematics Plant Proteins Phaseolus Messenger RNA Base Sequence biology food and beverages General Medicine Fabaceae biology.organism_classification Protein Structure Tertiary MicroRNAs 030104 developmental biology Nucleic Acid Conformation Sequence Alignment Genome Plant |
| Zdroj: | Europe PubMed Central |
| ISSN: | 1435-8603 |
| DOI: | 10.1111/plb.12377 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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