title: Long-read sequence assembly of the gorilla genome.
abstract: Accurate sequence and assembly of genomes is a critical first step for studies of genetic variation. We generated a high-quality assembly of the gorilla genome using single-molecule, real-time sequence technology and a string graph de novo assembly algorithm. The new assembly improves contiguity by two to three orders of magnitude with respect to previously released assemblies, recovering 87% of missing reference exons and incomplete gene models. Although regions of large, high-identity segmental duplications remain largely unresolved, this comprehensive assembly provides new biological insight into genetic diversity, structural variation, gene loss, and representation of repeat structures within the gorilla genome. The approach provides a path forward for the routine assembly of mammalian genomes at a level approaching that of the current quality of the human genome.
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
authors.forename: David
authors.initials: D
authors.lastname: Gordon
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
authors.forename: John
authors.initials: J
authors.lastname: Huddleston
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
authors.forename: Mark J P
authors.initials: MJ
authors.lastname: Chaisson
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Hill
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
authors.forename: Zev N
authors.initials: ZN
authors.lastname: Kronenberg
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
authors.forename: Katherine M
authors.initials: KM
authors.lastname: Munson
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
authors.forename: Maika
authors.initials: M
authors.lastname: Malig
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
authors.forename: Archana
authors.initials: A
authors.lastname: Raja
authors.affiliation: Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, CA 95064, USA.
authors.forename: Ian
authors.initials: I
authors.lastname: Fiddes
authors.affiliation: McDonnell Genome Institute, Department of Medicine, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA.
authors.forename: LaDeana W
authors.initials: LW
authors.lastname: Hillier
authors.affiliation: Pacific Biosciences of California, Menlo Park, CA 94025, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Dunn
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
authors.forename: Carl
authors.initials: C
authors.lastname: Baker
authors.affiliation: Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, CA 95064, USA.
authors.forename: Joel
authors.initials: J
authors.lastname: Armstrong
authors.affiliation: Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, CA 95064, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Diekhans
authors.affiliation: Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, CA 95064, USA.
authors.forename: Benedict
authors.initials: B
authors.lastname: Paten
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
authors.forename: Jay
authors.initials: J
authors.lastname: Shendure
authors.affiliation: McDonnell Genome Institute, Department of Medicine, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA.
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson
authors.affiliation: Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, CA 95064, USA.
authors.forename: David
authors.initials: D
authors.lastname: Haussler
authors.affiliation: Pacific Biosciences of California, Menlo Park, CA 94025, USA.
authors.forename: Chen-Shan
authors.initials: CS
authors.lastname: Chin
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. eee@gs.washington.edu.
authors.forename: Evan E
authors.initials: EE
authors.lastname: Eichler
mesh_terms: D000818:Animals; D020451:Contig Mapping; D019143:Evolution, Molecular; D020224:Expressed Sequence Tags; D005260:Female; D014644:Genetic Variation; D015894:Genome, Human; D023281:Genomics; D006071:Gorilla gorilla / Q000235:genetics*; D006801:Humans; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*