Improved Brassica oleracea JZS assembly reveals significant changing of LTR-RT dynamics in different morphotypes

文献类型： 外文期刊

第一作者： Cai, Xu

作者： Cai, Xu;Wu, Jian;Liang, Jianli;Lin, Runmao;Zhang, Kang;Cheng, Feng;Wang, Xiaowu

作者机构：

期刊名称：THEORETICAL AND APPLIED GENETICS （ 影响因子：5.699； 五年影响因子：5.565 ）

ISSN： 0040-5752

年卷期： 2020 年 133 卷 11 期

页码：

收录情况： SCI

摘要： Brassica oleracea is an important vegetable crop that has provided ancestor genomes of the two most important Brassica oil crops,Brassica napus and Brassica carinata. The current B. oleracea reference genome (JZS, also named 02-12) displays problems of large mis-assemblies, low sequence continuity, and low assembly integrity, thus limiting genomic analysis. We reported an updated assembly of the B. oleracea reference genome (JZS v2) obtained through single-molecule sequencing and chromosome conformation capture technologies. We assembled an additional 83.16 Mb of genomic sequences, and the updated genome features a contig N50 size of 2.37 Mb, representing an similar to 88-fold improvement. We detected a new round of long terminal repeat retrotransposon (LTR-RT) burst in the new assembly. Comparative analysis with the reported genome sequences of two other genomes of B. oleracea (TO1000 and HDEM) identified extensive gene order and gene structural variation. In addition, we found that the genome-specific amplification of Gypsy-like LTR-RTs occurred around 0-1 million years ago (MYA). In particular, theathila,tat,andDelfamilies were extensively amplified in JZS around 0-1 MYA. Moreover, we identified that the syntenic genes were modified due to the insertion of genome-specific LTR-RTs. These results indicated that the genome-specific LTR-RT dynamics were associated with genome diversification in B. oleracea.

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