Gapless assembly of maize chromosomes using long-read technologies

Jianing Liu; Arun S Seetharam; Kapeel Chougule; Shujun Ou; Kyle W Swentowsky; Jonathan I Gent; Victor Llaca; Margaret R Woodhouse; Nancy Manchanda; Gernot G Presting; David A Kudrna; Magdy Alabady; Candice N Hirsch; Kevin A Fengler; Doreen Ware; Todd P Michael; Matthew B Hufford; R Kelly Dawe

doi:10.1186/s13059-020-02029-9

Gapless assembly of maize chromosomes using long-read technologies

Genome Biol. 2020 May 20;21(1):121. doi: 10.1186/s13059-020-02029-9.

Authors

Jianing Liu¹, Arun S Seetharam², Kapeel Chougule³, Shujun Ou⁴, Kyle W Swentowsky⁵, Jonathan I Gent⁵, Victor Llaca⁶, Margaret R Woodhouse⁷, Nancy Manchanda⁴, Gernot G Presting⁸, David A Kudrna⁹, Magdy Alabady^{5

10}, Candice N Hirsch¹¹, Kevin A Fengler⁶, Doreen Ware^{3

12}, Todd P Michael¹³, Matthew B Hufford⁴, R Kelly Dawe^{14

15}

Affiliations

¹ Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
² Genome Informatics Facility, Iowa State University, Ames, IA, 50011, USA.
³ Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
⁴ Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA.
⁵ Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
⁶ Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA.
⁷ USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA.
⁸ Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, 96822, USA.
⁹ Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
¹⁰ Georgia Genomics and Bioinformatics Core Laboratory, University of Georgia, Athens, GA, 30602, USA.
¹¹ Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
¹² USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY, 14853, USA.
¹³ Informatics Department, J. Craig Venter Institute, La Jolla, CA, USA.
¹⁴ Department of Genetics, University of Georgia, Athens, GA, 30602, USA. kdawe@uga.edu.
¹⁵ Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA. kdawe@uga.edu.

Abstract

Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We use two independent assemblies and an optical map-based merging pipeline to produce a maize genome (B73-Ab10) composed of 63 contigs and a contig N50 of 162 Mb. This genome includes gapless assemblies of chromosome 3 (236 Mb) and chromosome 9 (162 Mb), and 53 Mb of the Ab10 meiotic drive haplotype. The data also reveal the internal structure of seven centromeres and five heterochromatic knobs, showing that the major tandem repeat arrays (CentC, knob180, and TR-1) are discontinuous and frequently interspersed with retroelements.

Keywords: Gapless assembly; Knob structure; Long-read technology; Maize genome; Meiotic drive.

Publication types

Evaluation Study
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Chromosomes, Plant*
Genome, Plant*
Genomics / methods*
Physical Chromosome Mapping / methods*
Zea mays / genetics*