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Chromosome level comparative analysis of Brassica genomes

  • Wenliang Wang
  • Rui Guan
  • Xing Liu
  • Haorui Zhang
  • Bo Song
  • Qiwu Xu
  • Guangyi Fan
  • Wenbin Chen
  • Xiaoming Wu
  • Xin Liu
  • Jianbo Wang
Article
  • 162 Downloads

Abstract

Key message

We provided a chromosome-length assembly of B. nigra and show the comprehensive chromosome-scale variations among Brassica genomes.

Abstract

Chromosome-level assembly of the Brassica species, which include many important crops, is essential for the agricultural and evolutionary studies. While the present B. nigra chromosomes was connected with genetic map of B. juncea, hindering the comparative analysis of the B chromosomes. Here we present a chromosome-length B. nigra assembly constructed with Hi-C connections and its variations on chromosome level compared with other Brassica species. We produced an assembly of 484 Mb annotated with 51,829 genes, of which 393 Mb were anchored onto 8 chromosomes, taking 81.26% of the assembly. Comparison of the B chromosomes shows high concordance of the two B. nigra assemblies and reveals comprehensive variations of the B chromosomes after polyploidization and gene loss in syntenic regions. Chromosome blocks with variations have lower gene density and higher TE content. Furthermore, we compared the chromosomes of the three major Brassica diploids, which showed that most of the variations between B and A/C had completed before A/C divergence and there are more variations on C chromosomes after their divergence. In summary, our work presents a chromosome-length assembly of B. nigra and comprehensive comparative analysis of the Brassica chromosomes, which provides a useful reference for other studies and comprehensive information of Brassica chromosome evolution.

Keywords

Brassica nigra Hi-C Chromosome variation 

Notes

Acknowledgements

This work was supported by the National Natural Science Foundation of China (31570539, 31370258, 31601042) and Basic Research Program Support by Shenzhen Municipal Government (JCYJ20151015162041454 to W. C. and JCYJ20150529150505656 to X. Liu).

Author contributions

Jianbo Wang and Xin Liu are the principle investigators and designed the project. Xiaoming Wu provided the samples sequenced in this research. Wenbin Chen, Qiwu Xu, Guangyi Fan extracted the DNA and RNA. Qiwu Xu and Guangyi Fan did the Hi-C experiment. Wenliang Wang did the genomic assembly, Hi-C data analysis, genome annotation and chromosome comparative analysis. Xing Liu and Haorui Zhang performed quality control analysis of the assembly. Rui Guan performed transcriptome analysis. Wenliang Wang wrote this manuscript. Bo Song, Jianbo Wang and Wenbin Chen edited the manuscript. All authors read and commented on the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Research involving human participants and/or animals

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

11103_2018_814_MOESM1_ESM.docx (36 kb)
Supplementary material 1 (DOCX 35 KB)
11103_2018_814_MOESM2_ESM.docx (1.4 mb)
Supplementary material 2 (DOCX 1448 KB)

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
  2. 2.BGI-ShenzhenShenzhenChina
  3. 3.China National GeneBank-Shenzhen, BGI-ShenzhenShenzhenChina
  4. 4.Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
  5. 5.State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical EngineeringSoutheast UniversityNanjingChina
  6. 6.Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina

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