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A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour

Author

Listed:
  • Liyi Zhang

    (Chinese Academy of Agricultural Science)

  • Jiang Hu

    (Nextomics Biosciences Institute)

  • Xiaolei Han

    (Chinese Academy of Agricultural Science)

  • Jingjing Li

    (Nextomics Biosciences Institute)

  • Yuan Gao

    (Chinese Academy of Agricultural Science)

  • Christopher M. Richards

    (USDA-ARS National Center for Genetic Resources Preservation)

  • Caixia Zhang

    (Chinese Academy of Agricultural Science)

  • Yi Tian

    (Chinese Academy of Agricultural Science)

  • Guiming Liu

    (Beijing Academy of Agriculture and Forestry Sciences)

  • Hera Gul

    (Chinese Academy of Agricultural Science)

  • Dajiang Wang

    (Chinese Academy of Agricultural Science)

  • Yu Tian

    (Nextomics Biosciences Institute)

  • Chuanxin Yang

    (Nextomics Biosciences Institute)

  • Minghui Meng

    (Nextomics Biosciences Institute)

  • Gaopeng Yuan

    (Chinese Academy of Agricultural Science)

  • Guodong Kang

    (Chinese Academy of Agricultural Science)

  • Yonglong Wu

    (Chinese Academy of Agricultural Science)

  • Kun Wang

    (Chinese Academy of Agricultural Science)

  • Hengtao Zhang

    (Chinese Academy of Agricultural Science)

  • Depeng Wang

    (Nextomics Biosciences Institute)

  • Peihua Cong

    (Chinese Academy of Agricultural Science)

Abstract

A complete and accurate genome sequence provides a fundamental tool for functional genomics and DNA-informed breeding. Here, we assemble a high-quality genome (contig N50 of 6.99 Mb) of the apple anther-derived homozygous line HFTH1, including 22 telomere sequences, using a combination of PacBio single-molecule real-time (SMRT) sequencing, chromosome conformation capture (Hi-C) sequencing, and optical mapping. In comparison to the Golden Delicious reference genome, we identify 18,047 deletions, 12,101 insertions and 14 large inversions. We reveal that these extensive genomic variations are largely attributable to activity of transposable elements. Interestingly, we find that a long terminal repeat (LTR) retrotransposon insertion upstream of MdMYB1, a core transcriptional activator of anthocyanin biosynthesis, is associated with red-skinned phenotype. This finding provides insights into the molecular mechanisms underlying red fruit coloration, and highlights the utility of this high-quality genome assembly in deciphering agriculturally important trait in apple.

Suggested Citation

  • Liyi Zhang & Jiang Hu & Xiaolei Han & Jingjing Li & Yuan Gao & Christopher M. Richards & Caixia Zhang & Yi Tian & Guiming Liu & Hera Gul & Dajiang Wang & Yu Tian & Chuanxin Yang & Minghui Meng & Gaope, 2019. "A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-09518-x
    DOI: 10.1038/s41467-019-09518-x
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    Cited by:

    1. Ting Wang & Shiyao Duan & Chen Xu & Yi Wang & Xinzhong Zhang & Xuefeng Xu & Liyang Chen & Zhenhai Han & Ting Wu, 2023. "Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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