Accurate assembly of the olive baboon ( Papio anubis ) genome using long-read and Hi-C data
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Abstract
Background
Baboons are a widely used nonhuman primate model for biomedical, evolutionary, and basic genetics research. Despite this importance, the genomic resources for baboons are limited. In particular, the current baboon reference genome Panu_3.0 is a highly fragmented, reference-guided (i.e., not fully de novo) assembly, and its poor quality inhibits our ability to conduct downstream genomic analyses.
Findings
Here we present a de novo genome assembly of the olive baboon (Papio anubis) that uses data from several recently developed single-molecule technologies. Our assembly, Panubis1.0, has an N50 contig size of ∼1.46 Mb (as opposed to 139 kb for Panu_3.0) and has single scaffolds that span each of the 20 autosomes and the X chromosome.
Conclusions
We highlight multiple lines of evidence (including Bionano Genomics data, pedigree linkage information, and linkage disequilibrium data) suggesting that there are several large assembly errors in Panu_3.0, which have been corrected in Panubis1.0.
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Now published in GigaScience doi: 10.1093/gigascience/giaa134
Sanjit Singh Batra 1Computer Science Division, University of California, Berkeley, CA 94720Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichal Levy-Sakin 2Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94143Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteJacqueline Robinson 3Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteJoseph Guillory 4Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080Find this author on Google ScholarFind this author on PubMedSearch for …
Now published in GigaScience doi: 10.1093/gigascience/giaa134
Sanjit Singh Batra 1Computer Science Division, University of California, Berkeley, CA 94720Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichal Levy-Sakin 2Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94143Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteJacqueline Robinson 3Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteJoseph Guillory 4Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteSteffen Durinck 4Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 940805Bioinformatics and Computational Biology Department, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080Find this author on Google ScholarFind this author on PubMedSearch for this author on this sitePui-Yan Kwok 2Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 941433Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteLaura A. Cox 6Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 271017Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78245Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteSomasekar Seshagiri 4Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteYun S. Song 1Computer Science Division, University of California, Berkeley, CA 947208Department of Statistics, University of California, Berkeley, CA 947209Chan Zuckerberg Biohub, San Francisco, CA 94158Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteJeffrey D. Wall 3Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: jeff.wall@ucsf.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa134 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102514 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102515 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102517
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