Genome-wide identification of the plant U-box (<i>PUB</i>) gene family and their global expression analysis in tomato (<i>Solanum lycopersicum</i>)

Abstract

Plant ubiquitination plays an important role in proteins post-translational changes that occurs in a wide variety of eukaryotic organisms and regulating a broad range of biological processes. However, little is known about the evolutionary relationships, gene duplication, and functional evolution of <italic>PUB</italic> genes in tomato. Herein, we explored 48 <italic>PUB</italic> genes in the tomato genome and were further classified into 7 major groups based on their sequences and relative genetic similarities with <italic>Arabidopsis</italic>. Gene structure analysis suggested that most of the PUBs carry similar features and with slight differentiation in their sources of functions during the process of evolution. Collinear analysis showed a high degree of conservation among SlPUBs, with a total of ten pairs identified as collinear with potential interactions with each other and another family. Based on their duplication forms, a total of 23 pairs were chosen for <italic>Ka/Ks</italic> calculation: 13 pairs of dispersed, 1 tandem, and 9 pairs of WGD or segmental. The majority of the gene pairs from the three forms of duplication had a <italic>Ka/Ks</italic> ratio of less than 1.00, indicating purifying selection and reduced divergence after duplication. Only 3 pairs i.e., <italic>SlPUB16-SlPUB22, SlPUB30-SlPUB32,</italic> and <italic>SlPUB36-SlPUB37</italic> were perceived by higher than 1.00 values, signifying positive selection. In addition, three major RNA-seq datasets analyses from the cultivated and its relatives, as well as Micro-Tom (MT), revealed their highly tissue-specific role, with the expression correlation analysis of duplicated pairs indicating highly putative neo-functionalization as compared to functional conservation or sub-functionalization after duplication. <italic>SlPUB10</italic> was screened out and preliminary verified as a key gene in salt and cold stress response with validation of transgenic strains. These results are indicative of their response during the gene duplication and evolution process, while further functional validation step is required to determine their specific role.