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

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

Agronomy and Plant Genetics

Research output: Contribution to journal › Article › peer-review

82 Scopus citations

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.

Original language	English (US)
Article number	121
Journal	Genome biology
Volume	21
Issue number	1
DOIs	https://doi.org/10.1186/s13059-020-02029-9
State	Published - 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).

Keywords

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

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10.1186/s13059-020-02029-9

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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. 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(1), Article 121. https://doi.org/10.1186/s13059-020-02029-9

Liu, J, Seetharam, AS, Chougule, K, Ou, S, Swentowsky, KW, Gent, JI, Llaca, V, Woodhouse, MR, Manchanda, N, Presting, GG, Kudrna, DA, Alabady, M, Hirsch, CN, Fengler, KA, Ware, D, Michael, TP, Hufford, MB & Dawe, RK 2020, 'Gapless assembly of maize chromosomes using long-read technologies', Genome biology, vol. 21, no. 1, 121. https://doi.org/10.1186/s13059-020-02029-9

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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.",

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doi = "10.1186/s13059-020-02029-9",

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AU - Seetharam, Arun S.

AU - Chougule, Kapeel

AU - Ou, Shujun

AU - Swentowsky, Kyle W.

AU - Gent, Jonathan I.

AU - Llaca, Victor

AU - Woodhouse, Margaret R.

AU - Manchanda, Nancy

AU - Presting, Gernot G.

AU - Kudrna, David A.

AU - Alabady, Magdy

AU - Hirsch, Candice N.

AU - Fengler, Kevin A.

AU - Ware, Doreen

AU - Michael, Todd P.

AU - Hufford, Matthew B.

AU - Dawe, R. Kelly

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N2 - 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.

AB - 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.

KW - Gapless assembly

KW - Knob structure

KW - Long-read technology

KW - Maize genome

KW - Meiotic drive

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Gapless assembly of maize chromosomes using long-read technologies

Abstract

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