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Title: Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

Abstract

Plant genomes, and eukaryotic genomes in general, are typically repetitive, polyploid and heterozygous, which complicates genome assembly1. The short read lengths of early Sanger and current next-generation sequencing platforms hinder assembly through complex repeat regions, and many draft and reference genomes are fragmented, lacking skewed GC and repetitive intergenic sequences, which are gaining importance due to projects like the Encyclopedia of DNA Elements (ENCODE). Here we report the whole-genome sequencing and assembly of the desiccation-tolerant grass Oropetium thomaeum. Using only single-molecule real-time sequencing, which generates long (>16 kilobases) reads with random errors, we assembled 99% (244 megabases) of the Oropetium genome into 625 contigs with an N50 length of 2.4 megabases. Oropetium is an example of a ‘near-complete’ draft genome which includes gapless coverage over gene space as well as intergenic sequences such as centromeres, telomeres, transposable elements and rRNA clusters that are typically unassembled in draft genomes. Oropetium has 28,466 protein-coding genes and 43% repeat sequences, yet with 30% more compact euchromatic regions it is the smallest known grass genome. As a result, the Oropetium genome demonstrates the utility of single-molecule real-time sequencing for assembling high-quality plant and other eukaryotic genomes, and serves as a valuable resource for themore » plant comparative genomics community.« less

Authors:
 [1];  [1];  [2];  [3];  [4];  [5];  [6];  [6];  [6];  [7];  [4];  [8];  [9];  [9];  [10];  [1]
  1. Donal Danforth Plant Science Center, St. Louis, MO (United States)
  2. Univ. of California, Berkeley, CA (United States); Michigan State Univ., East Lansing, MI (United States)
  3. Univ. of Arizona, Tucson, AZ (United States); Fujan Agriculture and Forestry Univ., Fuzhou (China)
  4. Univ. of California, Berkeley, CA (United States)
  5. Univ. of Bonn, Bonn (Germany); Central Univ. of Tamil Nadu, Thiruvarur (India)
  6. Pacific Biosciences, Menlo Park, CA (United States)
  7. Univ. of Arizona, Tucson, AZ (United States)
  8. Univ. of Bonn, Bonn (Germany)
  9. BioNano Genomics, San Diego, CA (United States)
  10. Ibis Biosciences, Carlsbad, CA (United States)
Publication Date:
Research Org.:
Donald Danforth Plant Science Center, St. Louis, MO (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1436509
Grant/Contract Number:  
SC0012639
Resource Type:
Accepted Manuscript
Journal Name:
Nature (London)
Additional Journal Information:
Journal Name: Nature (London); Journal Volume: 527; Journal Issue: 7579; Journal ID: ISSN 0028-0836
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Comparative genomics; Drought; Genome evolution; Plant evolution

Citation Formats

VanBuren, Robert, Bryant, Doug, Edger, Patrick P., Tang, Haibao, Burgess, Diane, Challabathula, Dinakar, Spittle, Kristi, Hall, Richard, Gu, Jenny, Lyons, Eric, Freeling, Michael, Bartels, Dorothea, Ten Hallers, Boudewijn, Hastie, Alex, Michael, Todd P., and Mockler, Todd C. Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum. United States: N. p., 2015. Web. https://doi.org/10.1038/nature15714.
VanBuren, Robert, Bryant, Doug, Edger, Patrick P., Tang, Haibao, Burgess, Diane, Challabathula, Dinakar, Spittle, Kristi, Hall, Richard, Gu, Jenny, Lyons, Eric, Freeling, Michael, Bartels, Dorothea, Ten Hallers, Boudewijn, Hastie, Alex, Michael, Todd P., & Mockler, Todd C. Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum. United States. https://doi.org/10.1038/nature15714
VanBuren, Robert, Bryant, Doug, Edger, Patrick P., Tang, Haibao, Burgess, Diane, Challabathula, Dinakar, Spittle, Kristi, Hall, Richard, Gu, Jenny, Lyons, Eric, Freeling, Michael, Bartels, Dorothea, Ten Hallers, Boudewijn, Hastie, Alex, Michael, Todd P., and Mockler, Todd C. Wed . "Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum". United States. https://doi.org/10.1038/nature15714. https://www.osti.gov/servlets/purl/1436509.
@article{osti_1436509,
title = {Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum},
author = {VanBuren, Robert and Bryant, Doug and Edger, Patrick P. and Tang, Haibao and Burgess, Diane and Challabathula, Dinakar and Spittle, Kristi and Hall, Richard and Gu, Jenny and Lyons, Eric and Freeling, Michael and Bartels, Dorothea and Ten Hallers, Boudewijn and Hastie, Alex and Michael, Todd P. and Mockler, Todd C.},
abstractNote = {Plant genomes, and eukaryotic genomes in general, are typically repetitive, polyploid and heterozygous, which complicates genome assembly1. The short read lengths of early Sanger and current next-generation sequencing platforms hinder assembly through complex repeat regions, and many draft and reference genomes are fragmented, lacking skewed GC and repetitive intergenic sequences, which are gaining importance due to projects like the Encyclopedia of DNA Elements (ENCODE). Here we report the whole-genome sequencing and assembly of the desiccation-tolerant grass Oropetium thomaeum. Using only single-molecule real-time sequencing, which generates long (>16 kilobases) reads with random errors, we assembled 99% (244 megabases) of the Oropetium genome into 625 contigs with an N50 length of 2.4 megabases. Oropetium is an example of a ‘near-complete’ draft genome which includes gapless coverage over gene space as well as intergenic sequences such as centromeres, telomeres, transposable elements and rRNA clusters that are typically unassembled in draft genomes. Oropetium has 28,466 protein-coding genes and 43% repeat sequences, yet with 30% more compact euchromatic regions it is the smallest known grass genome. As a result, the Oropetium genome demonstrates the utility of single-molecule real-time sequencing for assembling high-quality plant and other eukaryotic genomes, and serves as a valuable resource for the plant comparative genomics community.},
doi = {10.1038/nature15714},
journal = {Nature (London)},
number = 7579,
volume = 527,
place = {United States},
year = {2015},
month = {11}
}

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