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.
Highlights
Maize (Zea mays) is a classical genetic model and an important crop worldwide
All nine bacterial artificial chromosome (BAC) sequences were covered by a single scaffold with high consistency and coverage (Supplementary Table 3), indicating high quality of the assembled genome
With a high-density genetic map containing approximately 4.4 million genotype-by-sequencing (GBS) tags[27], we anchored and oriented 362 scaffolds onto ten pseudochromosomes, which account for 96.42% (2,104 Mb) of the genome assembly (Supplementary Table 4)
Summary
The maize genome exhibits high levels of genetic diversity among different inbred lines[1,2,3,4,5,6]. Owing to the high level of intraspecific genome diversity, hybrid maize resulting from crosses between lines from different heterotic groups shows extremely high levels of hybrid vigor. The draft genome sequences of the maize PH207 inbred line assembled from short reads have been reported[16]. We report the assembly of a high-quality Mo17 reference genome through single-molecule sequencing and BioNano opticalmapping technologies. The generation of an additional reference genome provides an unprecedented opportunity for extensive comparison of intraspecific genome diversity in maize. These large gene-order and gene structural variations were observed in a comparison of the PH207 genome with the B73 and Mo17 genomes
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