@article{a3cb460c004f4b35b386af9dfe20f2f7,
title = "The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species",
abstract = "The Bovine Pangenome Consortium (BPC) is an international collaboration dedicated to the assembly of cattle genomes to develop a more complete representation of cattle genomic diversity. The goal of the BPC is to provide genome assemblies and a community-agreed pangenome representation to replace breed-specific reference assemblies for cattle genomics. The BPC invites partners sharing our vision to participate in the production of these assemblies and the development of a common, community-approved, pangenome reference as a public resource for the research community ( https://bovinepangenome.github.io/ ). This community-driven resource will provide the context for comparison between studies and the future foundation for cattle genomic selection.",
keywords = "Animals, Cattle/genetics, Genome, Genomics, Polymorphism, Single Nucleotide",
author = "Smith, {Timothy P.L.} and Bickhart, {Derek M.} and Boichard, {Didier A} and Amanda Chamberlain and Appolinaire Djikeng and Yu Jiang and Low, {Wai Yee} and Hubert Pausch and Sebastian Demyda‑Peyr{\'a}s and James Prendergast and Schnabel, {Robert D} and Rosen, {Benjamin D.}",
note = "Funding Information: The BPC was established as a means to coordinate bovine global genome assembly efforts and not as a means to override, interfere, or take credit for local efforts. We encourage researchers that want to participate in the pangenome effort to join us. The initial assembly of diverse bovine species/breeds is supported by the US Department of Agriculture in part because of the historical role of the Agricultural Research Service (ARS) in the early cattle genome assembly efforts, development of methods for genome assembly, and ongoing presence in the generation of bovine genome assemblies. However, the BPC has an international steering committee and encourages open discussion of any topics related to data sharing, publication strategy, or logistics of sampling animals around the world. Resources for creating genome assemblies are available through ARS, and we are open to discussion of providing sequencing and/or assembly for breeds where local resources are not available. Any such collaborations will provide only the support requested, i.e., any combination of sequencing, assembly, data deposition, or advice. Experts participating in the consortium can assist in manuscript writing as requested. The sole requirement is that ARS-funded genome assemblies will be made public and will be available for the final pangenome representation. All collaborators will be offered the opportunity for coauthorship on manuscript(s) describing the community-standard pangenome, assuming they materially contributed to composite assemblies. Funding Information: The work presented here originated from the discussions at scientific meetings starting in 2020. We are grateful to the members of the Bovine Pangenome Consortium for their comments, suggestions, and willingness to provide samples. We thank Alexander S. Leonard for designing the bovine pangenome representation for Fig. 1. We thank the USDA for funding. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. The USDA is an equal opportunity provider and employer. Andrew Cosgrove was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team. The review history is available as Additional file 1. Funding Information: The work presented here originated from the discussions at scientific meetings starting in 2020. We are grateful to the members of the Bovine Pangenome Consortium for their comments, suggestions, and willingness to provide samples. We thank Alexander S. Leonard for designing the bovine pangenome representation for Fig. . We thank the USDA for funding. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. The USDA is an equal opportunity provider and employer. Publisher Copyright: {\textcopyright} 2023, This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.",
year = "2023",
month = jun,
day = "19",
doi = "10.1186/s13059-023-02975-0",
language = "English",
volume = "24",
pages = "1--13",
journal = "Genome Biology",
issn = "1465-6906",
publisher = "BioMed Central",
number = "1",
}