Graph construction method impacts variation representation and analyses in a bovine super-pangenome

Abstract

Background Several models and algorithms have been proposed to build pangenomes from multiple input assemblies, but their impact on variant representation, and consequently downstream analyses, is largely unknown. Results We create multi-species super-pangenomes using pggb, cactus, and minigraph with the Bos taurus taurus reference sequence and eleven haplotype-resolved assemblies from taurine and indicine cattle, bison, yak, and gaur. We recover 221 k nonredundant structural variations (SVs) from the pangenomes, of which 135 k (61%) are common to all three. SVs derived from assembly-based calling show high agreement with the consensus calls from the pangenomes (96%), but validate only a small proportion of variations private to each graph. Pggb and cactus, which also incorporate base-level variation, have approximately 95% exact matches with assembly-derived small variant calls, which significantly improves the edit rate when realigning assemblies compared to minigraph. We use the three pangenomes to investigate 9566 variable number tandem repeats (VNTRs), finding 63% have identical predicted repeat counts in the three graphs, while minigraph can over or underestimate the count given its approximate coordinate system. We examine a highly variable VNTR locus and show that repeat unit copy number impacts the expression of proximal genes and non-coding RNA. Conclusions Our findings indicate good consensus between the three pangenome methods but also show their individual strengths and weaknesses that need to be considered when analysing different types of variants from multiple input assemblies.

Taurine pangenome uncovers a segmental duplication upstream ofKITassociated with depigmentation in white-headed cattle

“…We also observe that the colored-head associated “deletion” allele (with respect to the Hereford-based ARS-UCD1.2 reference) is extremely common and therefore most likely represents the ancestral bovine KIT allele. In addition to the 12 color-headed taurine breeds examined here, we identified the same 20.6 kb deletion in optical mapping data from six Sanga (African taurine x indicine) cattle breeds (Talenti et al, 2022), as well as in pangenomes containing three further taurine breeds (Jang et al, 2023) and two indicine breeds and three non-cattle bovids (Leonard et al, 2023a) (Supplementary Table 3). Thus, it is very likely that the color-headed phenotype is the ancestral state, while the white-headed phenotype has evolved by mutation(s).…”

“…A Simmental haplotype (SIM_2) produced through trio-binning required some manual curation to correct an under assembled region of interest introduced later (see Methods). We further collected nine publicly available long read-based haplotype assemblies including a Simmental (Heaton et al, 2021) and a Highland (Rice et al, 2020) haplotype assembled with ONT reads, as well as seven HiFi-assembled Brown Swiss and Original Braunvieh haplotypes (Leonard et al, 2023a, 2023b, 2022) (Supplementary Table 1). We also included the cattle reference genome (ARS-UCD1.2) which was assembled from PacBio Continuous Long Read data collected from a Hereford cow (Rosen et al, 2020).…”

“…We used the merged VCF file of structural variants called from optical mapping data from (Talenti et al, 2022) to investigate the presence of the candidate SV in taurine and indicine cattle. We also examined the 14-breed pangenome from (Jang et al, 2023), first realigning the constituent assemblies to the pangenome using minigraph --call (v0.20) (Li et al, 2020), followed by examining the paths taken through bubble variation as described in (Leonard et al, 2023a). We also aligned PacBio Continuous Long Read data from the Simmental, Holstein, Hereford, Original Braunvieh and Evolèner breeds available at the study accession PRJEB72196 to the reference genome using minimap2 with the “map-pb” preset.…”

Pangenome graphs improve the analysis of structural variants in rare genetic diseases

“…Here, we relied on a progressive pangenome construction technique where each proband genome was added one at a time, revealing the SVs that are common and those that are less common. Such a progressive method is efficient, but it depends on the order of genomes that are incorporated and might miss events such as translocations 26 . An alternative could be a reference-free method such as the PanGenome Graph Builder 15 , but further developments would be needed to implement adding genomes to an existing pangenome.…”

Pig pangenome graph reveals functional features of non-reference sequences

“…The fundamental units of a graph genome are nodes, which represent sequence segments interconnected by edges (also known as links) that depict the relationships between various sequence segments [ 13 ]. Pangenome graphs have been well applied to human and plant genomes [ 14 , 17 – 20 ], but their utilization on farm animals (except cattle) is still few [ 11 , 21 – 23 ]. To date, we have only found one study reporting the pig pangenome graph.…”