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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #334120

Research Project: Enhancing Plant Genome Function Maps Through Genomic, Genetic, Computational and Collaborative Research

Location: Plant, Soil and Nutrition Research

Title: Improved maize reference genome with single-molecule technologies

Author
item Jiao, Yinping
item PELUSO, PAUL - Pacific Biosciences Inc
item LIANG, TIFFANY - Bionano Genomics, Inc
item SHI, JINGHUA - Bionano Genomics, Inc
item STITZER, MICHELLE - Institute Of Population Health Sciences
item WANG, BO - Cold Spring Harbor Laboratory
item CAMPBELL, MICHAEL - Cold Spring Harbor Laboratory
item STEIN, JOSHUA - Cold Spring Harbor Laboratory
item WEI, XUEHONG - Cold Spring Harbor Laboratory
item CHIN, JASON - Pacific Biosciences Inc
item Guill, Katherine
item REGULSKI, MICHAEL - Cold Spring Harbor Laboratory
item SUNITA, KUMARI - Cold Spring Harbor Laboratory
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item GENT, JONATHAN - University Of Georgia
item SCHNEIDER, KEVIN - University Of Hawaii
item WOLFGRUBER, THOMAS - University Of Hawaii
item MAY, MICHAEL - University Of Minnesota
item SPRINGER, NATHAN - University Of Minnesota
item ANTONIOU, ERIC - Cold Spring Harbor Laboratory
item MCCOMBIE, RICHARD - Cold Spring Harbor Laboratory
item PRESTING, GERNOT - University Of Hawaii
item McMullen, Michael
item ROSS-IBARRA, JEFFREY - University Of California
item KELLY, DAWE - University Of Georgia
item HASTIE, ALEX - Bionano Genomics, Inc
item RANK, DAVID - Pacific Biosciences Inc
item Ware, Doreen

Submitted to: Nature
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/14/2017
Publication Date: 6/12/2017
Citation: Jiao, Y., Peluso, P., Liang, T., Shi, J., Stitzer, M., Wang, B., Campbell, M., Stein, J., Wei, X., Chin, J., Guill, K.E., Regulski, M., Sunita, K., Olson, A., Gent, J., Schneider, K., Wolfgruber, T., May, M., Springer, N., Antoniou, E., McCombie, R., Presting, G., McMullen, M.D., Ross-Ibarra, J., Kelly, D., Hastie, A., Rank, D., Ware, D. 2017. Improved maize reference genome with single-molecule technologies. Nature. doi: 10.1038/nature22971.

Interpretive Summary: Corn (maize) is one of the most important crops in the United States and the world, providing livestock feed and a wide range of food and industrial products. Continued genetic improvement of maize through application of genomics research and breeding is essential for ensuring food and energy security in the future. This research utilized new sequencing technologies to vastly increase our knowledge of maize genome.

Technical Abstract: Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate elucidation 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 maize, a genetic and agricultural model organism, using sequence data generated by the PacBio® Single Molecule Real-Time (SMRT®) Sequencing platform and a high-resolution optical map. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and significant improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed over 130,000 intact transposable elements (TEs), allowing us to identify TE lineage expansions unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by SMRT Sequencing. In addition, comparative optical mapping of two other inbreds revealed a prevalence of deletions in the low gene density region with less conservered genes.