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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Publications at this Location » Publication #371045
Research Project: MaizeGDB: Enabling Access to Basic, Translational, and Applied Research Information

Location: Corn Insects and Crop Genetics Research

Title: Gapless assembly of maize chromosomes using long-read technologies

Author
item LIU, JIANING - University Of Georgia
item SEETHARAM, ARUN - Iowa State University
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item OU, SHUJUN - Iowa State University
item SWENTOWSKY, KYLE - University Of Georgia
item GENT, JONATHAN - University Of Georgia
item LLACA, VICTOR - Corteva Agriscience
item Woodhouse, Margaret
item MANCHANDA, NANCY - Iowa State University
item PRESTING, GERNOT - University Of Hawaii
item KURDNA, DAVID - University Of Arizona
item ALABADY, MAGDY - University Of Georgia
item HIRSCH, CANDICE - University Of Minnesota
item FENGLER, KEVIN - Corteva Agriscience
item Ware, Doreen
item MICHAEL, T. - J Craig Venter Institute
item HUFFORD, MATTHEW - Iowa State University
item DAWE, R. - University Of Georgia

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/22/2020
Publication Date: 5/20/2020
Citation: Liu, J., Seetharam, A.S., Chougule, K.M., Ou, S., Swentowsky, K.W., Gent, J.I., Llaca, V., Woodhouse, M.H., Manchanda, N., Presting, G.G., Kurdna, D.A., Alabady, M., Hirsch, C.N., Fengler, K.A., Ware, D., Michael, T.P., Hufford, M.B., Dawe, R.K. 2020. Gapless assembly of maize chromosomes using long-read technologies. Genome Biology. 21. https://doi.org/10.1186/s13059-020-02029-9.
DOI: https://doi.org/10.1186/s13059-020-02029-9

Interpretive Summary: While genome sequencing has been able to efficiently capture gene space for at least a decade, sequencing through non-genic, repetitive regions in a genome has remained problematic until now. These repeat regions often contain chromosome-level features that can play a role in cell function. Recent advances in sequencing technology, however, have made it possible to sequence through these difficult regions. This article describes a new technology used to sequence a maize genome containing a large repeat-sequence knob on Chromosome 10 that controls chromosome orientation during meiosis; this new technology allows researchers to better understand this controlling region, and other repetitive regions that may play a role in maize cell function.

Technical Abstract: Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We used long read technologies and an optical map based approach to produce a maize genome assembly composed of only 63 contigs. The B73-Ab10 genome includes gapless assemblies of chromosome 3 (236 Mb) and chromosome 9 (162 Mb), multiple highly repetitive centromeres and heterochromatic knobs, and 53 Mb of the Ab10 meiotic drive haplotype.