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Nat Genet. 2018 Sep;50(9):1289-1295. doi: 10.1038/s41588-018-0182-0. Epub 2018 Jul 30.

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

Author information

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. jlai@cau.edu.cn.
15
Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China. jlai@cau.edu.cn.

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.

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

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