The bovine lactation genome: insights into the evolution of mammalian milk

Abstract

Background: The newly assembled Bos taurus genome sequence enables the linkage of bovine milk and lactation data with other mammalian genomes.

Results: Using publicly available milk proteome data and mammary expressed sequence tags, 197 milk protein genes and over 6,000 mammary genes were identified in the bovine genome. Intersection of these genes with 238 milk production quantitative trait loci curated from the literature decreased the search space for milk trait effectors by more than an order of magnitude. Genome location analysis revealed a tendency for milk protein genes to be clustered with other mammary genes. Using the genomes of a monotreme (platypus), a marsupial (opossum), and five placental mammals (bovine, human, dog, mice, rat), gene loss and duplication, phylogeny, sequence conservation, and evolution were examined. Compared with other genes in the bovine genome, milk and mammary genes are: more likely to be present in all mammals; more likely to be duplicated in therians; more highly conserved across Mammalia; and evolving more slowly along the bovine lineage. The most divergent proteins in milk were associated with nutritional and immunological components of milk, whereas highly conserved proteins were associated with secretory processes.

Conclusions: Although both copy number and sequence variation contribute to the diversity of milk protein composition across species, our results suggest that this diversity is primarily due to other mechanisms. Our findings support the essentiality of milk to the survival of mammalian neonates and the establishment of milk secretory mechanisms more than 160 million years ago.

Figure 1

Simplified phylogenetic tree illustrates relationships of representative extant Mammalian species. Estimates in millions of years ago (MYA) of origin of each major branch were derived from Bininda-Emonds et al. [2]. The two earliest splits established monotremes, (166.2 MYA), and marsupials and placentals (147.7 MYA). Approximately 50 million years pass before the origination of any extant groups, and then the four placental superorders (italicized capitals) arose within 2.4 million years of each other.

Figure 2

Distribution of milk and mammary genes across all bovine chromosomes. In this chromosome map, each of the 30 bovine chromosomes is illustrated by a pair of columns, with genomic locations of milk and mammary genes in the first column, and milk-trait QTL in the second column. Note that the milk and mammary genes are distributed across all chromosomes.

Figure 3

Heatmap of milk protein gene copy numbers across mammals. Milk protein genes were clustered by copy number using the K-means algorithm followed by seriation within each cluster. Major trends, which convey the consensus profile of the cluster, are delineated by brackets. Most milk protein genes are either present as a single copy in each mammalian genome or as a single copy in all therian genomes. Duplicated genes are expanded after platypus in either a general or a species- or clade-specific manner. Black squares indicate that the gene was not found in a particular species, yellow-green squares indicate a single copy of the gene, and red squares indicate two or more copies of the gene. Brighter red squares indicate higher copy numbers.

Figure 4

Relationships between the milk protein sequences of mammalian taxa. This milk protein consensus tree, which is incongruous with the accepted phylogeny shown in Figure 1, was derived from a super-alignment of milk protein amino acid sequences for those genes with single copy orthologs in all seven species. The numbers indicate the percent of bootstraps that support the internal branch and the length of the scale bar represents the number of amino acid substitutions per unit site.

Figure 5

Pairwise percent identity of human milk proteins with milk proteins of other species. Bars depict the average amino acid (AA) pairwise percent identity between human milk proteins and those of the species named on the x-axis. Note that human milk proteins are more similar to those of dog and bovine than to rodents and the other species depicted.

Figure 6

Average pairwise percent identities of milk and mammary genes across mammals. The distribution of average amino acid pairwise PID of amino acid sequences across the seven taxa - human, mouse, rat, bovine, dog, opossum, and platypus - is plotted for those genes in the virgin, pregnancy, lactation, involution, and mastitis mammary gene sets, the milk protein gene set, and all bovine consensus genes. Only genes with a single copy in each of the seven genomes were used for the analysis. Milk and mammary genes are more conserved across mammals than other genes in the genome.