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Nature genetics
06, 2022;54 (6): 885-896.

Genomic insights into the recent chromosome reduction of autopolyploid sugarcane Saccharum spontaneum.

Qing Zhang, Yiying Qi, Haoran Pan, Haibao Tang, Gang Wang, Xiuting Hua, Yongjun Wang, Lianyu Lin, Zhen Li, Yihan Li, Fan Yu, Zehuai Yu, Yongji Huang, Tianyou Wang, Panpan Ma, Meijie Dou, Zongyi Sun, Yibin Wang, Hengbo Wang, Xingtan Zhang, Wei Yao, Yuntong Wang, Xinlong Liu, Maojun Wang, Jianping Wang, Zuhu Deng, Jingsheng Xu, Qinghui Yang, ZhongJian Liu, Baoshan Chen, Muqing Zhang, Ray Ming, Jisen Zhang
Author Information
  1. Qing Zhang: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
  2. Yiying Qi: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
  3. Haoran Pan: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
  4. Haibao Tang: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China. ORCID
  5. Gang Wang: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
  6. Xiuting Hua: Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China.
  7. Yongjun Wang: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
  8. Lianyu Lin: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
  9. Zhen Li: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
  10. Yihan Li: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
  11. Fan Yu: Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China.
  12. Zehuai Yu: Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China.
  13. Yongji Huang: Institute of Oceanography, Marine Biotechnology Center, Minjiang University, Fuzhou, China.
  14. Tianyou Wang: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
  15. Panpan Ma: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
  16. Meijie Dou: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
  17. Zongyi Sun: GrandOmics Biosciences, Beijing, China.
  18. Yibin Wang: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
  19. Hengbo Wang: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
  20. Xingtan Zhang: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
  21. Wei Yao: Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China.
  22. Yuntong Wang: Biomarker Technologies Corporation, Beijing, China.
  23. Xinlong Liu: Yunnan Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China.
  24. Maojun Wang: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. ORCID
  25. Jianping Wang: Department of Agronomy, University of Florida, Gainesville, FL, USA. ORCID
  26. Zuhu Deng: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
  27. Jingsheng Xu: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
  28. Qinghui Yang: Sugarcane Research Institute, Yunnan Agricultural University, Kunming, China.
  29. ZhongJian Liu: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China. ORCID
  30. Baoshan Chen: Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China.
  31. Muqing Zhang: Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China.
  32. Ray Ming: Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA. ORCID
  33. Jisen Zhang: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China. zjisen@fafu.edu.cn. ORCID
PMID: 35654976 DOI: 10.1038/s41588-022-01084-1

Abstract

Saccharum spontaneum is a founding Saccharum species and exhibits wide variation in ploidy levels. We have assembled a high-quality autopolyploid genome of S. spontaneum Np-X (2n = 4x = 40) into 40 pseudochromosomes across 10 homologous groups, that better elucidates recent chromosome reduction and polyploidization that occurred circa 1.5 million years ago (Mya). One paleo-duplicated chromosomal pair in Saccharum, NpChr5 and NpChr8, underwent fission followed by fusion accompanied by centromeric split around 0.80 Mya. We inferred that Np-X, with x = 10, most likely represents the ancestral karyotype, from which x = 9 and x = 8 evolved. Resequencing of 102 S. spontaneum accessions revealed that S. spontaneum originated in northern India from an x = 10 ancestor, which then radiated into four major groups across the Indian subcontinent, China, and Southeast Asia. Our study suggests new directions for accelerating sugarcane improvement and expands our knowledge of the evolution of autopolyploids.

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MeSH Term

Chromosomes
Genome, Plant
Genomics
Ploidies
Saccharum
Journal Article Research Support, Non-U.S. Gov't
Article has an altmetric score of 14

Word Cloud

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