The Bovine Pangenome Consortium is an international scientific research collaboration that was designed to organize genome assembly efforts within the tribe Bovini. Our goals are to provide the sequencing resources and bioinformatics expertise to collaborative groups interested in generating an assembly of their favorite species or breed of Bovini.
The creation of reference-quality genome assemblies based on long-read platforms has recently become sufficiently cost-effective to consider generating at least one example for many of the over 700 existing cattle breeds, and other species in the Bovidae phylogeny. We have applied both Pacific Biosciences Sequel and Oxford Nanopore PromethiION instruments to demonstrate successful high-quality assemblies of several breeds, species, and hybrids. We pioneered a method to create the highest-quality assemblies, called trio-binning, which depends on F1 crosses between breeds and sampling of the parents. Where possible, this is the most efficient method since one can achieve very high contiguity for two breeds from sequencing reads of the F1. High quality assemblies, albeit less efficient, can also be generated from individual breeds where creation of F1 and sampling of parents is not feasible or practical.
- Generate high-quality (haplotype-resolved) references for bovid species
- Identify species-specific genetic loci
- Enhance genomic tools and resources for bovids
Our short-term aim is to generate enough high quality reference assemblies of bovid species to fuel the next generation of comparative assembly projects. We want to specifically identify species- and breed-specific variation that underlies phenotypic diversity in bovids. If successful, our next aim is to assist with development or to create new resources for bovid genomics.
In short: if you contribute samples to our consortium, you own the assemblies, data and analysis. All that we ask in return is acknowledgment on your future projects/publications.
To facilitate our overall project goals, we will ask your permission to use the assemblies we generate in our priority comparative genomics project, and we will grant you acknowledgment as a full fledged consortium member in the publication.