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Different divergence events for three pairs of PEBPs in Gossypium as implied by evolutionary analysis

  • Youjun Lu
  • Wei Chen
  • Lanjie Zhao
  • Jinbo Yao
  • Yan Li
  • Weijun Yang
  • Ziyang Liu
  • Yongshan Zhang
  • Jie Sun
Research Article

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.

Keywords

Gossypium PEBP Evolution Selective pressure Gene loss 

Notes

Acknowledgements

The study was supported, in part, by the National Natural Science Foundation of China (Item Number: 31671740), the Natural Science Foundation of Henan Province (Item Number: 112300410019) and the State Key Laboratory of Cotton Biology (Item Number: CB2015C16).

Author contributions

YL, YZ and JS: designed the study; LZ, WC, JY, WY and YL: performed the experiments; YL, LZ and ZL: performed the data analysis; and YL and YZ: wrote the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing financial interests.

Supplementary material

13258_2018_775_MOESM1_ESM.docx (2.3 mb)
Supplementary material 1 (DOCX 2316 KB)
13258_2018_775_MOESM2_ESM.xlsx (178 kb)
Supplementary material 2 (XLSX 177 KB)
13258_2018_775_MOESM3_ESM.xlsx (15 kb)
Supplementary Information 3: Gene expression data of the PEBP in G. hirsutum. (XLSX 15 KB)
13258_2018_775_MOESM4_ESM.pdf (156 kb)
Supplementary Information 4: Predicted gene structure of the cotton PEBPs. (PDF 156 KB)
13258_2018_775_MOESM5_ESM.rar (7.9 mb)
Supplementary material 5 (RAR 8054 KB)

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Copyright information

© The Genetics Society of Korea 2019

Authors and Affiliations

  1. 1.College of Agriculture/The Key Laboratory of Oasis Eco-AgricultureShihezi UniversityShiheziChina
  2. 2.Cotton Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)/State Key Laboratory of Cotton BiologyAnyangChina
  3. 3.Research Base, Anyang Institute of TechnologyState Key Laboratory of Cotton BiologyAnyangChina
  4. 4.University of SaskatchewanSaskatoonCanada

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