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Reply to: ‘Organization of the genome sequence of the polyploid crop species Brassica juncea’

Nature Genetics volume 50, pages 1497–1498 (2018)Cite this article

Subjects

Yang et al. reply — He and Bancroft have commented on shortcomings in the organization of the draft genome sequence of Brassica juncea, assembled using a hybrid strategy, and the characteristics of this genome evolution under crop selection1. B. juncea is a recent allopolyploid species that resulted from hybridization between Brassica rapa (A genome) and Brassica nigra (B genome) followed by chromosome doubling and evolution into vegetable and oilseed types for agricultural usage.

We are aware of scaffold chimerism in this genome after checking the genome-ordered graphical genotypes (GOGG). For better understanding of this allopolyploid genome, we have improved and updated a new version of the genome sequence of B. juncea, although the updated genome assembly does not impact the conclusions of homoeolog transcriptional behavior influencing selection in this allopolyploid B. juncea.

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Fig. 1: Genome sequence organization of B. juncea with assessment using genome-ordered graphical genotypes and chromosomes A01 and J01 as examples.

Data availability

The genome assembly has now been improved as V1.5, and the updated genome assembly is available to be downloaded from the website (http://brassicadb.org/brad/datasets/pub/Genomes/Brassica_juncea/V1.5/).

References

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Acknowledgements

We thank S.A. Mackenzie for her opinions and discussions on this reply.

Author information

Authors and Affiliations

  1. Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China

    Jinghua Yang & Mingfang Zhang

  2. Biomarker Technologies Corporation, Beijing, China

    Changmian Ji & Dongyuan Liu

  3. Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China

    Xiaowu Wang

Authors
  1. Jinghua Yang
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  2. Changmian Ji
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  3. Dongyuan Liu
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  4. Xiaowu Wang
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  5. Mingfang Zhang
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Contributions

J.Y., C.J., X.W. and M.Z. designed the project. C.J. and D.L. performed genome assembly and bioinformatics analyses. J.Y. wrote the manuscript.

Corresponding authors

Correspondence to Jinghua Yang, Changmian Ji or Mingfang Zhang.

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The authors declare no competing interests.

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Supplementary Tables 6, 8a, 9, 14a,b, 16a,b, 17, 22, 23 and 27b

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Yang, J., Ji, C., Liu, D. et al. Reply to: ‘Organization of the genome sequence of the polyploid crop species Brassica juncea’. Nat Genet 50, 1497–1498 (2018). https://doi.org/10.1038/s41588-018-0240-7

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