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 assembly. 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. 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.
authors.affiliation: Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: VanBuren
authors.affiliation: Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA.
authors.forename: Doug
authors.initials: D
authors.lastname: Bryant
authors.affiliation: Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720, USA.|Department of Horticulture, Michigan State University, East Lansing, Michigan 48823, USA.
authors.forename: Patrick P
authors.initials: PP
authors.lastname: Edger
authors.affiliation: iPlant Collaborative, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA.|Center for Genomics and Biotechnology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou 350002, China.
authors.forename: Haibao
authors.initials: H
authors.lastname: Tang
authors.affiliation: Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720, USA.
authors.forename: Diane
authors.initials: D
authors.lastname: Burgess
authors.affiliation: IMBIO, University of Bonn, Kirschallee 1, D-53115 Bonn, Germany.
authors.forename: Dinakar
authors.initials: D
authors.lastname: Challabathula
authors.affiliation: Pacific Biosciences, Menlo Park, California 94025, USA.
authors.forename: Kristi
authors.initials: K
authors.lastname: Spittle
authors.affiliation: Pacific Biosciences, Menlo Park, California 94025, USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Hall
authors.affiliation: Pacific Biosciences, Menlo Park, California 94025, USA.
authors.forename: Jenny
authors.initials: J
authors.lastname: Gu
authors.affiliation: iPlant Collaborative, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Lyons
authors.affiliation: Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Freeling
authors.affiliation: IMBIO, University of Bonn, Kirschallee 1, D-53115 Bonn, Germany.
authors.forename: Dorothea
authors.initials: D
authors.lastname: Bartels
authors.affiliation: BioNano Genomics, San Diego, California 92121, USA.
authors.forename: Boudewijn
authors.initials: B
authors.lastname: Ten Hallers
authors.affiliation: BioNano Genomics, San Diego, California 92121, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Hastie
authors.affiliation: Ibis Biosciences, Carlsbad, California 92008, USA.
authors.forename: Todd P
authors.initials: TP
authors.lastname: Michael
authors.affiliation: Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA.
authors.forename: Todd C
authors.initials: TC
authors.lastname: Mockler
mesh_terms: D000064:Acclimatization / Q000235:genetics; D020451:Contig Mapping; D003681:Dehydration; D003890:Desiccation; D055864:Droughts; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D008969:Molecular Sequence Data; D006109:Poaceae / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*