Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle

Abstract

Background: The gaur (Bos gaurus) is the largest extant wild bovine species, native to South and Southeast Asia, with unique traits, and is listed as vulnerable by the International Union for Conservation of Nature (IUCN).

Results: We report the first gaur reference genome and identify three biological pathways including lysozyme activity, proton transmembrane transporter activity, and oxygen transport with significant changes in gene copy number in gaur compared to other mammals. These may reflect adaptation to challenges related to climate and nutrition. Comparative analyses with domesticated indicine (Bos indicus) and taurine (Bos taurus) cattle revealed genomic signatures of artificial selection, including the expansion of sperm odorant receptor genes in domesticated cattle, which may have important implications for understanding selection for male fertility.

Conclusions: Apart from aiding dissection of economically important traits, the gaur genome will also provide the foundation to conserve the species.

Keywords: Domestication; Gaur; Genome assembly; Odorant receptors; Sperm.

Fig. 1

Genome assembly of gaur and comparison with cattle. a A picture of a female herd mate that looks similar to the sequenced gaur individual. b Flowchart of assembly procedure. c A circos plot of B. gaurus chromosome scaffold matching to B. taurus (ARS-UCD1.2)

Fig. 2

Number of assembly gaps and repeats resolution. a Barplot showing the number of gaps in chromosomes or scaffolds of gaur compared to other high quality mammalian assemblies. b Violin plot of LINE/L1, LINE/RTE-BovB, and satellite/centromeric repeat families. Only repeats that are larger than 2.5 kb are used in the plot

Fig. 3

Gene family expansion and contraction across the nine study species. a The number of gene families involved in expansions and contractions are shown in red and blue, respectively, with the size of each node representing the significance of the expansion or contraction. Human was the outgroup used for this analysis. The species tree was based on the Species Tree Inference from All Genes (STAG) method. b The ancestor chart of the nine GO terms of genes from gene families with significant gene gains and losses in gaur. The terms are coloured in a gradient of increasing redness to indicate significance of enrichment.

Fig. 4

Expansion of sperm odorant receptors in cattle. a Microsynteny plot showing a divergent region on chromosome 15 that contains odorant receptors between gaur, indicine and taurine breeds. The gaur coordinates are on chromosome 15, from 46,744,541 to 45,417,056 against the homologous taurine cattle (ARS-UCD1.2) chromosome between positions 78,791,037 to 80,120,961. The indicine cattle (UOA_Brahman_1) coordinates are chromosome 15, from 3,748,952 to 5,140,465. b Gene gains and losses of odorant receptors from six PANTHER gene families (PTHR24242, PTHR24248, PTHR26452, PTHR26453, PTHR48002, PTHR48018), which represent all odorant receptors gene families flanked by the gene PTPRJ and LRRC55 on chromosome 15, mapped onto species phylogenetic tree

Fig. 5

Heat map of gene expression in the surrounding of the divergent region in chromosome 15. Genes on the x-axis are arranged as per their gene order on chromosome 15, starting from gene ENSBTAG00000018742 (MTCH2) at position 77,409,614, ending with gene ENSBTAG00000020285 (PRG3) at position 80,584,707. Refer to Supplementary Table 11 for annotation details of these genes. The y-axis shows the 91 tissues from Cattle Gene Atlas. Expression values are given in FPKM