Youjun Lu1,2,3, Wei Chen2, Lanjie Zhao2, Jinbo Yao2, Yan Li2, Weijun Yang3, Ziyang Liu4, Yongshan Zhang5, Jie Sun6. 1. College of Agriculture/The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi, 832003, China. 2. Cotton Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China. 3. Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Huanghe Road, Anyang, 455000, Henan, China. 4. University of Saskatchewan, Saskatoon, SK, S7N 5A5, Canada. 5. Cotton Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China. 13938698299@163.com. 6. College of Agriculture/The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi, 832003, China. sunjie@shzu.edu.cn.
Abstract
INTRODUCTION: The phosphatidylethanolamine-binding protein (PEBP) gene family plays a crucial role in seed germination, reproductive transformation, and other important developmental processes in plants, but its distribution in Gossypium genomes or species, evolutionary properties, and the fates of multiple duplicated genes remain unclear. OBJECTIVES: The primary objectives of this study were to elucidate the distribution and characteristics of PEBP genes in Gossypium, as well as the evolutionary pattern of duplication and deletion, and functional differentiation of PEBPs in plants. METHODS: Using the PEBP protein sequences in Arabidopsis thaliana as queries, blast alignment was carried out for the identification of PEBP genes in four sequenced cotton species. Using the primers designed according to the PEBP genome sequences, PEBP genes were cloned from 15 representative genomes of Gossypium genus, and the gene structure, CDS sequence, protein sequence and properties were predicted and phylogenetic analysis was performed. Taking PEBP proteins of grape as reference, grouping of orthologous gene, analysis of phylogeny and divergence of PEBPs in nine species were conducted to reconstruct the evolutionary pattern of PEBP genes in plants. RESULTS: We identified and cloned 160 PEBPs from 15 cotton species, and the phylogenetic analysis showed that the genes could be classified into the following three subfamilies: MFT-like, FT-like and TFL1-like. There were eight single orthologous group (OG) members in each diploid and 16 double OG members in each tetraploid. An analysis of the expression and selective pressure indicated that expression divergence and strong purification selection within the same OG presented in the PEBP gene family. CONCLUSION: An evolutionary pattern of duplication and deletion of the PEBP family in the evolutionary history of Gossypium was suggested, and three pairs of genes resulted from different whole-genome duplication events.
INTRODUCTION: The phosphatidylethanolamine-binding protein (PEBP) gene family plays a crucial role in seed germination, reproductive transformation, and other important developmental processes in plants, but its distribution in Gossypium genomes or species, evolutionary properties, and the fates of multiple duplicated genes remain unclear. OBJECTIVES: The primary objectives of this study were to elucidate the distribution and characteristics of PEBP genes in Gossypium, as well as the evolutionary pattern of duplication and deletion, and functional differentiation of PEBPs in plants. METHODS: Using the PEBP protein sequences in Arabidopsis thaliana as queries, blast alignment was carried out for the identification of PEBP genes in four sequenced cotton species. Using the primers designed according to the PEBP genome sequences, PEBP genes were cloned from 15 representative genomes of Gossypium genus, and the gene structure, CDS sequence, protein sequence and properties were predicted and phylogenetic analysis was performed. Taking PEBP proteins of grape as reference, grouping of orthologous gene, analysis of phylogeny and divergence of PEBPs in nine species were conducted to reconstruct the evolutionary pattern of PEBP genes in plants. RESULTS: We identified and cloned 160 PEBPs from 15 cotton species, and the phylogenetic analysis showed that the genes could be classified into the following three subfamilies: MFT-like, FT-like and TFL1-like. There were eight single orthologous group (OG) members in each diploid and 16 double OG members in each tetraploid. An analysis of the expression and selective pressure indicated that expression divergence and strong purification selection within the same OG presented in the PEBP gene family. CONCLUSION: An evolutionary pattern of duplication and deletion of the PEBP family in the evolutionary history of Gossypium was suggested, and three pairs of genes resulted from different whole-genome duplication events.
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