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

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, Zongling Liu, Fan Yu, Jiaming Song, Youzong Huang, Jisen Zhang, Haifeng Wang, Baoshan Chen (), Xingtan Zhang () and Muqing Zhang ()
Additional contact information
Yixue Bao: Guangxi University
Qing Zhang: Guangxi University
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

Nature Communications, 2024, vol. 15, issue 1, 1-14

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-47390-6

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