The bracteatus pineapple genome and domestication of clonally propagated crops

Li Yu Chen, Robert VanBuren, Margot Paris, Hongye Zhou, Xingtan Zhang, Ching Man Wai, Hansong Yan, Shuai Chen, Michael Alonge, Srividya Ramakrishnan, Zhenyang Liao, Juan Liu, Jishan Lin, Jingjing Yue, Mahpara Fatima, Zhicong Lin, Jisen Zhang, Lixian Huang, Hao Wang, Teh Yang HwaShu Min Kao, Jae Young Choi, Anupma Sharma, Jian Song, Lulu Wang, Won C. Yim, John C. Cushman, Robert E. Paull, Tracie Matsumoto, Yuan Qin, Qingsong Wu, Jianping Wang, Qingyi Yu, Jun Wu, Shaoling Zhang, Peter Boches, Chih Wei Tung, Ming Li Wang, Geo Coppens d’Eeckenbrugge, Garth M. Sanewski, Michael D. Purugganan, Michael C. Schatz, Jeffrey L. Bennetzen, Christian Lexer, Ray Ming

Research output: Contribution to journalArticle

Abstract

Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a ‘one-step operation’. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars ‘Smooth Cayenne’ and ‘Queen’ exhibited ancient and recent admixture, while ‘Singapore Spanish’ supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops.

Original languageEnglish (US)
Pages (from-to)1549-1558
Number of pages10
JournalNature Genetics
Volume51
Issue number10
DOIs
StatePublished - Oct 1 2019

Fingerprint

Ananas
Genome
Bromelains
Capsicum
South America
Singapore
Genetic Recombination
Genes
Fruit
Color
Chromosomes
Domestication

ASJC Scopus subject areas

  • Genetics

Cite this

Chen, L. Y., VanBuren, R., Paris, M., Zhou, H., Zhang, X., Wai, C. M., ... Ming, R. (2019). The bracteatus pineapple genome and domestication of clonally propagated crops. Nature Genetics, 51(10), 1549-1558. https://doi.org/10.1038/s41588-019-0506-8

The bracteatus pineapple genome and domestication of clonally propagated crops. / Chen, Li Yu; VanBuren, Robert; Paris, Margot; Zhou, Hongye; Zhang, Xingtan; Wai, Ching Man; Yan, Hansong; Chen, Shuai; Alonge, Michael; Ramakrishnan, Srividya; Liao, Zhenyang; Liu, Juan; Lin, Jishan; Yue, Jingjing; Fatima, Mahpara; Lin, Zhicong; Zhang, Jisen; Huang, Lixian; Wang, Hao; Hwa, Teh Yang; Kao, Shu Min; Choi, Jae Young; Sharma, Anupma; Song, Jian; Wang, Lulu; Yim, Won C.; Cushman, John C.; Paull, Robert E.; Matsumoto, Tracie; Qin, Yuan; Wu, Qingsong; Wang, Jianping; Yu, Qingyi; Wu, Jun; Zhang, Shaoling; Boches, Peter; Tung, Chih Wei; Wang, Ming Li; Coppens d’Eeckenbrugge, Geo; Sanewski, Garth M.; Purugganan, Michael D.; Schatz, Michael C.; Bennetzen, Jeffrey L.; Lexer, Christian; Ming, Ray.

In: Nature Genetics, Vol. 51, No. 10, 01.10.2019, p. 1549-1558.

Research output: Contribution to journalArticle

Chen, LY, VanBuren, R, Paris, M, Zhou, H, Zhang, X, Wai, CM, Yan, H, Chen, S, Alonge, M, Ramakrishnan, S, Liao, Z, Liu, J, Lin, J, Yue, J, Fatima, M, Lin, Z, Zhang, J, Huang, L, Wang, H, Hwa, TY, Kao, SM, Choi, JY, Sharma, A, Song, J, Wang, L, Yim, WC, Cushman, JC, Paull, RE, Matsumoto, T, Qin, Y, Wu, Q, Wang, J, Yu, Q, Wu, J, Zhang, S, Boches, P, Tung, CW, Wang, ML, Coppens d’Eeckenbrugge, G, Sanewski, GM, Purugganan, MD, Schatz, MC, Bennetzen, JL, Lexer, C & Ming, R 2019, 'The bracteatus pineapple genome and domestication of clonally propagated crops', Nature Genetics, vol. 51, no. 10, pp. 1549-1558. https://doi.org/10.1038/s41588-019-0506-8
Chen LY, VanBuren R, Paris M, Zhou H, Zhang X, Wai CM et al. The bracteatus pineapple genome and domestication of clonally propagated crops. Nature Genetics. 2019 Oct 1;51(10):1549-1558. https://doi.org/10.1038/s41588-019-0506-8
Chen, Li Yu ; VanBuren, Robert ; Paris, Margot ; Zhou, Hongye ; Zhang, Xingtan ; Wai, Ching Man ; Yan, Hansong ; Chen, Shuai ; Alonge, Michael ; Ramakrishnan, Srividya ; Liao, Zhenyang ; Liu, Juan ; Lin, Jishan ; Yue, Jingjing ; Fatima, Mahpara ; Lin, Zhicong ; Zhang, Jisen ; Huang, Lixian ; Wang, Hao ; Hwa, Teh Yang ; Kao, Shu Min ; Choi, Jae Young ; Sharma, Anupma ; Song, Jian ; Wang, Lulu ; Yim, Won C. ; Cushman, John C. ; Paull, Robert E. ; Matsumoto, Tracie ; Qin, Yuan ; Wu, Qingsong ; Wang, Jianping ; Yu, Qingyi ; Wu, Jun ; Zhang, Shaoling ; Boches, Peter ; Tung, Chih Wei ; Wang, Ming Li ; Coppens d’Eeckenbrugge, Geo ; Sanewski, Garth M. ; Purugganan, Michael D. ; Schatz, Michael C. ; Bennetzen, Jeffrey L. ; Lexer, Christian ; Ming, Ray. / The bracteatus pineapple genome and domestication of clonally propagated crops. In: Nature Genetics. 2019 ; Vol. 51, No. 10. pp. 1549-1558.
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abstract = "Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a ‘one-step operation’. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars ‘Smooth Cayenne’ and ‘Queen’ exhibited ancient and recent admixture, while ‘Singapore Spanish’ supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops.",
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AU - Matsumoto, Tracie

AU - Qin, Yuan

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AU - Wang, Jianping

AU - Yu, Qingyi

AU - Wu, Jun

AU - Zhang, Shaoling

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AU - Tung, Chih Wei

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AU - Purugganan, Michael D.

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AU - Lexer, Christian

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