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A chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution

Author

Listed:
  • Yixue Bao

    (Guangxi University)

  • Qing Zhang

    (Guangxi University
    Chinese Academy of Agricultural Sciences)

  • Jiangfeng Huang

    (Guangxi University)

  • Shengcheng Zhang

    (Chinese Academy of Agricultural Sciences)

  • Wei Yao

    (Guangxi University)

  • Zehuai Yu

    (Guangxi University)

  • Zuhu Deng

    (Guangxi University)

  • Jiaxin Yu

    (Chinese Academy of Agricultural Sciences)

  • Weilong Kong

    (Chinese Academy of Agricultural Sciences)

  • Xikai Yu

    (Guangxi University)

  • Shan Lu

    (Guangxi University)

  • Yibin Wang

    (Chinese Academy of Agricultural Sciences)

  • Ru Li

    (Guangxi University)

  • Yuhan Song

    (Chinese Academy of Agricultural Sciences)

  • Chengwu Zou

    (Guangxi University)

  • Yuzhi Xu

    (Guangxi University)

  • Zongling Liu

    (Guangxi University)

  • Fan Yu

    (Guangxi University)

  • Jiaming Song

    (Guangxi University)

  • Youzong Huang

    (Guangxi University)

  • Jisen Zhang

    (Guangxi University)

  • Haifeng Wang

    (Guangxi University)

  • Baoshan Chen

    (Guangxi University)

  • Xingtan Zhang

    (Chinese Academy of Agricultural Sciences)

  • Muqing Zhang

    (Guangxi University)

Abstract

Sugarcane is a vital crop with significant economic and industrial value. However, the cultivated sugarcane’s ultra-complex genome still needs to be resolved due to its high ploidy and extensive recombination between the two subgenomes. Here, we generate a chromosomal-scale, haplotype-resolved genome assembly for a hybrid sugarcane cultivar ZZ1. This assembly contains 10.4 Gb genomic sequences and 68,509 annotated genes with defined alleles in two sub-genomes distributed in 99 original and 15 recombined chromosomes. RNA-seq data analysis shows that sugar accumulation-associated gene families have been primarily expanded from the ZZSO subgenome. However, genes responding to pokkah boeng disease susceptibility have been derived dominantly from the ZZSS subgenome. The region harboring the possible smut resistance genes has expanded significantly. Among them, the expansion of WAK and FLS2 families is proposed to have occurred during the breeding of ZZ1. Our findings provide insights into the complex genome of hybrid sugarcane cultivars and pave the way for future genomics and molecular breeding studies in sugarcane.

Suggested Citation

  • Yixue Bao & Qing Zhang & Jiangfeng Huang & Shengcheng Zhang & Wei Yao & Zehuai Yu & Zuhu Deng & Jiaxin Yu & Weilong Kong & Xikai Yu & Shan Lu & Yibin Wang & Ru Li & Yuhan Song & Chengwu Zou & Yuzhi Xu, 2024. "A chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-47390-6
    DOI: 10.1038/s41467-024-47390-6
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    References listed on IDEAS

    as
    1. Yinping Jiao & Paul Peluso & Jinghua Shi & Tiffany Liang & Michelle C. Stitzer & Bo Wang & Michael S. Campbell & Joshua C. Stein & Xuehong Wei & Chen-Shan Chin & Katherine Guill & Michael Regulski & S, 2017. "Improved maize reference genome with single-molecule technologies," Nature, Nature, vol. 546(7659), pages 524-527, June.
    2. Olivier Garsmeur & Gaetan Droc & Rudie Antonise & Jane Grimwood & Bernard Potier & Karen Aitken & Jerry Jenkins & Guillaume Martin & Carine Charron & Catherine Hervouet & Laurent Costet & Nabila Yahia, 2018. "A mosaic monoploid reference sequence for the highly complex genome of sugarcane," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    Full references (including those not matched with items on IDEAS)

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