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A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0)

Kuderna, Lukas F. K. (author)
Univ Pompeu Fabra, CSIC, Inst Biol Evolut, PRBB, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.;BIST, CRG, CNAG, Baldiri & Reixac 4, Barcelona 08028, Spain.
Tomlinson, Chad (author)
Washington Univ, Sch Med, Dept Genet, McDonnell Genome Inst,Dept Med, 4444 Forest Pk Ave, St Louis, MO 63108 USA.
Hillier, LaDeana W. (author)
Washington Univ, Sch Med, Dept Genet, McDonnell Genome Inst,Dept Med, 4444 Forest Pk Ave, St Louis, MO 63108 USA.
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Tran, Annabel (author)
UCL, UCL Canc Inst, Bill Lyons Informat Ctr, 72 Huntley St, London WC1E 6DD, England.
Fiddes, Ian T. (author)
Univ Calif Santa Cruz, Genom Inst, 1156 High St, Santa Cruz, CA 95064 USA.;Howard Hughes Med Inst, 1156 High St, Santa Cruz, CA 95064 USA.
Armstrong, Joel (author)
Univ Calif Santa Cruz, Genom Inst, 1156 High St, Santa Cruz, CA 95064 USA.;Howard Hughes Med Inst, 1156 High St, Santa Cruz, CA 95064 USA.
Laayouni, Hafid (author)
Univ Pompeu Fabra, CSIC, Inst Biol Evolut, PRBB, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.;UPF, ESCI, Bioinformat Studies, Pg Pujades 1, Barcelona 08003, Spain.
Gordon, David (author)
Univ Washington, Sch Med, Dept Genome Sci, Box 355065, Seattle, WA 98195 USA.;Univ Washington, Howard Hughes Med Inst, Box 355065, Seattle, WA 98195 USA.
Huddleston, John (author)
Univ Washington, Sch Med, Dept Genome Sci, Box 355065, Seattle, WA 98195 USA.;Univ Washington, Howard Hughes Med Inst, Box 355065, Seattle, WA 98195 USA.
Garcia Perez, Raquel (author)
Univ Pompeu Fabra, CSIC, Inst Biol Evolut, PRBB, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.
Povolotskaya, Inna (author)
Univ Pompeu Fabra, CSIC, Inst Biol Evolut, PRBB, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.
Serres Armero, Aitor (author)
Univ Pompeu Fabra, CSIC, Inst Biol Evolut, PRBB, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.
Gomez Garrido, Jessica (author)
Univ Pompeu Fabra, CSIC, Inst Biol Evolut, PRBB, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.;BIST, CRG, CNAG, Baldiri & Reixac 4, Barcelona 08028, Spain.
Ho, Daniel (author)
Icahn Sch Med Mt Sinai, Dept Genet & Genom Sci, New York, NY 10029 USA.
Ribeca, Paolo (author)
Pirbright Inst, Ash Rd, Woking GU24 0NF, Surrey, England.
Alioto, Tyler (author)
Univ Pompeu Fabra, CSIC, Inst Biol Evolut, PRBB, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.;BIST, CRG, CNAG, Baldiri & Reixac 4, Barcelona 08028, Spain.
Green, Richard E. (author)
Univ Calif Santa Cruz, Dept Biomol Engn, 1156 High St, Santa Cruz, CA 95060 USA.;Dovetail Genom, 2161 Delaware Ave, Santa Cruz, CA 95060 USA.
Paten, Benedict (author)
Univ Calif Santa Cruz, Genom Inst, 1156 High St, Santa Cruz, CA 95064 USA.;Howard Hughes Med Inst, 1156 High St, Santa Cruz, CA 95064 USA.
Navarro, Arcadi (author)
Univ Pompeu Fabra, CSIC, Inst Biol Evolut, PRBB, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.;BIST, CRG, CNAG, Baldiri & Reixac 4, Barcelona 08028, Spain.;ICREA, Passeig Lluis Co 23, Barcelona 08010, Catalonia, Spain.
Betranpetit, Jaume (author)
Univ Pompeu Fabra, CSIC, Inst Biol Evolut, PRBB, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.
Herrero, Javier (author)
UCL, UCL Canc Inst, Bill Lyons Informat Ctr, 72 Huntley St, London WC1E 6DD, England.
Eichler, Evan E. (author)
Univ Washington, Sch Med, Dept Genome Sci, Box 355065, Seattle, WA 98195 USA.;Univ Washington, Howard Hughes Med Inst, Box 355065, Seattle, WA 98195 USA.
Sharp, Andrew J. (author)
Icahn Sch Med Mt Sinai, Dept Genet & Genom Sci, New York, NY 10029 USA.
Feuk, Lars (author)
Uppsala universitet,Science for Life Laboratory, SciLifeLab,Medicinsk genetik och genomik
Warren, Wesley C. (author)
Washington Univ, Sch Med, Dept Genet, McDonnell Genome Inst,Dept Med, 4444 Forest Pk Ave, St Louis, MO 63108 USA.
Marques-Bonet, Tomas (author)
Univ Pompeu Fabra, CSIC, Inst Biol Evolut, PRBB, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.;BIST, CRG, CNAG, Baldiri & Reixac 4, Barcelona 08028, Spain.;ICREA, Passeig Lluis Co 23, Barcelona 08010, Catalonia, Spain.
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Univ Pompeu Fabra, CSIC, Inst Biol Evolut, PRBB, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain;BIST, CRG, CNAG, Baldiri & Reixac 4, Barcelona 08028, Spain. Washington Univ, Sch Med, Dept Genet, McDonnell Genome Inst,Dept Med, 4444 Forest Pk Ave, St Louis, MO 63108 USA. (creator_code:org_t)
2017-10-30
2017
English.
In: GigaScience. - : Oxford University Press (OUP). - 2047-217X. ; 6:11, s. 1-6
Related links:
https://academic.oup...
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https://urn.kb.se/re...
https://doi.org/10.1...
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  • Journal article (peer-reviewed)
Abstract Subject headings
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  • The chimpanzee is arguably the most important species for the study of human origins. A key resource for these studies is a high-quality reference genome assembly; however, as with most mammalian genomes, the current iteration of the chimpanzee reference genome assembly is highly fragmented. In the current iteration of the chimpanzee reference genome assembly (Pan tro 2.1.4), the sequence is scattered across more then 183 000 contigs, incorporating more than 159 000 gaps, with a genome-wide contig N50 of 51 Kbp. In this work, we produce an extensive and diverse array of sequencing datasets to rapidly assemble a new chimpanzee reference that surpasses previous iterations in bases represented and organized in large scaffolds. To this end, we show substantial improvements over the current release of the chimpanzee genome (Pan tro 2.1.4) by several metrics, such as increased contiguity by > 750% and 300% on contigs and scaffolds, respectively, and closure of 77% of gaps in the Pan tro 2.1.4 assembly gaps spanning > 850 Kbp of the novel coding sequence based on RNASeq data. We further report more than 2700 genes that had putatively erroneous frame-shift predictions to human in Pan tro 2.1.4 and show a substantial increase in the annotation of repetitive elements. We apply a simple 3-way hybrid approach to considerably improve the reference genome assembly for the chimpanzee, providing a valuable resource for the study of human origins. Furthermore, we produce extensive sequencing datasets that are all derived from the same cell line, generating a broad non-human benchmark dataset.

Subject headings

NATURVETENSKAP  -- Biologi -- Genetik (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Genetics (hsv//eng)

Keyword

chimpanzee reference genome
assembly
genomics

Publication and Content Type

ref (subject category)
art (subject category)

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