Molecular Characterization, Evolution, and Expression Profiling of the Dirigent (DIR) Family Genes in Chinese White Pear (Pyrus bretschneideri)

Abstract

Stone cells content and size are the key factors determining the internal quality of the pear fruit. Synthesis of lignin and thickening of secondary cell wall are the keys to the development of stone cells. The polymerization of monolignols and secondary cell wall formation requires the participation of dirigent proteins (DIRs). In recent years, <i>DIR</i> family have been studied in higher plants, but lack of comprehensive study in the pear <i>DIR</i> (<i>PbDIR</i>) family. This study focuses on the identification and analysis of <i>PbDIR</i> family for the first time. We identified 35 <i>PbDIR</i>s from the pear genome, 89% of which are intronless genes. Phylogenetic tree and chromosome localization analysis showed that 35 <i>PbDIR</i>s were divided into four subfamilies (DIR-a, -b/d, -e, and -g) and irregularly distributed among 10 chromosomes. In addition, we identified 29, 26, and 14 DIRs from the other three Rosids (peach, Mei, and grape), respectively. Interspecies microsynteny analysis revealed the collinear gene pairs between pear and peach are the most. Temporal expression analysis showed that the expression changes of seven <i>PbDIR</i>s (DIR-a subfamily: <i>PbDIR4</i> and <i>PbDIR5</i>; DIR-b/d subfamily: <i>PbDIR11</i>; DIR-g subfamily: <i>PbDIR19</i>; DIR-e subfamily: <i>PbDIR23, 25</i> and <i>26</i>) in fruits were consistent with the changes of fruit lignin and stone cells contents. In addition, the subfamily of <i>PbDIR</i>s in fruits showed significant responses after treatment with ABA, SA, and MeJA. According to the protein tertiary structure, key amino acid residues and expression patterns analysis found that PbDIR4 might be involved in the metabolism of lignin and related to stone cells contents in pear fruits. In this study, we systematically analyzed the structure, evolution, function and expression of <i>PbDIR</i> family, which not only confirmed the characteristics of <i>PbDIR</i> family, but also laid the foundation for revealing the role of <i>DIR</i> in pear stone cell development and lignin polymerization.