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Gigascience. 2017 Nov 1;6(11):1-6. doi: 10.1093/gigascience/gix098.

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

Author information

Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.
McDonnell Genome Institute, Department of Medicine, Department of Genetics, Washington University School of Medicine, 4444 Forest Park Ave., St. Louis, MO 63108, USA.
Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK.
Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, 1156 High Street, Santa Cruz, CA 95064, USA.
Bioinformatics Studies, ESCI-UPF, Pg. Pujades 1, 08003, Barcelona, Spain.
Department of Genome Sciences, University of Washington School of Medicine, Box 355065, Seattle, WA 98195, USA.
Howard Hughes Medical Institute, University of Washington, Box 355065, Seattle, WA 98195, USA.
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, UK.
Department of Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95060, USA.
Dovetail Genomics, Santa Cruz, 2161 Delaware Ave., Santa Cruz, CA 95060, USA.
Institucio Catalana de Recerca i Estudis Avancats (ICREA), Passeig Lluís Companys 23, Barcelona, Catalonia 08010, Spain.
Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Box 815, Uppsala University 751 08 Uppsala, Sweden.


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.


assembly, genomics; chimpanzee reference genome

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