Gapless Assembly of Maize Chromosomes Using Long-Read Technologies

Liu, J., Seetharam, A.S., Chougule, K., Ou, S., Swentowsky, K.W., Gent, J.I., Llaca, V., Woodhouse, M.R., Manchanda, N., Presting, G.G., Kudrna, D., Alabady, M., Hirsch, C.N., Fengler, K.A., Ware, D., Michael, T.P., Hufford, M. B., Dawe, R.K. (May 2020) Gapless Assembly of Maize Chromosomes Using Long-Read Technologies. Genome Biology, 21 (1). p. 121. ISSN 1474-7596

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URL: https://pubmed.ncbi.nlm.nih.gov/32434565/

DOI: 10.1186/s13059-020-02029-9

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.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics organism description > plant > maize bioinformatics > genomics and proteomics > Mapping and Rendering bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosome bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosomes, structure and function > chromosome bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosomes, structure and function organism description > plant
CSHL Authors:	Ware, Doreen H. Chougule, Kapeel Swentowsky, Kyle
Communities:	CSHL labs > Ware lab
Depositing User:	Adrian Gomez
Date:	20 May 2020
Date Deposited:	22 May 2020 14:25
Last Modified:	01 Feb 2024 15:59
PMCID:	PMC7238635
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/39476

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