Computational identification of microRNAs in Phaseolus vulgaris L.

What is it about?

The common bean (Phaseolus vulgaris L.) is an important legume for global food security and is an essential staple crop for more than 400 million people. In addition, it plays an important role in sustainable agriculture by fixing atmospheric nitrogen. Although much is known about the biology of P. vulgaris, relatively little is known about how gene expression networks regulate its development. The miRNAs are endogenous small RNAs, ~21 nucleotides in length that regulate gene expression by inhibiting translation through the nucleic acid sequence complementarity between the miRNA and its target. Many important biological functions in plants are mediated by miRNAs, including regulation of leaf development and floral transitions, adaptation to stress against pathogens and control of cell proliferation. The study of plant miRNAs has now become a powerful tool to for elucidating the control of biological processes. The aims of this study were to identify and characterise, by in silico analysis, the genes involved in miRNA-processing pathway, the mature miRNAs (and their precursors) and their predicted targets using available P. vulgaris genomic and transcriptomic resources. This study will allow a better understanding of miRNAs in this important staple crop, and provide targets for future investigation.

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Why is it important?

Identification of the miRNAs present in a plant, and the genes that they regulate, are important for understanding plant biology. To further understand this in a major legume crop, we applied an integrated computational analysis to EST, GSS and genome resources, and identified 68 proteins involved in processing small RNAs. At least 31 of these proteins participate in the miRNA-processing pathway. We identified 221 mature miRNAs and 136 pre-miRNAs within 52 different families, including 129 previously unreported mature miRNAs within 24 families. The 221 miRNAs target the mRNA of at least 483 P. vulgaris genes, suggesting that miRNAs have major roles in development, stress, hormone response, pathogen defence and other processes important for the biology, breeding and agricultural use of this plant. A phylogenetic study of these genes indicates that there is a high level of conservation of both miRNAs and miRNA target sites. This suggests that results obtained in other plant species, and especially in other legumes such as soybean, can also be applied in Phaseolus vulgaris. Overall, our results advance the study of miRNAs in plants, providing new targets for experimental validation to understand the functional significance of miRNA-based regulation in common bean.