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Natural variation and evolutionary dynamics of transposable elements in Brassica oleracea based on next-generation sequencing data

Authors
  • Liu, Zhen1
  • Fan, Miao1
  • Yue, Er-Kui1
  • Li, Yu1
  • Tao, Ruo-Fu1
  • Xu, Hai-Ming1
  • Duan, Ming-Hua2
  • Xu, Jian-Hong1
  • 1 Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, People’s Republic of China , Hangzhou (China)
  • 2 Zhejiang Zhengjingyuan Pharmacy Chain Co., Ltd. & Hangzhou Zhengcaiyuan Pharmaceutical Co., Ltd., Hangzhou, 310021, People’s Republic of China , Hangzhou (China)
Type
Published Article
Journal
Horticulture Research
Publisher
Nature Publishing Group UK
Publication Date
Sep 01, 2020
Volume
7
Issue
1
Identifiers
DOI: 10.1038/s41438-020-00367-0
Source
Springer Nature
License
Green

Abstract

Brassica oleracea comprises various economically important vegetables and presents extremely diverse morphological variations. They provide a rich source of nutrition for human health and have been used as a model system for studying polyploidization. Transposable elements (TEs) account for nearly 40% of the B. oleracea genome and contribute greatly to genetic diversity and genome evolution. Although the proliferation of TEs has led to a large expansion of the B. oleracea genome, little is known about the population dynamics and evolutionary activity of TEs. A comprehensive mobilome profile of 45,737 TE loci was obtained from resequencing data from 121 diverse accessions across nine B. oleracea morphotypes. Approximately 70% (32,195) of the loci showed insertion polymorphisms between or within morphotypes. In particular, up to 1221 loci were differentially fixed among morphotypes. Further analysis revealed that the distribution of the population frequency of TE loci was highly variable across different TE superfamilies and families, implying a diverse expansion history during host genome evolution. These findings provide better insight into the evolutionary dynamics and genetic diversity of B. oleracea genomes and will potentially serve as a valuable resource for molecular markers and association studies between TE-based genomic variations and morphotype-specific phenotypic differentiation.

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