NEW YORK (GenomeWeb News) - In a study appearing online today in Science, members of the International Sheep Genomics Consortium described findings from a genome sequencing study of sheep, Ovis aries — a resource that's being used to explore the basis of the animal's digestive capabilities, woolly coat, metabolism, and more.
In addition to that high-quality reference genome, the first so far for sheep, the team generated transcriptome sequences representing 40 sheep tissues, which contributed to its subsequent analysis of sheep features.
"Sheep were one of the first animals to be domesticated for farming and are still an important part of the global agricultural economy," The Roslin Institute's Alan Archibald, a co-corresponding author on the study, said in a statement. "Understanding more about their genetic make-up will help us to breed healthier and more productive flocks."
With transcript sequence data from skin and other samples, for example, the researchers identified ties between lipid metabolism and wool production. The so-called rumen chamber of the sheep's four-chambered stomach, meanwhile, showed elevated expression of genes believed to cross link keratin, consistent with a role for keratin in not only sheep skin, wool, and hoof formation, but also in the evolution of ruminant digestion in the animal.
Like cattle, sheep are known for noshing on plant material that's not especially nutritious for other animals, deriving useful proteins from lignocellulose-laden plant material with the help of fermentation and microbes in the rumen. Specialized features of the sheep metabolism go to work on volatile fatty acids that gut bugs produce during that process.
But sheep seem to have other unusual metabolic capabilities as well, the study's authors explained. For instance, they noted that fatty acid metabolism features seem to feed into the production of wool fibers, which contain lanolin, or "wool grease," formed from waxy ester molecules.
To explore these and other features of sheep biology and evolution, the researchers sequenced genomic DNA from two Texel sheep, a breed that's experienced selection for muscle hypertrophy.
The team placed the resulting sequences into an assembly that spans 2.61 billion bases of the sheep genome to an average depth of around 150-fold. That assembly, dubbed Oar v3.1, covers around 99 percent of the sheep's 26 autosomal chromosomes and X chromosome.
By adding in transcript sequence data for almost 100 samples taken from 40 sheep tissue types, the researchers looked at the protein-coding genes present in the sheep genome and their relationship to those found in 11 other ruminant and non-ruminant mammals.
In particular, the group detected more than 300 protein sub-families that are either specific to ruminant animals or mushroomed in that lineage. Meanwhile, a phylogenetic analysis of the animal genomes pointed to a split between goats and sheep at roughly the same time that so-called C4 grasses — which fix carbon by forming a four carbon molecule — started becoming more prominent.
The comparison pointed to genes that have undergone copy number or tissue-specific expression shifts in sheep, the researchers reported. It also provided new details about the keratin-related proteins encoded in the sheep version of the mammalian epidermal development complex, which appears to influence the animal's skin, wool, and even digestive features.
In rumen tissue, for example, they tracked down a highly expressed gene called TCHHL2 that appears to code for a previously unknown keratin cross-linking protein. And TCHHL2 was not the only keratin player present in the rumen. The keratin and structure-related gene PRD-SPRRII and others resembling it were also found at elevated expression in the rumen.
Yet another epidermal development complex gene called LCE7 that showed signs of positive selection in sheep was more highly expressed in sheep skin tissue rather than the rumen, the researchers found, and is suspected of contributing to wool development.
Results of their subsequent analyses suggest wool production also benefits from fatty acid metabolism involving skin-expressed lipid enzymes, including some that are expressed in the intestine of other, non-ruminant animals such as humans.
Together, the study's authors noted, the genomic data pointed to complex interactions between sheep diet, digestion, and metabolism that impact a range of physical features in the animal, from their outer coat to inner ruminations.