Accurate assembly of the olive baboon (Papio anubis) genome using long-read and Hi-C data. Issue 12 (7th December 2020)

• Record Type: Journal Article
• Authors: Batra, Sanjit Singh; Levy-Sakin, Michal; Robinson, Jacqueline; Guillory, Joseph; Durinck, Steffen; Vilgalys, Tauras P; Kwok, Pui-Yan; Cox, Laura A; Seshagiri, Somasekar; Song, Yun S; Wall, Jeffrey D
• Is Part Of: GigaScience. Volume 9:Issue 12(2020)
• Publication Date: 2020-12-07
• Subjects: Information storage and retrieval systems -- Research -- Periodicals; Biology -- Research -- Periodicals; Medical sciences -- Research -- Periodicals; Database management -- Periodicals; 570.285
• DOI: 10.1093/gigascience/giaa134
• Languages: English
• ISSNs: 2047-217X

Abstract

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.