Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.
USDA, ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, USA.
J Hered. 2021 Mar 29;112(2):174-183. doi: 10.1093/jhered/esab003.
Bison are an icon of the American West and an ecologically, commercially, and culturally important species. Despite numbering in the hundreds of thousands today, conservation concerns remain for the species, including the impact on genetic diversity of a severe bottleneck around the turn of the 20th century and genetic introgression from domestic cattle. Genetic diversity and admixture are best evaluated at genome-wide scale, for which a high-quality reference is necessary. Here, we use trio binning of long reads from a bison-Simmental cattle (Bos taurus taurus) male F1 hybrid to sequence and assemble the genome of the American plains bison (Bison bison bison). The male haplotype genome is chromosome-scale, with a total length of 2.65 Gb across 775 scaffolds (839 contigs) and a scaffold N50 of 87.8 Mb. Our bison genome is ~13× more contiguous overall and ~3400× more contiguous at the contig level than the current bison reference genome. The bison genome sequence presented here (ARS-UCSC_bison1.0) will enable new research into the evolutionary history of this iconic megafauna species and provide a new tool for the management of bison populations in federal and commercial herds.
野牛是美国西部的标志性动物，也是一种具有生态、商业和文化重要性的物种。尽管今天的数量达到了数十万头，但该物种仍然存在保护问题，包括 20 世纪之交的严重瓶颈对遗传多样性的影响，以及与家养牛的基因渗透。遗传多样性和混合情况最好在全基因组范围内进行评估，这需要高质量的参考基因组。在这里，我们使用野牛-西门塔尔牛（Bos taurus taurus）雄性 F1 杂种的长读段三重组装，对美洲野牛（Bison bison bison）的基因组进行测序和组装。该雄性单倍型基因组是染色体规模的，总长度为 26.5Gb，跨越 775 个支架（839 个重叠群），支架 N50 为 87.8Mb。与现有的野牛参考基因组相比，我们的野牛基因组在整体上更加连续，连续度提高了约 13 倍；在重叠群水平上的连续度提高了约 3400 倍。本文提供的野牛基因组序列（ARS-UCSC_bison1.0）将使人们能够对这种标志性巨型动物物种的进化历史进行新的研究，并为联邦和商业牛群中野牛种群的管理提供新的工具。
