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

Research output: Contribution to journalArticlepeer-review

71 Scopus citations


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.

Original languageEnglish (US)
Article number121
JournalGenome biology
Issue number1
StatePublished - May 20 2020

Bibliographical note

Funding Information:
This study was supported by the National Science Foundation grants MCB-1412063 and IOS-1744001.

Publisher Copyright:
© 2020 The Author(s).


  • Gapless assembly
  • Knob structure
  • Long-read technology
  • Maize genome
  • Meiotic drive


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