The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

J. Yang; D. Liu; X. Wang; C. Ji; F. Cheng; B. Liu; Z. Hu; Sheng Chen; D. Pental; Y. Ju; P. Yao; X. Li; K. Xie; J. Zhang; J. Wang; W. Ma; J. Shopan; H. Zheng; S.A. Mackenzie; M. Zhang

doi:10.1038/ng.3657

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

J. Yang, D. Liu, X. Wang, C. Ji, F. Cheng, B. Liu, Z. Hu, Sheng Chen, D. Pental, Y. Ju, P. Yao, X. Li, K. Xie, J. Zhang, J. Wang, W. Ma, J. Shopan, H. Zheng, S.A. Mackenzie, M. Zhang

UWA School of Agriculture and Environment

Research output: Contribution to journal › Article › peer-review

342 Citations (Scopus)

Abstract

© 2016 Nature America, Inc. All rights reserved.The Brassica genus encompasses three diploid and three allopolyploid genomes, but a clear understanding of the evolution of agriculturally important traits via polyploidy is lacking. We assembled an allopolyploid Brassica juncea genome by shotgun and single-molecule reads integrated to genomic and genetic maps. We discovered that the A subgenomes of B. juncea and Brassica napus each had independent origins. Results suggested that A subgenomes of B. juncea were of monophyletic origin and evolved into vegetable-use and oil-use subvarieties. Homoeolog expression dominance occurs between subgenomes of allopolyploid B. juncea, in which differentially expressed genes display more selection potential than neutral genes. Homoeolog expression dominance in B. juncea has facilitated selection of glucosinolate and lipid metabolism genes in subvarieties used as vegetables and for oil production. These homoeolog expression dominance relationships among Brassicaceae genomes have contributed to selection response, predicting the directional effects of selection in a polyploid crop genome.

Original language	English
Pages (from-to)	1225-1232
Number of pages	8
Journal	Nature Genetics
Volume	48
Issue number	10
DOIs	https://doi.org/10.1038/ng.3657
Publication status	Published - 1 Oct 2016

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Yang, J., Liu, D., Wang, X., Ji, C., Cheng, F., Liu, B., Hu, Z., Chen, S., Pental, D., Ju, Y., Yao, P., Li, X., Xie, K., Zhang, J., Wang, J., Ma, W., Shopan, J., Zheng, H., Mackenzie, S. A., & Zhang, M. (2016). The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection. Nature Genetics, 48(10), 1225-1232. https://doi.org/10.1038/ng.3657

@article{6835f4b0e10e44d29ded63f1f16cf845,

title = "The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection",

abstract = "{\textcopyright} 2016 Nature America, Inc. All rights reserved.The Brassica genus encompasses three diploid and three allopolyploid genomes, but a clear understanding of the evolution of agriculturally important traits via polyploidy is lacking. We assembled an allopolyploid Brassica juncea genome by shotgun and single-molecule reads integrated to genomic and genetic maps. We discovered that the A subgenomes of B. juncea and Brassica napus each had independent origins. Results suggested that A subgenomes of B. juncea were of monophyletic origin and evolved into vegetable-use and oil-use subvarieties. Homoeolog expression dominance occurs between subgenomes of allopolyploid B. juncea, in which differentially expressed genes display more selection potential than neutral genes. Homoeolog expression dominance in B. juncea has facilitated selection of glucosinolate and lipid metabolism genes in subvarieties used as vegetables and for oil production. These homoeolog expression dominance relationships among Brassicaceae genomes have contributed to selection response, predicting the directional effects of selection in a polyploid crop genome.",

author = "J. Yang and D. Liu and X. Wang and C. Ji and F. Cheng and B. Liu and Z. Hu and Sheng Chen and D. Pental and Y. Ju and P. Yao and X. Li and K. Xie and J. Zhang and J. Wang and W. Ma and J. Shopan and H. Zheng and S.A. Mackenzie and M. Zhang",

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Yang, J, Liu, D, Wang, X, Ji, C, Cheng, F, Liu, B, Hu, Z, Chen, S, Pental, D, Ju, Y, Yao, P, Li, X, Xie, K, Zhang, J, Wang, J, Ma, W, Shopan, J, Zheng, H, Mackenzie, SA & Zhang, M 2016, 'The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection', Nature Genetics, vol. 48, no. 10, pp. 1225-1232. https://doi.org/10.1038/ng.3657

TY - JOUR

T1 - The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

AU - Yang, J.

AU - Liu, D.

AU - Wang, X.

AU - Ji, C.

AU - Cheng, F.

AU - Liu, B.

AU - Hu, Z.

AU - Chen, Sheng

AU - Pental, D.

AU - Ju, Y.

AU - Yao, P.

AU - Li, X.

AU - Xie, K.

AU - Zhang, J.

AU - Wang, J.

AU - Ma, W.

AU - Shopan, J.

AU - Zheng, H.

AU - Mackenzie, S.A.

AU - Zhang, M.

PY - 2016/10/1

Y1 - 2016/10/1

N2 - © 2016 Nature America, Inc. All rights reserved.The Brassica genus encompasses three diploid and three allopolyploid genomes, but a clear understanding of the evolution of agriculturally important traits via polyploidy is lacking. We assembled an allopolyploid Brassica juncea genome by shotgun and single-molecule reads integrated to genomic and genetic maps. We discovered that the A subgenomes of B. juncea and Brassica napus each had independent origins. Results suggested that A subgenomes of B. juncea were of monophyletic origin and evolved into vegetable-use and oil-use subvarieties. Homoeolog expression dominance occurs between subgenomes of allopolyploid B. juncea, in which differentially expressed genes display more selection potential than neutral genes. Homoeolog expression dominance in B. juncea has facilitated selection of glucosinolate and lipid metabolism genes in subvarieties used as vegetables and for oil production. These homoeolog expression dominance relationships among Brassicaceae genomes have contributed to selection response, predicting the directional effects of selection in a polyploid crop genome.

AB - © 2016 Nature America, Inc. All rights reserved.The Brassica genus encompasses three diploid and three allopolyploid genomes, but a clear understanding of the evolution of agriculturally important traits via polyploidy is lacking. We assembled an allopolyploid Brassica juncea genome by shotgun and single-molecule reads integrated to genomic and genetic maps. We discovered that the A subgenomes of B. juncea and Brassica napus each had independent origins. Results suggested that A subgenomes of B. juncea were of monophyletic origin and evolved into vegetable-use and oil-use subvarieties. Homoeolog expression dominance occurs between subgenomes of allopolyploid B. juncea, in which differentially expressed genes display more selection potential than neutral genes. Homoeolog expression dominance in B. juncea has facilitated selection of glucosinolate and lipid metabolism genes in subvarieties used as vegetables and for oil production. These homoeolog expression dominance relationships among Brassicaceae genomes have contributed to selection response, predicting the directional effects of selection in a polyploid crop genome.

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DO - 10.1038/ng.3657

M3 - Article

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VL - 48

SP - 1225

EP - 1232

JO - Nature Genetics

JF - Nature Genetics

SN - 1061-4036

IS - 10

ER -

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

Abstract

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