De novo assembly and annotation of the North American bison (Bison bison) reference genome and subsequent variant identification

Abstract

Genomic tools have improved the ability to manage bison populations and enhanced efforts to conserve this iconic species. These tools have been particularly useful for detecting introgression of cattle genome within bison herds but are limited by the need to use the cattle genome as a surrogate for mapping reads. This complicates efforts to distinguish the species of origin of chromosomal segments in individual bison at the genomic level. An assembly (Bison_UMD1.0) based on 75X genome coverage by Illumina and 454 reads was generated using the MaSuRCA assembler, generating a 2.81 Gigbases de novo reference genome from American bison. Comparison of bison and domestic cattle references identified 28 443 364 single nucleotide variants and 2 627 645 insertions/deletions distinguishing the species. Sequence alignment of an additional 12 modern bison samples and two historic bison samples to domestic cattle and bison references provides a dataset of genomic variants defining the different species and within-species variation. This first annotated draft assembly represents a resource for the management and conservation of bison, as well as a means to study the effects on the genome of interspecies hybridization. The comparisons of historical bison sequences with the new bison reference identified genomic differences between modern and pre-population bottleneck bison. The results support the application of genomics to enhance future research on disease, the establishment of satellite conservation herds and insight into bison and cattle speciation. The first genome assembly for bison and dataset provides a foundation that can be built upon as genetic technologies improve over the years.

Genomic evaluation of hybridization in historic and modern North American Bison (Bison bison)

“…Multiple recent and ongoing investigations to fully annotate the bison genome 37 , 38 will provide the necessary bison genomic reference information to investigate specific regions and genes and identify signatures of genomic selection. Due to the size and uniquely distributed genomic regions of introgression, methods utilizing reduced representation such as RADseq would likely not detect all regions.…”

Wisent genome assembly uncovers extended runs of homozygosity and a large deletion that inactivates the thyroid hormone responsive gene

“…We hypothesized that deletion of the first exon including the entire protein-coding sequence in wisent and bison represents a functional knock-out of THRSP . Transcriptomic data are not available for wisent but bison RNA-seq data are publicly available for liver, spleen, lung, skeletal muscle, kidney and supramammary lymph node tissues (Dobson et al, 2021). We mapped the bison transcriptomes to the Bos taurus taurus reference sequence and, as expected given the deletion, did not detect expression of the coding exon of THRSP ( Supplementary Fig.…”

A draft genome of Drung cattle reveals clues to its chromosomal fusion and environmental adaptation

“…To estimate Drung cattle speciation times and explore their genetic relationships, we constructed a phylogenetic tree based on 2301 single-copy gene families of six species in the Bovinae subfamily ( B. frontalis, B. taurus 8 , B. indicus 9 , B. grunniens 12 , B. bubalis 13 , and B. bison 10 ), with the other five mammals ( Ovis aries 28 , Capra hircus 29 , Pantholops hodgsonii 30 , Ceratotherium simum simum 31 , and Homo sapiens 32 ) as the outgroup (Fig. 2a ).…”

“…We selected six species in the Bovinae subfamily ( B. frontalis , B. taurus 8 , B. indicus 9 , B. grunniens 12 , B. bubalis 13 , and B. bison 10 ) and other five mammals ( O. aries 28 , C. hircus 29 , P. hodgsonii 30 , C. simum simum 31 , and Homo sapiens 32 ) as the outgroup for phylogenetic analysis of the B. frontalis . The genes and protein-coding sequences of the ten mammalian species downloaded from NCBI and our B. frontalis assembly genome were used to define gene families.…”

“…To date, the genomes of several bovine species under the tribe Bovini , including B. taurus (cattle) 8 , B. indicus (zebu) 9 , Bison bison (American bison) 10 , Bison bonasus (wisent) 11 , Bos grunniens (yak) 12 , Bubalus bubalis (water buffalo) 13 – 15 and Syncerus caffer (African buffalo) 16 , 17 , have been sequenced and annotated (Supplementary Data 1 ). High-quality reference genome sequences and gene annotations can be used as genomic resources to facilitate further functional and evolutionary studies.…”