The genome sequence of taurine cattle: a window to ruminant biology and evolution

Abstract

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

Fig. 1

Protein orthology comparison among genomes of cattle, dog, human, mouse and rat (Bos taurus, Canis familiaris, Homo sapiens, Mus musculus, Rattus norvegicus, representing placental mammals), opossum (Monodelphis domestica; marsupial), and platypus (Ornithorhynchus anatinus; monotreme). (A) The majority of mammalian genes are orthologous, with over half preserved as single-copies (dark blue); a few thousand have species-specific duplications (blue); another few thousand have been lost in specific lineages (orange). We also show those lacking confident orthology assignment (green), and those that are apparently lineage specific [unique (white)]. Placental-specific orthologs are shown in pink. Single- or multiple-copy genes were defined on the basis of representatives in human, bovine or dog, mouse or rat, and opossum or platypus. (B) Venn diagram showing shared orthologous groups (duplicated genes were counted as one) between laurasiatherians (cattle and dog), human, rodents (mouse and rat), and non-placental mammals (opossum and platypus) on the basis of the presence of a representative gene in at least one of the grouped species (as in A). (C) Distribution of ortholog protein identities between human and the other species for a subset of strictly conserved single-copy orthologs. (D) A maximum likelihood phylogenetic tree using all single-copy orthologs supports the accepted phylogeny and quantifies the relative rates of molecular evolution expressed as the branch lengths.

Fig. 2

Examples of evolutionary breakpoint regions (EBRs). Ferungulate- artiodactyl- and primate-specific EBRs on HSA1 at 175-247 Mbp (other lineage-specific EBRs not shown). Homologous synteny blocks constructed for the macaque, chimp, cattle, dog, mouse, rat and pig genomes were used for pair-wise comparisons (4). White areas correspond to EBRs. Arrows to the right of the chromosome ideogram indicate positions of representative cattle-specific, artiodactyl-specific (specific to the chromosomes of pigs and cattle), ferungulate-specific (cattle, dog and pig), primate-specific (human, macaque, chimp), and hominoid-specific (human and chimp) rearrangements. Opossum is shown as an outgroup to the eutherian clade, which allows classification of ferungulate-specific EBRs.