Structural, Evolutionary, and Functional Analysis of the Class III Peroxidase Gene Family in Chinese Pear (Pyrus bretschneideri)

Abstract

Peroxidases (PRXs) are widely existed in various organisms and could be divided into different types according to their structures and functions. Specifically, the Class III Peroxidase, a plant-specific multi-gene family, involves in many physiological processes, such as the metabolism of auxin, the extension and thickening of cell wall, as well as the formation of lignin. By searching the pear genome database, 94 non-redundant <i>PRXs</i> from <i>Pyrus bretschneideri</i> (<i>PbPRXs</i>) were identified. Subsequently, analysis of phylogenetic relationships, gene structures, conserved motifs, and microsynteny was performed. These <i>PbPRXs</i> were unevenly distributed among 17 chromosomes of pear. In addition, 26 segmental duplication events but only one tandem duplication were occurred in these <i>PbPRXs</i>, implying segmental duplication was the main contributor to the expansion of the <i>PbPRX</i> family. By the Ka/Ks analysis, 26 out of 27 duplicated <i>PbPRXs</i> has experienced purifying selection. Twenty motifs were identified in PbPRXs based on the MEME analysis, 11 of which were enriched in pear. A total of 41 expressed genes were identified from ESTs of pear fruit. According to qRT-PCR, the expression trends of five <i>PbPRXs</i> in subgroup C were consistent with the change of lignin content during pear fruit development. So we inferred that the five <i>PbPRXs</i> were candidate genes involved in the lignin synthesis pathway. These results provided useful information for further researches of <i>PRX</i> genes in pear.