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

Abstract

Besides macaques, baboons are the most commonly used nonhuman primate in biomedical research. Despite this importance, the genomic resources for baboons are quite 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. Here we present a truly 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. 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.

High-quality carnivore genomes from roadkill samples enable species delimitation in aardwolf and bat-eared fox

“…The use of less GC-biased long reads of single DNA molecules and ultra-long reads spanning repeated genomic regions provides a powerful solution for obtaining assemblies with high contiguity and completeness, although long-read sequencing has limited accuracy (10-20% errors). Long reads can indeed be used alone at a high depth of coverage permitting autocorrection (Koren et al, 2017; Shafin et al, 2020) or in combination with short reads for (1) scaffolding short-read contigs (Armstrong et al, 2020; Kwan et al, 2019), (2) using short reads to polish long-read contigs (Batra et al, 2019b; Datema et al, 2016; Jansen et al, 2017; Michael et al, 2018), or (3) optimizing the assembly process by using information from both long and short reads (Díaz-Viraqué et al, 2019; Gan et al, 2019; Jiang et al, 2019; Kadobianskyi et al, 2019; Tan et al, 2018; Wang et al, 2020; Zimin et al, 2017). Given the previously demonstrated efficiency of the MaSuRCA tool for the assembly of large genomes (Scott et al, 2020; Wang et al, 2020; Zimin et al, 2017), we decided to rely on hybrid sequencing data combining the advantages of Illumina short-read and Nanopore long-read sequencing technologies.…”

“…This approach is particularly suitable for sequencing roadkill specimens for which it is notoriously difficult to obtain a large amount of high-quality DNA because of post-mortem DNA degradation processes. Furthermore, it is possible to correct errors in ONT long reads by combining them with Illumina short reads, either to polish de novo long read-based genome assemblies (Batra et al, 2019a; Jain et al, 2018; Nicholls et al, 2019; Walker et al, 2014) or to construct hybrid assemblies (Di Genova et al, 2018; Gan et al, 2019; Tan et al, 2018; Zimin et al, 2013). In hybrid assembly approaches, the accuracy of short reads with high depth of coverage (50-100x) allows the use of long reads at lower depth of coverage (10-30x) essentially for scaffolding (Armstrong et al, 2020; Kwan et al, 2019).…”

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

“…We constructed indexed RNA-seq libraries using the NEBNext Ultra I or II library prep kits, followed by paired-end sequencing on an Illumina HiSeq 2500 (for samples collected from 2013 – 2016) or single-end on a HiSeq 4000 (for samples collected after 2016) to a mean depth of 17.4 million reads (± 7.7 million SD; Table S1). Trimmed reads were mapped to the Panubis 1.0 genome (GCA_008728515.1) using the STAR 2-pass aligner [112,113]. Finally, we generated gene-level counts using HTSeq and the Panubis1.0 annotation (GCF_008728515.1) [114].…”

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

“…The genome annotation report and raw files can be found at [ 52 ]. All supporting data and materials are available in the GigaScience GigaDB database [ 53 ].…”