Accurate assembly of the olive baboon (Papio anubis) genome using long-read and Hi-C data

Sanjit Singh Batra; Michal Levy-Sakin; Jacqueline Robinson; Joseph Guillory; Steffen Durinck; Tauras P Vilgalys; Pui-Yan Kwok; Laura A Cox; Somasekar Seshagiri; Yun S Song; Jeffrey D Wall

doi:10.1093/gigascience/giaa134

Accurate assembly of the olive baboon (Papio anubis) genome using long-read and Hi-C data

Gigascience. 2020 Dec 7;9(12):giaa134. doi: 10.1093/gigascience/giaa134.

Authors

Sanjit Singh Batra¹, Michal Levy-Sakin², Jacqueline Robinson³, Joseph Guillory⁴, Steffen Durinck^{4

5}, Tauras P Vilgalys⁶, Pui-Yan Kwok^{2

3}, Laura A Cox^{7

8}, Somasekar Seshagiri⁴, Yun S Song^{1

9

10}, Jeffrey D Wall³

Affiliations

¹ Computer Science Division, University of California Berkeley, 2626 Hearst Avenue, Berkeley, CA 94720, USA.
² Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Boulevard South, San Francisco, CA 94158, USA.
³ Institute for Human Genetics, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.
⁴ Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
⁵ Bioinformatics and Computational Biology Department, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
⁶ Department of Evolutionary Anthropology, Duke University, 130 Science Drive, Durham, NC 27705, USA.
⁷ Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, 475 Vine Drive, Winston-Salem, NC 27101, USA.
⁸ Southwest National Primate Research Center, Texas Biomedical Research Institute, 8715 W. Military Drive, San Antonio, TX 78227, USA.
⁹ Department of Statistics, University of California Berkeley, 367 Evans Hall, Berkeley, CA 94720, USA.
¹⁰ Chan Zuckerberg Biohub, Mission Bay, San Francisco, CA 94158, USA.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Biological Evolution
Chromosomes
Genome*
Genomics
Papio anubis* / genetics

Abstract

Publication types

MeSH terms

Grants and funding