Improved Brassica oleracea JZS assembly reveals significant changing of LTR-RT dynamics in different morphotypes
- PDF / 2,552,242 Bytes
- 13 Pages / 595.276 x 790.866 pts Page_size
- 49 Downloads / 173 Views
ORIGINAL ARTICLE
Improved Brassica oleracea JZS assembly reveals significant changing of LTR‑RT dynamics in different morphotypes Xu Cai1 · Jian Wu1 · Jianli Liang1 · Runmao Lin1 · Kang Zhang1 · Feng Cheng1 · Xiaowu Wang1 Received: 15 March 2020 / Accepted: 3 August 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract 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 ~ 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, the athila, tat, and Del families 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.
Introduction Brassica oleracea is one of the most economically important Brassica species cultivated worldwide, mainly as a vegetable crop that includes cabbage, broccoli, and cauliflower subspecies/morphotypes (Kopsell and Kopsell 2006; Liu et al. 2014). B. oleracea also provided the ancestor genome of Brassica napus and Brassica carinata, both of which are cultivated as important oil crops. A high-quality genome assembly has been pursued for the improvement of the genetics and breeding in these crops. The whole-genome sequences of JZS (B. oleracea sp. capitata, heading type) and TO1000 (B. oleracea ssp. Alboglabrata, kale-like type), Communicated by Isobel A. P. Parkin. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00122-020-03664-3) contains supplementary material, which is available to authorized users. * Xiaowu Wang [email protected] 1
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Haidian District, No.12. Zhongguancun South St, Beijing 100081, China
which were assembled using the next-generation sequencing data, were released in 2014 (Liu et al. 2014; Parkin et al. 2014). While NGS technology provided high-accuracy and high-throughput reads to assemble the genome at relatively low
Data Loading...
