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

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...

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Bibliographic Details
Published in:Gigascience 2020-12, Vol.9 (12)
Main 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
Format: Article
Language:English
Subjects:
Animals
Assembly
Baboons
Biological Evolution
Chromosomes
Data Note
Genome
Genomic analysis
Genomics
Linkage disequilibrium
Papio anubis
Papio anubis - genetics
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Summary: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.
ISSN:2047-217X
2047-217X
DOI:10.1093/gigascience/giaa134