Genome-wide identification, phylogeny, and expression analysis of PEBP gene family in Castanea mollissima

The phosphatidylethanolamine binding protein (PEBP) family plays an important part in growth and development of plants. <i>Castanea mollissima</i> is an economic plant with significant financial value and has become an important food source in the Northern Hemisphere. However, the <i>PEBP</i> genes in <i>C. mollissima</i> have not been studied yet. In this study, six <i>PEBP</i> genes (<i>CmPEBP1</i> ∼ <i>CmPEBP6</i>) were identified in <i>C. mollissima</i> and comprehensively analyzed in terms of physicochemical properties, phylogeny, gene structures, <i>cis</i>-regulatory elements (<i>CREs</i>), transcription factor interaction, and expression profiles. The six <i>CmPEBP</i> genes were categorized into three subfamilies according to the phylogeny analysis, and all of them share extremely similar gene and protein structures. A total of 136 <i>CREs</i> were identified in the promoter regions of the <i>CmPEBP</i> genes, mainly related to growth and development, environmental stress, hormone response, and light response. Comparative genomic analysis indicated that the expansion of the <i>CmPEBP</i> genes was mainly driven by dispersed duplication, and the <i>CmPEBP3</i>/<i>CmPEBP5</i> derived from eudicot common hexaploidization (ECH) events retained orthologous genes in all species studied. A total of 259 transcription factors (TFs) belonging to 39 families were predicted to be regulators of <i>CmPEBP</i> genes, and <i>CmPEBP4</i> was predicted to interact with the most TFs. The RNA-seq data analysis indicated the potential roles of <i>CmPEBP</i> genes in the ovule, bud, and flower development of <i>C. mollissima</i>, as well as in the response to temperature stress, drought stress, and the gall wasp <i>Dryocosmus kuriphilus</i> (GWDK) infestation. Additionally, the expression of <i>CmPEBP</i> genes in <i>C. mollissima</i> seed kernel development and their response to temperature stress were confirmed by RT-qPCR assays. This study gives references and directions for future in-depth studies of <i>PEBP</i> genes.