The genome sequence of the wisent (Bison bonasus)

Abstract

The wisent, also known as the European bison, was rescued from extinction approximately 80 years ago through the conservation of 12 individuals. Here, we present the draft genome sequence of a male wisent individual descended from this founding stock. A total of 366 billion base pairs (Gb) of raw reads from whole-genome sequencing of this wisent were generated using the Illumina HiSeq2000 platform. The final genome assembly (2.58 Gb) is composed of 29,074 scaffolds with an N50 of 4.7 Mb. 47.3% of the genome is composed of repetitive elements. We identified 21,542 genes and 58,385 non-coding RNAs. A phylogenetic tree based on nuclear genomes indicated sister relationships between bison and wisent and between the wisent-bison clade and yak. For 75 genes we obtained evidence of positive evolution in the wisent lineage. We provide the first genome sequence and gene annotation for the wisent. The availability of these resources will be of value for the future conservation of this endangered large mammal and for reconstructing the evolutionary history of the Bovini tribe.

The sequence and de novo assembly of the wild yak genome

“…BUSCO analysis carried out to assess the completeness of our assembly resulted in a BUSCO score of 96.8% (complete = 93.8%, single = 92.4%, duplicated = 1.4%, fragmented = 3.0%, missed = 3.2%, genes = 4,104). These results are comparable with those for the published European bison (wisent) 34 and domestic yak 4 genomes, suggesting our assembly has high quality and is quite complete.…”

The Evolution and Population Diversity of Bison in Pleistocene and Holocene Eurasia: Sex Matters

“…The analyses of the mitogenomes indicate the alternation of two bison populations with mitotypes for which the age of the MRCA can be estimated to 1.55 [1.74-1.37] Mya whereas the age of the MRCA between the Bison bonasus and Bos primigenius mitotypes can be estimated to 1.27 [1.44-1.12] Mya. This is at odds with the distance separating the genome of Bison bonasus from that of Bison bison (0.37%) and of Bos primigenius f. taurus (0.93%) and reveals that the two bison species are closely related and have diverged long after the divergence of bisontine and taurine groups [8]. The analysis of two modern B. bonasus genomes has revealed that the bison and cattle lineages started diverging about 1.7 Mya followed by an extended period of limited gene flow lasting up to about 850 kya [7].…”

“…Finally, comparative analyses of the wisent and American bison genomes revealed the proximity of these two genomes compared to the cattle genome [8]. The percentage of nucleotide differences between the two bison genomes was low, 0.37%, while either of these genomes was equally distant to the cattle genome with 0.93% differences.…”

“…Following Gautier et al [7], the estimation of divergence between the B. bonasus and B. bison lineages was performed under the coalescent hidden Markov models (CoalHMM) framework [40] considering an isolation (I) model that assumes that the ancestral population split into two populations at time τ into the past [41]. To that end, the alignments of the B. bison genome assembly (GCA_000754665.1) onto the recently published B. bonasus assembly by Wang et al [8] were extracted from the synteny alignments (bovine.SixSpecies.maf file) accompanying the latter publication using the program MafFilter [42]. The bovine sequence was used as a reference to merge the identified synteny blocks between the two lineages with a maximum distance of 50 kb between them and a minimal size of 10 Mb.…”

“…For this, genomic information from both modern and ancient specimens is needed. This situation was achieved only around 2016 when the genome of the extant B. bonasus (wisent) was sequenced [7,8], partial genomic information from historical specimens was obtained [9] and ancient Bison specimens from the Upper Pleistocene and the Holocene in Eurasia yielded sequencing results [10][11][12]. As a consequence, 2016 was declared the year of the wisent [13].…”