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

Silong Sun¹, Yingsi Zhou¹, Jian Chen¹, Junpeng Shi¹, Haiming Zhao¹, Hainan Zhao¹, Weibin Song¹, Mei Zhang^{1

2}, Yang Cui¹, Xiaomei Dong¹, Han Liu¹, Xuxu Ma¹, Yinping Jiao³, Bo Wang³, Xuehong Wei³, Joshua C Stein³, Jeff C Glaubitz⁴, Fei Lu^{5

6

7}, Guoliang Yu⁸, Chengzhi Liang⁹, Kevin Fengler¹⁰, Bailin Li¹¹, Antoni Rafalski¹¹, Patrick S Schnable¹², Doreen H Ware^{3

13}, Edward S Buckler^{5

13}, Jinsheng Lai^{14

15}

Affiliations

¹ State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China.
² Department of Biology, Stanford University, Stanford, CA, USA.
³ Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
⁴ Genomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA.
⁵ Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA.
⁶ State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
⁷ CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
⁸ Nextomics Biosciences Co., Ltd, Wuhan, China.
⁹ State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
¹⁰ DuPont Pioneer, Johnston, IA, USA.
¹¹ DuPont Pioneer, Wilmington, DE, USA.
¹² Department of Agronomy, Iowa State University, Ames, IA, USA.
¹³ USDA-ARS, NEA Robert W. Holley Center, Cornell University, Ithaca, NY, USA.
¹⁴ State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China. [email protected].
¹⁵ Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China. [email protected].

PMID: 30061735
DOI: 10.1038/s41588-018-0182-0

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

Silong Sun et al. Nat Genet. 2018 Sep.

. 2018 Sep;50(9):1289-1295.

doi: 10.1038/s41588-018-0182-0. Epub 2018 Jul 30.

Authors

Affiliations

¹ State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China.
² Department of Biology, Stanford University, Stanford, CA, USA.
³ Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
⁴ Genomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA.
⁵ Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA.
⁶ State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
⁷ CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
⁸ Nextomics Biosciences Co., Ltd, Wuhan, China.
⁹ State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
¹⁰ DuPont Pioneer, Johnston, IA, USA.
¹¹ DuPont Pioneer, Wilmington, DE, USA.
¹² Department of Agronomy, Iowa State University, Ames, IA, USA.
¹³ USDA-ARS, NEA Robert W. Holley Center, Cornell University, Ithaca, NY, USA.
¹⁴ State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China. [email protected].
¹⁵ Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China. [email protected].

PMID: 30061735
DOI: 10.1038/s41588-018-0182-0

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.

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

Affiliations

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

Authors

Affiliations

Abstract

Publication types

MeSH terms

LinkOut - more resources

Full Text Sources

Other Literature Sources

Miscellaneous