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

Research output: Contribution to journalArticlepeer-review

189 Scopus citations


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 languageEnglish
Pages (from-to)1289-1295
Number of pages7
JournalNature Genetics
Issue number9
StatePublished - Sep 1 2018


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