Journal Article

Comprehensive genomic analysis of the expansin gene family in pecan (Carya illinoinensis) and their transcriptional responses to stresses and fruit abscission

Xuan, Ji-ping, Wang, Gang, Wang, Tao, Zhang, Ji-yu, Jia, Zhan-hui, Wang, Guo-ming

2025

Overview

Background Expansins (EXPs) are important components of the plant cell wall. They are involved in plant growth and development and diverse environmental stress responses by promoting cell-wall loosening and cell enlargement. Although EXPs have been characterized in many plant species, little is known about the EXPs in Carya illinoinensis . Methods The CiEXP gene family was systematically analyzed using bioinformatics. RNA-seq data (both from our study and public databases) and qRT-PCR were employed to analyze the expression patterns of the CiEXP family in different tissues, under biotic and abiotic stress, and in persistent versus abscised fruit. Results In this study, a total of 39 EXP genes unevenly distributed on 14 chromosomes were identified in the C. illinoinensis genome, which were classified into four subfamilies (27 CiEXPAs, 3 CiEXPBs, 2 CiEXLAs, and 7 CiEXLBs), and the motif and gene structures were consistent with this subfamily classification. Thirty-six pairs of duplicated genes were identified, suggesting that gene duplication may have contributed to the expansion of the EXP gene family. Collinearity analysis provided further phylogenetic insights into the EXP gene family. Cis -acting element analysis revealed that the promoter regions of the CiEXPs gene were associated with hormone-responsive, plant growth and development, and stress-responsive, particularly ABA response element (ABRE) and MeJA-responsive element. The expression results showed that most CiEXPs exhibited tissue-specific expression patterns, and some CiEXPs were highly responsive to abiotic and biotic stresses. Additionally, most CiEXPA genes, CiEXPB1/2 , and CiEXLA2 were up-regulated in persistent fruit. Conclusions Our study findings enhance the understanding of the CiEXP gene family and facilitate the selection of suitable candidate genes for further study, which lays a foundation for future investigations into the functional roles of specific CiEXPs .

• Publisher: BioMed Central,BioMed Central Ltd,BMC
• Subject: abiotic stress / Agriculture / Analysis / Bioinformatics / Biomedical and Life Sciences / Carya - genetics / Carya - physiology / Carya illinoinensis / cell growth / cell walls / Computational biology / Diseases and pests / Expansin / expansins / Expression patterns / family / Fruit - genetics / Fruit - growth & development / Fruit - physiology / fruit drop / fruits / gene duplication / Gene expression / Gene Expression Regulation, Plant / genes / Genes, Plant / Genetic aspects / Genome, Plant / genomics / Growth / growth and development / Life Sciences / Multigene Family / Pecan / Pecan (Carya illinoinensis) / pecans / Phylogeny / plant growth / Plant Proteins - genetics / Plant Proteins - metabolism / Plant Sciences / Polymerase chain reaction / regulatory sequences / sequence analysis / species / Stress, Physiological - genetics / Stresses response / subfamily / Testing / transcription (genetics) / Tree Biology