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 (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.

Molecular Approaches for the Validation of the Baboon as a Nonhuman Primate Model for the Study of Zika Virus Infection

“…These primary analyses provided approximately 10 million high-quality, 100 bp paired end reads per sample in FASTQ format, which were then used for secondary data analyses performed with a pipeline of software tools available from Partek Flow (Partek Inc.). These secondary analyses included steps such as additional filtering of reads to base quality of Phred 30, and alignment of reads to the publicly available assembly of the olive baboon genome, Panubis 1.0 ( Batra et al., 2020 ), with the RNA-Seq aligner pipeline STAR 2.5.3a ( Dobin et al., 2013 ), post alignment quality assessment, and transcript abundance estimation according to Ensembl transcriptome annotation by expectation- maximization algorithm.…”

Distinct gene regulatory signatures of dominance rank and social bond strength in wild baboons

“…; electronic supplementary material, table S1). Trimmed reads were mapped to the Panubis 1.0 genome (GCA_008728515.1) using the STAR 2pass aligner [113,114]. Finally, we generated gene-level counts royalsocietypublishing.org/journal/rstb Phil.…”

Genomic variation in baboons from central Mozambique unveils complex evolutionary relationships with other Papio species

“…After we started to analyze the GNP sample, an additional baboon reference genome became available (Panubis1.0 [ 53 ]). Structural differences between the Panu_3.0 and Panubis1.0 assemblies have been highlighted.…”

“…The recombination map produced using a block penalty value of 5 was used as those were the rates focused on in the Robinson et al [ 78 ] study. Recombination rates for the Panu_3.0 assembly from the Panu_2.0 assembly were generated using the liftOver chain provided by Robinson et al Furthermore, regions which were found to be erroneously assembled in Panu_3.0 [ 53 ] were masked for both aforementioned analyzes.…”