Evolution of PEPC gene family in Gossypium reveals functional diversification and GhPEPC genes responding to abiotic stresses

Yanpeng Zhao; Anhui Guo; Yumei Wang; Jinping Hua

doi:10.1016/j.gene.2019.02.061

Evolution of PEPC gene family in Gossypium reveals functional diversification and GhPEPC genes responding to abiotic stresses

Gene. 2019 May 25:698:61-71. doi: 10.1016/j.gene.2019.02.061. Epub 2019 Feb 28.

Authors

Yanpeng Zhao¹, Anhui Guo², Yumei Wang³, Jinping Hua⁴

Affiliations

¹ Laboratory of Cotton Genetics, Genomics and Breeding, Beijing Key Laboratory of Crop Genetic Improvement, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China. Electronic address: yanpeng_zhao@cau.edu.cn.
² Laboratory of Cotton Genetics, Genomics and Breeding, Beijing Key Laboratory of Crop Genetic Improvement, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China. Electronic address: guoah@cau.edu.cn.
³ Research Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China.
⁴ Laboratory of Cotton Genetics, Genomics and Breeding, Beijing Key Laboratory of Crop Genetic Improvement, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China. Electronic address: jinping_hua@cau.edu.cn.

PMID: 30825597
DOI: 10.1016/j.gene.2019.02.061

Abstract

Phosphoenolpyruvate carboxylase (PEPC) family genes play important roles in regulating plant growth and abiotic stress response. Based on the sequenced Gossypium genomes, we performed comprehensive analysis of PEPC homolog genes in cotton, which six, six, eleven and ten PEPC genes were identified in Gossypium arboreum (A₂), G. raimondii (D₅), G. hirsutum (AD₁) and G. barbadense (AD₂), respectively. These genes were divided into six subgroups: PEPC-i, PEPC-ii, PEPC-iii, PEPC-iv, PEPC-v and PEPC-vi; PEPC genes in each subgroup displayed conserved gene structure and motifs. Segmental duplication and whole genome duplication (WGD) events yielded the expansion of PEPC genes. Expression assays showed that the duplicated PEPC genes displayed diverse expression patterns, indicating that they experienced functional divergence. Of which, genes in PEPC-iv subgroup played crucial role for substrate distribution in cottonseed. Cis-elements, putative miRNAs and expression analyses showed that GhPEPC homologs might respond to abiotic stresses, expression levels of GhPEPC1 and GhPEPC2/GhPEPC2D genes were larger induced than other GhPEPC genes under cold, heat, salt, and drought stresses, indicating the crucial roles in abiotic stresses response. Present study serves new information to decipher the evolution and function of PEPC genes in Gossypium.

Keywords: Abiotic stresses; Evolution; Functional diversification; Gossypium; Phosphoenolpyruvate carboxylase (PEPC).

MeSH terms

Chromosome Mapping / methods
Evolution, Molecular
Gene Duplication / genetics
Gene Expression Profiling / methods
Gene Expression Regulation, Plant / genetics
Genome, Plant / genetics
Genome-Wide Association Study / methods
Gossypium / genetics*
Phosphoenolpyruvate Carboxylase / genetics*
Phosphoenolpyruvate Carboxylase / metabolism
Phylogeny
Plant Proteins / genetics
Stress, Physiological / genetics*
Stress, Physiological / physiology

Substances

Plant Proteins
Phosphoenolpyruvate Carboxylase