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.
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Code availability
The misjoins correction pipeline can be downloaded from https://github.com/caixu0518/MisjoinDetect.
Data availability
The genome assembly and gene annotations are freely available through BRAD website (https://brassicadb.org/brad/datasets/pub/Genomes/Brassica_oleracea/V2.0/) or in the Genome Warehouse database (Members 2019) under bioproject number (PRJCA001832) and accession number GWHAASO00000000 (https://bigd.big.ac.cn/gwh).
Change history
27 November 2023
A Correction to this paper has been published: https://doi.org/10.1007/s00122-023-04498-5
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Acknowledgments
We would like to thank Ian Bancroft and Zhesi He for the help of the evaluation of JZS v2 assembly.
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This work is supported by the National Program on Key Research Project (2016YFD0100307), the National Natural Science Foundation of China (NSFC grants 31630068), Central Public-interest Scientific Institution Basal Research Fund (No.Y2017PT52), China Agriculture Research System, the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences, the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, P.R. China.
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XC wrote the manuscript. XW, JW and FC designed the experiments. XC performed the experiments. XW, JW, FC, JL, RL and KZ helped to improve the manuscript. All authors agree with the current statement.
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Cai, X., Wu, J., Liang, J. et al. Improved Brassica oleracea JZS assembly reveals significant changing of LTR-RT dynamics in different morphotypes. Theor Appl Genet 133, 3187–3199 (2020). https://doi.org/10.1007/s00122-020-03664-3
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DOI: https://doi.org/10.1007/s00122-020-03664-3