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; Zhong Jian Liu; Baoshan Chen; Muqing Zhang; Ray Ming; Jisen Zhang

doi:10.1038/s41588-022-01084-1

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 ZhangWei Yao, Yuntong Wang, Xinlong Liu, Maojun Wang, Jianping Wang, Zuhu Deng, Jingsheng Xu, Qinghui Yang, Zhong Jian Liu, Baoshan Chen, Muqing Zhang, Ray Ming, Jisen Zhang

Plant Biology

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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.

Original language	English (US)
Pages (from-to)	885-896
Number of pages	12
Journal	Nature Genetics
Volume	54
Issue number	6
DOIs	https://doi.org/10.1038/s41588-022-01084-1
State	Published - Jun 2022

ASJC Scopus subject areas

Genetics

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Zhang, Q., Qi, Y., Pan, H., Tang, H., Wang, G., Hua, X., Wang, Y., Lin, L., Li, Z., Li, Y., Yu, F., Yu, Z., Huang, Y., Wang, T., Ma, P., Dou, M., Sun, Z., Wang, Y., Wang, H., ... Zhang, J. (2022). Genomic insights into the recent chromosome reduction of autopolyploid sugarcane Saccharum spontaneum. Nature Genetics, 54(6), 885-896. https://doi.org/10.1038/s41588-022-01084-1

Zhang, Q, Qi, Y, Pan, H, Tang, H, Wang, G, Hua, X, Wang, Y, Lin, L, Li, Z, Li, Y, Yu, F, Yu, Z, Huang, Y, Wang, T, Ma, P, Dou, M, Sun, Z, Wang, Y, Wang, H, Zhang, X, Yao, W, Wang, Y, Liu, X, Wang, M, Wang, J, Deng, Z, Xu, J, Yang, Q, Liu, ZJ, Chen, B, Zhang, M, Ming, R & Zhang, J 2022, 'Genomic insights into the recent chromosome reduction of autopolyploid sugarcane Saccharum spontaneum', Nature Genetics, vol. 54, no. 6, pp. 885-896. https://doi.org/10.1038/s41588-022-01084-1

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title = "Genomic insights into the recent chromosome reduction of autopolyploid sugarcane Saccharum spontaneum",

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.",

author = "Qing Zhang and Yiying Qi and Haoran Pan and Haibao Tang and Gang Wang and Xiuting Hua and Yongjun Wang and Lianyu Lin and Zhen Li and Yihan Li and Fan Yu and Zehuai Yu and Yongji Huang and Tianyou Wang and Panpan Ma and Meijie Dou and Zongyi Sun and Yibin Wang and Hengbo Wang and Xingtan Zhang and Wei Yao and Yuntong Wang and Xinlong Liu and Maojun Wang and Jianping Wang and Zuhu Deng and Jingsheng Xu and Qinghui Yang and Liu, {Zhong Jian} and Baoshan Chen and Muqing Zhang and Ray Ming and Jisen Zhang",

note = "This work was supported by funding from the National Key Research and Development Program (2021YFF1000100), the Science and Technology Planting Project of Guangdong Province (2019B020238001), the National High-tech R&D Program (2013AA100604) and the Fujian Provincial Department of Education (JA12082) to J.Z.; the National Key Research and Development Program (2021YFF1000104) to H.T.; the Science and Technology Major Project of Guangxi (AA17202025) to M.Z.; and the China Scholarship Council (201707877011), the Scientific Research Foundation of the Graduate School of Fujian Agriculture and Forestry University Grant (324-1122yb050) and the fellowship of China Postdoctoral Science Foundation (2021M703555) to Q.Z.",

year = "2022",

month = jun,

doi = "10.1038/s41588-022-01084-1",

language = "English (US)",

volume = "54",

pages = "885--896",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Research",

number = "6",

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T1 - Genomic insights into the recent chromosome reduction of autopolyploid sugarcane Saccharum spontaneum

AU - Zhang, Qing

AU - Qi, Yiying

AU - Pan, Haoran

AU - Tang, Haibao

AU - Wang, Gang

AU - Hua, Xiuting

AU - Wang, Yongjun

AU - Lin, Lianyu

AU - Li, Zhen

AU - Li, Yihan

AU - Yu, Fan

AU - Yu, Zehuai

AU - Huang, Yongji

AU - Wang, Tianyou

AU - Ma, Panpan

AU - Dou, Meijie

AU - Sun, Zongyi

AU - Wang, Yibin

AU - Wang, Hengbo

AU - Zhang, Xingtan

AU - Yao, Wei

AU - Wang, Yuntong

AU - Liu, Xinlong

AU - Wang, Maojun

AU - Wang, Jianping

AU - Deng, Zuhu

AU - Xu, Jingsheng

AU - Yang, Qinghui

AU - Liu, Zhong Jian

AU - Chen, Baoshan

AU - Zhang, Muqing

AU - Ming, Ray

AU - Zhang, Jisen

N1 - This work was supported by funding from the National Key Research and Development Program (2021YFF1000100), the Science and Technology Planting Project of Guangdong Province (2019B020238001), the National High-tech R&D Program (2013AA100604) and the Fujian Provincial Department of Education (JA12082) to J.Z.; the National Key Research and Development Program (2021YFF1000104) to H.T.; the Science and Technology Major Project of Guangxi (AA17202025) to M.Z.; and the China Scholarship Council (201707877011), the Scientific Research Foundation of the Graduate School of Fujian Agriculture and Forestry University Grant (324-1122yb050) and the fellowship of China Postdoctoral Science Foundation (2021M703555) to Q.Z.

PY - 2022/6

Y1 - 2022/6

N2 - 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.

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

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