Dataset Information

A Reference Genome Assembly of American Bison, Bison bison bison.

ABSTRACT: 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.

SUBMITTER: Oppenheimer J

PROVIDER: S-EPMC8006816 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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A Reference Genome Assembly of American Bison, Bison bison bison.

Oppenheimer Jonas J Rosen Benjamin D BD Heaton Michael P MP Vander Ley Brian L BL Shafer Wade R WR Schuetze Fred T FT Stroud Brad B Kuehn Larry A LA McClure Jennifer C JC Barfield Jennifer P JP Blackburn Harvey D HD Kalbfleisch Theodore S TS Bickhart Derek M DM Davenport Kimberly M KM Kuhn Kristen L KL Green Richard E RE Shapiro Beth B Smith Timothy P L TPL

The Journal of heredity 20210301 2

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 bin ...[more]

PMID: 33595645

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Project description:During the late nineteenth century North American bison underwent a significant population bottleneck resulting in a reduction in population size of over 99% and a species-level near-extinction event. Factors responsible for this destruction included indiscriminate killing, loss of access to suitable habitat, and diseases. At the nadir of this population crash, very few wild plains bison survived and were restricted to Yellowstone National Park, USA and a small number of wild wood bison remained in Wood Buffalo National Park, Canada. However, most surviving bison in the late 1800's were maintained by cattle ranchers in private herds where hybridization between bison with various breeds of domestic cattle was often encouraged. Over the last 20 years, the legacy of this introgression has been identified using mitochondrial DNA and limited nuclear microsatellite analyses. However, no genome-wide assessment has been performed, and some herds were believed to be free of introgression based on current genetic testing strategies. Herein, we report detailed analyses using whole genome sequencing from nineteen modern and six historical bison, chosen to represent the major lineages of bison, to identify and quantitate signatures of nuclear introgression in their recent (within 200 years) history. Both low and high coverage genomes provided evidence for recent introgression, including animals from Yellowstone, Wind Cave, and Elk Island National Parks which were previously thought to be free from hybridization with domestic cattle. We employed multiple approaches, including one developed for this work, to identify putative cattle haplotypes in each bison genome. These regions vary greatly in size and frequency by sample and herd, though we detected domestic cattle introgression in all bison genomes tested. Since our sampling strategy spanned across the diversity of modern bison populations, these finding are best explained by multiple historical hybridization events between these two species with significant genetic recombination over the last 200 years. Our results demonstrate that whole genome sequencing approaches are required to accurately quantitate cattle introgression in bison.

Project description:BackgroundBison (Bison bison) and cattle (Bos taurus) are closely related (can interbreed) and they also share many parasites. Cattle are commonly infected with one or more of the eight named Sarcocystis species: Sarcocystis hirsuta, S. cruzi, S. hominis, S. bovifelis, S. heydorni, S. bovini, S. sigmoideus and S. rommeli. Among these, the full life-cycle is known only for S. cruzi. Sarcocystis cruzi (transmitted via canids) is recognized as the most pathogenic Sarcocystis species, causing abortion, low milk yield and poor body growth. It has been experimentally cross-transmitted from cattle to bison and vice versa.MethodsWe tested 200 bison tongues from three commercial sources (farms) (Nebraska #141; South Dakota #36; New Jersey and Pennsylvania #23). Frozen tongues were purchased and examined for Sarcocystis infection using light microscopy, histology and quantitative PCR (qPCR) targeting 18S ribosomal DNA (18S rRNA) of S. cruzi. Lesions associated with degenerating sarcocysts were studied. The intensity of Sarcocystis infection in histological sections was quantitated.ResultsSarcocystis cruzi-like infections were detected in 129 of 141 (91.5%) tongues from Nebraska, 36 of 36 (100%) tongues from South Dakota and two of 23 (8.6%) tongues from New Jersey and Pennsylvania. Sarcocysts were detected in histological sections stained with hematoxylin and eosin in 167 of 200 samples. Light microscopy examination revealed that the sarcocysts had thin walls (< 1 µm thick) and appeared to be S. cruzi. However, in two samples, sarcocysts had thicker walls measuring up to 2.3 µm wide and 154 µm long and the sarcocyst wall was not striated; these two samples could not be characterized further. In three tongues, degenerating sarcocysts were recognized; two of these were associated with thick-walled sarcocysts. Molecularly, S. cruzi from bison was identical to that in cattle.ConclusionsIn the present study of bison tongues, S. cruzi was the only species identified in bison using both molecular and morphological methods. An unidentified species of Sarcocystis found in two bison samples needs further study.

Dataset Information

A Reference Genome Assembly of American Bison, Bison bison bison.

Publications

A Reference Genome Assembly of American Bison, Bison bison bison.

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