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

212 Citations (Scopus)

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

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Zea mays
Genome
Technology
DNA Transposable Elements
Plant Genome
Molecular Sequence Annotation
Biological Phenomena
Centromere
Genetic Models
Genes
Research

Cite this

Jiao, Y., Peluso, P., Shi, J., Liang, T., Stitzer, M. C., Wang, B., ... Ware, D. (2017). Improved maize reference genome with single-molecule technologies. Nature, 546(7659), 524-527. https://doi.org/10.1038/nature22971

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

In: Nature, Vol. 546, No. 7659, 22.06.2017, p. 524-527.

Research output: Contribution to journalArticle

Jiao, Y, Peluso, P, Shi, J, Liang, T, Stitzer, MC, Wang, B, Campbell, MS, Stein, JC, Wei, X, Chin, CS, Guill, K, Regulski, M, Kumari, S, Olson, A, Gent, J, Schneider, KL, Wolfgruber, TK, May, MR, Springer, NM, Antoniou, E, McCombie, WR, Presting, GG, McMullen, M, Ross-Ibarra, J, Dawe, RK, Hastie, A, Rank, DR & Ware, D 2017, 'Improved maize reference genome with single-molecule technologies', Nature, vol. 546, no. 7659, pp. 524-527. https://doi.org/10.1038/nature22971
Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B et al. Improved maize reference genome with single-molecule technologies. Nature. 2017 Jun 22;546(7659):524-527. https://doi.org/10.1038/nature22971
Jiao, Yinping ; Peluso, Paul ; Shi, Jinghua ; Liang, Tiffany ; Stitzer, Michelle C. ; Wang, Bo ; Campbell, Michael S. ; Stein, Joshua C. ; Wei, Xuehong ; Chin, Chen Shan ; Guill, Katherine ; Regulski, Michael ; Kumari, Sunita ; Olson, Andrew ; Gent, Jonathan ; Schneider, Kevin L. ; Wolfgruber, Thomas K. ; May, Michael R. ; Springer, Nathan M. ; Antoniou, Eric ; McCombie, W. Richard ; Presting, Gernot G. ; McMullen, Michael ; Ross-Ibarra, Jeffrey ; Dawe, R. Kelly ; Hastie, Alex ; Rank, David R. ; Ware, Doreen. / Improved maize reference genome with single-molecule technologies. In: Nature. 2017 ; Vol. 546, No. 7659. pp. 524-527.
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