Improved maize reference genome with single-molecule technologies

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., Antoniou, E., McCombie, W. R., Presting, G. G., McMullen, M., Ross-Ibarra, J., Dawe, R. K., Hastie, A., Rank, D. R., Ware, D. (2017) Improved maize reference genome with single-molecule technologies. Nature, 546 (7659). pp. 524-527. ISSN 0028-0836

URL: https://www.ncbi.nlm.nih.gov/pubmed/28605751
DOI: 10.1038/nature22971

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.

Item Type: Paper
Subjects: organism description > plant > maize
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
CSHL Authors:
Communities: CSHL labs > McCombie lab
CSHL labs > Ware lab
Depositing User: Matt Covey
Date Deposited: 21 Jun 2017 20:42
Last Modified: 07 Sep 2017 18:26
Related URLs:
Dataset ID:
URI: http://repository.cshl.edu/id/eprint/35009

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving