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

Author

Listed:
  • Shujun Ou

    (Iowa State University)

  • Jianing Liu

    (University of Georgia)

  • Kapeel M. Chougule

    (Cold Spring Harbor Laboratory)

  • Arkarachai Fungtammasan

    (Mountain View)

  • Arun S. Seetharam

    (Iowa State University
    Iowa State University)

  • Joshua C. Stein

    (Cold Spring Harbor Laboratory)

  • Victor Llaca

    (Applied Science and Technology, Corteva Agriscience TM)

  • Nancy Manchanda

    (Iowa State University)

  • Amanda M. Gilbert

    (University of Minnesota)

  • Sharon Wei

    (Cold Spring Harbor Laboratory)

  • Chen-Shan Chin

    (Mountain View)

  • David E. Hufnagel

    (Iowa State University)

  • Sarah Pedersen

    (Iowa State University)

  • Samantha J. Snodgrass

    (Iowa State University)

  • Kevin Fengler

    (Applied Science and Technology, Corteva Agriscience TM)

  • Margaret Woodhouse

    (USDA ARS Corn Insects and Crop Genetics Research Unit)

  • Brian P. Walenz

    (National Institutes of Health)

  • Sergey Koren

    (National Institutes of Health)

  • Adam M. Phillippy

    (National Institutes of Health)

  • Brett T. Hannigan

    (Mountain View)

  • R. Kelly Dawe

    (University of Georgia)

  • Candice N. Hirsch

    (University of Minnesota)

  • Matthew B. Hufford

    (Iowa State University)

  • Doreen Ware

    (Cold Spring Harbor Laboratory
    Agricultural Research Service)

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.

Suggested Citation

  • 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 , 2020. "Effect of sequence depth and length in long-read assembly of the maize inbred NC358," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16037-7
    DOI: 10.1038/s41467-020-16037-7
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    Cited by:

    1. Weidong Wang & Liyang Chen & Kevin Fengler & Joy Bolar & Victor Llaca & Xutong Wang & Chancelor B. Clark & Tomara J. Fleury & Jon Myrvold & David Oneal & Maria Magdalena Dyk & Ashley Hudson & Jesse Mu, 2021. "A giant NLR gene confers broad-spectrum resistance to Phytophthora sojae in soybean," Nature Communications, Nature, vol. 12(1), pages 1-8, December.

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