Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

Silong Sun; Yingsi Zhou; Jian Chen; Junpeng Shi; Haiming Zhao; Hainan Zhao; Weibin Song; Mei Zhang; Yang Cui; Xiaomei Dong; Han Liu; Xuxu Ma; Yinping Jiao; Bo Wang; Xuehong Wei; Joshua C. Stein; Jeff C. Glaubitz; Fei Lu; Guoliang Yu; Chengzhi Liang; Kevin Fengler; Bailin Li; Antoni Rafalski; Patrick S. Schnable; Doreen H. Ware; Edward S. Buckler; Jinsheng Lai

doi:10.1038/s41588-018-0182-0

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

Silong Sun, Yingsi Zhou, Jian Chen, Junpeng Shi, Haiming Zhao, Hainan Zhao, Weibin Song, Mei Zhang, Yang Cui, Xiaomei Dong, Han Liu, Xuxu Ma, Yinping Jiao, Bo Wang, Xuehong Wei, Joshua C. Stein, Jeff C. Glaubitz, Fei Lu, Guoliang Yu, Chengzhi LiangKevin Fengler, Bailin Li, Antoni Rafalski, Patrick S. Schnable, Doreen H. Ware, Edward S. Buckler, Jinsheng Lai

Plant & Soil Science

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

110 Scopus citations

Abstract

Maize is an important crop with a high level of genome diversity and heterosis. The genome sequence of a typical female line, B73, was previously released. Here, we report a de novo genome assembly of a corresponding male representative line, Mo17. More than 96.4% of the 2,183 Mb assembled genome can be accounted for by 362 scaffolds in ten pseudochromosomes with 38,620 annotated protein-coding genes. Comparative analysis revealed large gene-order and gene structural variations: approximately 10% of the annotated genes were mutually nonsyntenic, and more than 20% of the predicted genes had either large-effect mutations or large structural variations, which might cause considerable protein divergence between the two inbred lines. Our study provides a high-quality reference-genome sequence of an important maize germplasm, and the intraspecific gene order and gene structural variations identified should have implications for heterosis and genome evolution.

Original language	English
Pages (from-to)	1289-1295
Number of pages	7
Journal	Nature Genetics
Volume	50
Issue number	9
DOIs	https://doi.org/10.1038/s41588-018-0182-0
State	Published - Sep 1 2018

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Sun, S., Zhou, Y., Chen, J., Shi, J., Zhao, H., Zhao, H., Song, W., Zhang, M., Cui, Y., Dong, X., Liu, H., Ma, X., Jiao, Y., Wang, B., Wei, X., Stein, J. C., Glaubitz, J. C., Lu, F., Yu, G., ... Lai, J. (2018). Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nature Genetics, 50(9), 1289-1295. https://doi.org/10.1038/s41588-018-0182-0

Sun, Silong ; Zhou, Yingsi ; Chen, Jian ; Shi, Junpeng ; Zhao, Haiming ; Zhao, Hainan ; Song, Weibin ; Zhang, Mei ; Cui, Yang ; Dong, Xiaomei ; Liu, Han ; Ma, Xuxu ; Jiao, Yinping ; Wang, Bo ; Wei, Xuehong ; Stein, Joshua C. ; Glaubitz, Jeff C. ; Lu, Fei ; Yu, Guoliang ; Liang, Chengzhi ; Fengler, Kevin ; Li, Bailin ; Rafalski, Antoni ; Schnable, Patrick S. ; Ware, Doreen H. ; Buckler, Edward S. ; Lai, Jinsheng. / Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. In: Nature Genetics. 2018 ; Vol. 50, No. 9. pp. 1289-1295.

@article{2785a7b781ea440984d6350b35b05793,

title = "Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes",

abstract = "Maize is an important crop with a high level of genome diversity and heterosis. The genome sequence of a typical female line, B73, was previously released. Here, we report a de novo genome assembly of a corresponding male representative line, Mo17. More than 96.4% of the 2,183 Mb assembled genome can be accounted for by 362 scaffolds in ten pseudochromosomes with 38,620 annotated protein-coding genes. Comparative analysis revealed large gene-order and gene structural variations: approximately 10% of the annotated genes were mutually nonsyntenic, and more than 20% of the predicted genes had either large-effect mutations or large structural variations, which might cause considerable protein divergence between the two inbred lines. Our study provides a high-quality reference-genome sequence of an important maize germplasm, and the intraspecific gene order and gene structural variations identified should have implications for heterosis and genome evolution.",

author = "Silong Sun and Yingsi Zhou and Jian Chen and Junpeng Shi and Haiming Zhao and Hainan Zhao and Weibin Song and Mei Zhang and Yang Cui and Xiaomei Dong and Han Liu and Xuxu Ma and Yinping Jiao and Bo Wang and Xuehong Wei and Stein, {Joshua C.} and Glaubitz, {Jeff C.} and Fei Lu and Guoliang Yu and Chengzhi Liang and Kevin Fengler and Bailin Li and Antoni Rafalski and Schnable, {Patrick S.} and Ware, {Doreen H.} and Buckler, {Edward S.} and Jinsheng Lai",

year = "2018",

month = sep,

day = "1",

doi = "10.1038/s41588-018-0182-0",

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Sun, S, Zhou, Y, Chen, J, Shi, J, Zhao, H, Zhao, H, Song, W, Zhang, M, Cui, Y, Dong, X, Liu, H, Ma, X, Jiao, Y, Wang, B, Wei, X, Stein, JC, Glaubitz, JC, Lu, F, Yu, G, Liang, C, Fengler, K, Li, B, Rafalski, A, Schnable, PS, Ware, DH, Buckler, ES & Lai, J 2018, 'Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes', Nature Genetics, vol. 50, no. 9, pp. 1289-1295. https://doi.org/10.1038/s41588-018-0182-0

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. / Sun, Silong; Zhou, Yingsi; Chen, Jian; Shi, Junpeng; Zhao, Haiming; Zhao, Hainan; Song, Weibin; Zhang, Mei; Cui, Yang; Dong, Xiaomei; Liu, Han; Ma, Xuxu; Jiao, Yinping; Wang, Bo; Wei, Xuehong; Stein, Joshua C.; Glaubitz, Jeff C.; Lu, Fei; Yu, Guoliang; Liang, Chengzhi; Fengler, Kevin; Li, Bailin; Rafalski, Antoni; Schnable, Patrick S.; Ware, Doreen H.; Buckler, Edward S.; Lai, Jinsheng.

In: Nature Genetics, Vol. 50, No. 9, 01.09.2018, p. 1289-1295.

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

TY - JOUR

T1 - Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

AU - Sun, Silong

AU - Zhou, Yingsi

AU - Chen, Jian

AU - Shi, Junpeng

AU - Zhao, Haiming

AU - Zhao, Hainan

AU - Song, Weibin

AU - Zhang, Mei

AU - Cui, Yang

AU - Dong, Xiaomei

AU - Liu, Han

AU - Ma, Xuxu

AU - Jiao, Yinping

AU - Wang, Bo

AU - Wei, Xuehong

AU - Stein, Joshua C.

AU - Glaubitz, Jeff C.

AU - Lu, Fei

AU - Yu, Guoliang

AU - Liang, Chengzhi

AU - Fengler, Kevin

AU - Li, Bailin

AU - Rafalski, Antoni

AU - Schnable, Patrick S.

AU - Ware, Doreen H.

AU - Buckler, Edward S.

AU - Lai, Jinsheng

PY - 2018/9/1

Y1 - 2018/9/1

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AB - Maize is an important crop with a high level of genome diversity and heterosis. The genome sequence of a typical female line, B73, was previously released. Here, we report a de novo genome assembly of a corresponding male representative line, Mo17. More than 96.4% of the 2,183 Mb assembled genome can be accounted for by 362 scaffolds in ten pseudochromosomes with 38,620 annotated protein-coding genes. Comparative analysis revealed large gene-order and gene structural variations: approximately 10% of the annotated genes were mutually nonsyntenic, and more than 20% of the predicted genes had either large-effect mutations or large structural variations, which might cause considerable protein divergence between the two inbred lines. Our study provides a high-quality reference-genome sequence of an important maize germplasm, and the intraspecific gene order and gene structural variations identified should have implications for heterosis and genome evolution.

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