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Position: Home > Articles > Hotspots of Independent and Multiple Rounds of LTR-retrotransposon Bursts in Brassica Species Horticultural Plant Journal 2018,4 (4)

Hotspots of Independent and Multiple Rounds of LTR-retrotransposon Bursts in Brassica Species

作者：

Xiaohua Cai;Yinan Cui;Lei Zhang;Jian Wu;Jiansheng Liang;Lin Cheng;Xiaowu Wang;Feng Chen

单位：

Shandong Provincial Key Laboratory of Protected Vegetable Molecular Breeding, Shandong Shouguang Vegetable Seed Industry Group Co. Ltd, Shouguang 262700, Shandong, China;Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, Chin;Shandong Provincial Key Laboratory of Protected Vegetable Molecular Breeding, Shandong Shouguang Vegetable Seed Industry Group Co. Ltd, Shouguang 262700, Shandong, China;Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China

关键词：

Brassica;LTR-retrotransposon;insertion time;Raphanus sativus;GENOME SEQUENCE;PHYLOGENETIC ANALYSIS;DIVERSITY;TOOL;ELEMENTS;ARABIS;SIZ

摘要：

Long terminal repeat retrotransposons (LTR-RTs) are a predominant group of plant transposable elements (TEs) that are an important component of plant genomes. A large number of LTR-RTs have been annotated in the genomes of the agronomically important oil and vegetable crops of the genus Brassica. Herein, full-length LTR-RTs in the genomes of Brassica and other closely related species were systematically analyzed. The full-length LTR-RT content varied greatly (from 0.43% to 23.4%) between different species, with Gypsy-like LTR-RTs constituting a primary group across these genomes. More importantly, many annotated LTR-RTs (from 10.03% to 33.25% of all detected LTR-RTs) were found to be enriched in localized hotspot regions. Furthermore, all of the analyzed species showed evidence of having experienced at least one round of a LTR-RT burst, with Raphanus sativus experiencing three or more. Moreover, these relatively ancient LTR-RT amplifications exhibited a clear expansion at specific time points. To gain a further understanding of this timing, Brassica rapa, B. oleracea, and R. sativus were examined for the presence of syntenic regions, but none were present. These findings indicate that these LTR-RT burst events were not inherited from a common ancestor, but instead were species-specific bursts that occurred after the divergence of Brassica species. This study further exemplifies the complexities of TE amplifications during the evolution of plant genomes and suggests that these LTR-RT bursts play an important role in genome expansion and divergence in Brassica species.

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Hotspots of Independent and Multiple Rounds of LTR-retrotransposon Bursts in Brassica Species

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