Browse Articles

Article|01 Sep 2020|OPEN
Natural variation and evolutionary dynamics of transposable elements in Brassica oleracea based on next-generation sequencing data
Zhen Liu1, Miao Fan1, Er-Kui Yue1, Yu Li1, Ruo-Fu Tao1, Hai-Ming Xu1, Ming-Hua Duan2 & Jian-Hong Xu1,
1Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, 310058 Hangzhou, People’s Republic of China
2Zhejiang Zhengjingyuan Pharmacy Chain Co., Ltd. & Hangzhou Zhengcaiyuan Pharmaceutical Co., Ltd., 310021 Hangzhou, People’s Republic of China

Horticulture Research 7,
Article number: 145 (2020)
doi: 10.1038/hortres.2020.145
Views: 346

Received: 06 Jan 2020
Revised: 22 May 2020
Accepted: 19 Jun 2020
Published online: 01 Sep 2020

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.