Improved maize reference genome with single-molecule technologies

Yinping Jiao, Paul Peluso, Jinghua Shi, Tiffany Liang, Michelle C. Stitzer, Bo Wang, Michael S. Campbell, Joshua C. Stein, Xuehong Wei, Chen Shan Chin, Katherine Guill, Michael Regulski, Sunita Kumari, Andrew Olson, Jonathan Gent, Kevin L. Schneider, Thomas K. Wolfgruber, Michael R. May, Nathan M. Springer, Eric AntoniouW. Richard McCombie, Gernot G. Presting, Michael McMullen, Jeffrey Ross-Ibarra, R. Kelly Dawe, Alex Hastie, David R. Rank, Doreen Ware

Research output: Contribution to journalArticle

313 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)524-527
Number of pages4
JournalNature
Volume546
Issue number7659
DOIs
StatePublished - Jun 22 2017

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    Jiao, Y., Peluso, P., Shi, J., Liang, T., Stitzer, M. C., Wang, B., Campbell, M. S., Stein, J. C., Wei, X., Chin, C. S., Guill, K., Regulski, M., Kumari, S., Olson, A., Gent, J., Schneider, K. L., Wolfgruber, T. K., May, M. R., Springer, N. M., ... Ware, D. (2017). Improved maize reference genome with single-molecule technologies. Nature, 546(7659), 524-527. https://doi.org/10.1038/nature22971