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Nature. 2017 Jun 22;546(7659):524-527. doi: 10.1038/nature22971. Epub 2017 Jun 12.

Improved maize reference genome with single-molecule technologies.

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Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
Pacific Biosciences, Menlo Park, California 94025, USA.
BioNano Genomics, San Diego, California 92121, USA.
Department of Plant Sciences and Center for Population Biology, University of California, Davis, Davis, California 95616, USA.
USDA-ARS, Plant Genetics Research Unit, Columbia, Missouri 65211, USA.
University of Georgia, Athens, Georgia 30602, USA.
Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, Hawaii 96822, USA.
Department of Evolution and Ecology, University of California, Davis, California 95616, USA.
Department of Plant Biology, University of Minnesota, St Paul, Minnesota 55108, USA.
Department of Plant Sciences, Center for Population Biology, and Genome Center, University of California, Davis, California 95616, USA.
USDA-ARS, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York 14853, USA.


Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and notable improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed more than 130,000 intact transposable elements, allowing us to identify transposable element lineage expansions that are unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by single-molecule real-time sequencing. In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes.

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