Effect of sequence depth and length in long-read assembly of the maize inbred NC358

Shujun Ou; Jianing Liu; Kapeel M. Chougule; Arkarachai Fungtammasan; Arun S. Seetharam; Joshua C. Stein; Victor Llaca; Nancy Manchanda; Amanda M. Gilbert; Sharon Wei; Chen Shan Chin; David E. Hufnagel; Sarah Pedersen; Samantha J. Snodgrass; Kevin Fengler; Margaret Woodhouse; Brian P. Walenz; Sergey Koren; Adam M. Phillippy; Brett T. Hannigan; R. Kelly Dawe; Candice N. Hirsch; Matthew B. Hufford; Doreen Ware

doi:10.1038/s41467-020-16037-7

Effect of sequence depth and length in long-read assembly of the maize inbred NC358

Shujun Ou, Jianing Liu, Kapeel M. Chougule, Arkarachai Fungtammasan, Arun S. Seetharam, Joshua C. Stein, Victor Llaca, Nancy Manchanda, Amanda M. Gilbert, Sharon Wei, Chen Shan Chin, David E. Hufnagel, Sarah Pedersen, Samantha J. Snodgrass, Kevin Fengler, Margaret Woodhouse, Brian P. Walenz, Sergey Koren, Adam M. Phillippy, Brett T. HanniganR. Kelly Dawe, Candice N. Hirsch, Matthew B. Hufford, Doreen Ware

Agronomy and Plant Genetics

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

19 Scopus citations

Abstract

Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an assessment of critical sequence depth and read length is important for allocating limited resources. To this end, we have generated eight assemblies for the complex genome of the maize inbred line NC358 using PacBio datasets ranging from 20 to 75 × genomic depth and with N50 subread lengths of 11–21 kb. Assemblies with ≤30 × depth and N50 subread length of 11 kb are highly fragmented, with even low-copy genic regions showing degradation at 20 × depth. Distinct sequence-quality thresholds are observed for complete assembly of genes, transposable elements, and highly repetitive genomic features such as telomeres, heterochromatic knobs, and centromeres. In addition, we show high-quality optical maps can dramatically improve contiguity in even our most fragmented base assembly. This study provides a useful resource allocation reference to the community as long-read technologies continue to mature.

Original language	English (US)
Article number	2288
Journal	Nature communications
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41467-020-16037-7
State	Published - May 8 2020

Bibliographical note

Funding Information:
This work was supported by NSF Plant Genome Research Program grant IOS-1744001 to R.K.D., D.W., and M.B.H., and grant IOS-1546727 to C.N.H., USDA ARS 5030-21000- 068-00D to M.W., and USDA ARS 58-8062-2100-044 to D.W. B.P.W., S.K., and A.M.P. were supported by the Intramural Research Program of the National Human Genome Research Institute. We acknowledge Jonathan Gent for helpful discussion on repeat space analyses. This research was supported in part by the U.S. Department of Agriculture, Agricultural Research Service. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer.

Publisher Copyright:
© 2020, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.

Keywords

Base Sequence
DNA Transposable Elements/genetics
Genome, Plant
High-Throughput Nucleotide Sequencing/methods
Inbreeding
Repetitive Sequences, Nucleic Acid/genetics
Zea mays/genetics

PubMed: MeSH publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Intramural
Journal Article

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10.1038/s41467-020-16037-7

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Ou, S., Liu, J., Chougule, K. M., Fungtammasan, A., Seetharam, A. S., Stein, J. C., Llaca, V., Manchanda, N., Gilbert, A. M., Wei, S., Chin, C. S., Hufnagel, D. E., Pedersen, S., Snodgrass, S. J., Fengler, K., Woodhouse, M., Walenz, B. P., Koren, S., Phillippy, A. M., ... Ware, D. (2020). Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nature communications, 11(1), [2288]. https://doi.org/10.1038/s41467-020-16037-7

Ou, S, Liu, J, Chougule, KM, Fungtammasan, A, Seetharam, AS, Stein, JC, Llaca, V, Manchanda, N, Gilbert, AM, Wei, S, Chin, CS, Hufnagel, DE, Pedersen, S, Snodgrass, SJ, Fengler, K, Woodhouse, M, Walenz, BP, Koren, S, Phillippy, AM, Hannigan, BT, Dawe, RK, Hirsch, CN, Hufford, MB & Ware, D 2020, 'Effect of sequence depth and length in long-read assembly of the maize inbred NC358', Nature communications, vol. 11, no. 1, 2288. https://doi.org/10.1038/s41467-020-16037-7

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abstract = "Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an assessment of critical sequence depth and read length is important for allocating limited resources. To this end, we have generated eight assemblies for the complex genome of the maize inbred line NC358 using PacBio datasets ranging from 20 to 75 × genomic depth and with N50 subread lengths of 11–21 kb. Assemblies with ≤30 × depth and N50 subread length of 11 kb are highly fragmented, with even low-copy genic regions showing degradation at 20 × depth. Distinct sequence-quality thresholds are observed for complete assembly of genes, transposable elements, and highly repetitive genomic features such as telomeres, heterochromatic knobs, and centromeres. In addition, we show high-quality optical maps can dramatically improve contiguity in even our most fragmented base assembly. This study provides a useful resource allocation reference to the community as long-read technologies continue to mature.",

keywords = "Base Sequence, DNA Transposable Elements/genetics, Genome, Plant, High-Throughput Nucleotide Sequencing/methods, Inbreeding, Repetitive Sequences, Nucleic Acid/genetics, Zea mays/genetics",

author = "Shujun Ou and Jianing Liu and Chougule, {Kapeel M.} and Arkarachai Fungtammasan and Seetharam, {Arun S.} and Stein, {Joshua C.} and Victor Llaca and Nancy Manchanda and Gilbert, {Amanda M.} and Sharon Wei and Chin, {Chen Shan} and Hufnagel, {David E.} and Sarah Pedersen and Snodgrass, {Samantha J.} and Kevin Fengler and Margaret Woodhouse and Walenz, {Brian P.} and Sergey Koren and Phillippy, {Adam M.} and Hannigan, {Brett T.} and Dawe, {R. Kelly} and Hirsch, {Candice N.} and Hufford, {Matthew B.} and Doreen Ware",

note = "Funding Information: This work was supported by NSF Plant Genome Research Program grant IOS-1744001 to R.K.D., D.W., and M.B.H., and grant IOS-1546727 to C.N.H., USDA ARS 5030-21000- 068-00D to M.W., and USDA ARS 58-8062-2100-044 to D.W. B.P.W., S.K., and A.M.P. were supported by the Intramural Research Program of the National Human Genome Research Institute. We acknowledge Jonathan Gent for helpful discussion on repeat space analyses. This research was supported in part by the U.S. Department of Agriculture, Agricultural Research Service. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer. Publisher Copyright: {\textcopyright} 2020, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.",

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doi = "10.1038/s41467-020-16037-7",

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AU - Ou, Shujun

AU - Liu, Jianing

AU - Chougule, Kapeel M.

AU - Fungtammasan, Arkarachai

AU - Seetharam, Arun S.

AU - Stein, Joshua C.

AU - Llaca, Victor

AU - Manchanda, Nancy

AU - Gilbert, Amanda M.

AU - Wei, Sharon

AU - Chin, Chen Shan

AU - Hufnagel, David E.

AU - Pedersen, Sarah

AU - Snodgrass, Samantha J.

AU - Fengler, Kevin

AU - Woodhouse, Margaret

AU - Walenz, Brian P.

AU - Koren, Sergey

AU - Phillippy, Adam M.

AU - Hannigan, Brett T.

AU - Dawe, R. Kelly

AU - Hirsch, Candice N.

AU - Hufford, Matthew B.

AU - Ware, Doreen

N1 - Funding Information: This work was supported by NSF Plant Genome Research Program grant IOS-1744001 to R.K.D., D.W., and M.B.H., and grant IOS-1546727 to C.N.H., USDA ARS 5030-21000- 068-00D to M.W., and USDA ARS 58-8062-2100-044 to D.W. B.P.W., S.K., and A.M.P. were supported by the Intramural Research Program of the National Human Genome Research Institute. We acknowledge Jonathan Gent for helpful discussion on repeat space analyses. This research was supported in part by the U.S. Department of Agriculture, Agricultural Research Service. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer. Publisher Copyright: © 2020, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.

PY - 2020/5/8

Y1 - 2020/5/8

N2 - Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an assessment of critical sequence depth and read length is important for allocating limited resources. To this end, we have generated eight assemblies for the complex genome of the maize inbred line NC358 using PacBio datasets ranging from 20 to 75 × genomic depth and with N50 subread lengths of 11–21 kb. Assemblies with ≤30 × depth and N50 subread length of 11 kb are highly fragmented, with even low-copy genic regions showing degradation at 20 × depth. Distinct sequence-quality thresholds are observed for complete assembly of genes, transposable elements, and highly repetitive genomic features such as telomeres, heterochromatic knobs, and centromeres. In addition, we show high-quality optical maps can dramatically improve contiguity in even our most fragmented base assembly. This study provides a useful resource allocation reference to the community as long-read technologies continue to mature.

AB - Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an assessment of critical sequence depth and read length is important for allocating limited resources. To this end, we have generated eight assemblies for the complex genome of the maize inbred line NC358 using PacBio datasets ranging from 20 to 75 × genomic depth and with N50 subread lengths of 11–21 kb. Assemblies with ≤30 × depth and N50 subread length of 11 kb are highly fragmented, with even low-copy genic regions showing degradation at 20 × depth. Distinct sequence-quality thresholds are observed for complete assembly of genes, transposable elements, and highly repetitive genomic features such as telomeres, heterochromatic knobs, and centromeres. In addition, we show high-quality optical maps can dramatically improve contiguity in even our most fragmented base assembly. This study provides a useful resource allocation reference to the community as long-read technologies continue to mature.

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KW - DNA Transposable Elements/genetics

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KW - High-Throughput Nucleotide Sequencing/methods

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KW - Repetitive Sequences, Nucleic Acid/genetics

KW - Zea mays/genetics

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Effect of sequence depth and length in long-read assembly of the maize inbred NC358

Abstract

Bibliographical note

Keywords

PubMed: MeSH publication types

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