Abstract
The identification of genes under positive selection is a central goal of evolutionary biology. Many legume species, including Phaseolus vulgaris (common bean) and Phaseolus lunatus (lima bean), have important ecological and economic value. In this study, we sequenced and assembled the transcriptome of one Phaseolus species, lima bean. A comparison with the genomes of six other legume species, including the common bean, Medicago, lotus, soybean, chickpea, and pigeonpea, revealed 15 and 4 orthologous groups with signatures of positive selection among the two Phaseolus species and among the seven legume species, respectively. Characterization of these positively selected genes using Non redundant (nr) annotation, gene ontology (GO) classification, GO term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that these genes are mostly involved in thylakoids, photosynthesis and metabolism. This study identified genes that may be related to the divergence of the Phaseolus and legume species. These detected genes are particularly good candidates for subsequent functional studies.
Highlights
The discovery of genes that are influenced by natural selection is a central goal of evolutionary biology
The genes identified in this study as most likely being under positive selection are good candidates for subsequent functional studies
Through the use of non redundant annotation, gene ontology (GO) classification, GO term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, we investigated the functional classifications for all orthologous groups (OGs)
Summary
The discovery of genes that are influenced by natural selection is a central goal of evolutionary biology. One widely used method for inferring the targets of positive Darwinian selection is to test the ratio, numbers, and patterns of nonsynonymous and synonymous substitutions in homologous protein coding regions. This approach has been widely employed to infer the selection of single genes and functional classes of genes, including on a genome-wide scale [1,2,3,4,5,6,7]. Advances in next-generation sequencing have made it possible to identify positively selected genes using more extensively sampled species. Backstrom et al [6]
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