Genome Wide Identification, Evolutionary, and Expression Analysis of VQ Genes from Two Pyrus Species

Abstract

The VQ motif-containing gene, a member of the plant-specific genes, is involved in the plant developmental process and various stress responses. The VQ motif-containing gene family has been studied in several plants, such as rice (<i>Oryza sativa</i>), maize (<i>Zea mays</i>), and Arabidopsis (<i>Arabidopsis thaliana</i>). However, no systematic study has been performed in <i>Pyrus</i> species, which have important economic value. In our study, we identified 41 and 28 VQ motif-containing genes in <i>Pyrus bretschneideri</i> and <i>Pyrus communis</i>, respectively. Phylogenetic trees were calculated using <i>A. thaliana</i> and <i>O. sativa</i> VQ motif-containing genes as a template, allowing us to categorize these genes into nine subfamilies. Thirty-two and eight paralogous of VQ motif-containing genes were found in <i>P. bretschneideri</i> and <i>P. communis</i>, respectively, showing that the VQ motif-containing genes had a more remarkable expansion in <i>P. bretschneideri</i> than in <i>P. communis</i>. A total of 31 orthologous pairs were identified from the <i>P. bretschneideri</i> and <i>P. communis</i> VQ motif-containing genes. Additionally, among the paralogs, we found that these duplication gene pairs probably derived from segmental duplication/whole-genome duplication (WGD) events in the genomes of <i>P. bretschneideri</i> and <i>P. communis</i>, respectively. The gene expression profiles in both <i>P. bretschneideri</i> and <i>P. communis</i> fruits suggested functional redundancy for some orthologous gene pairs derived from a common ancestry, and sub-functionalization or neo-functionalization for some of them. Our study provided the first systematic evolutionary analysis of the VQ motif-containing genes in <i>Pyrus</i>, and highlighted the diversification and duplication of VQ motif-containing genes in both <i>P. bretschneideri</i> and <i>P. communis</i>.