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A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0)
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..
Washington Univ, Sch Med, Dept Genet, McDonnell Genome Inst,Dept Med, 4444 Forest Pk Ave, St Louis, MO 63108 USA..
UCL, UCL Canc Inst, Bill Lyons Informat Ctr, 72 Huntley St, London WC1E 6DD, England..
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2017 (English)In: GigaScience, ISSN 2047-217X, E-ISSN 2047-217X, Vol. 6, no 11, p. 1-6Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2017. Vol. 6, no 11, p. 1-6
Keywords [en]
chimpanzee reference genome, assembly, genomics
National Category
Genetics
Identifiers
URN: urn:nbn:se:uu:diva-340340DOI: 10.1093/gigascience/gix098ISI: 000419634200001OAI: oai:DiVA.org:uu-340340DiVA, id: diva2:1178693
Note

De tre sista författarna delar sista författarskapet.

Available from: 2018-01-30 Created: 2018-01-30 Last updated: 2018-01-30Bibliographically approved

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Feuk, Lars

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