IN a collaborative study published online Dec. 24 in Nature Biotechnology, researchers from the Kunming Institute of Zoology in China, the Chinese Academy of Sciences, the Beijing Genomics Institute (BGI) and other institutes have completed the first genome sequence of the domesticated goat by a robust approach integrated with next-generation sequencing and whole-genome mapping technologies.
The goat genome is the first reference genome for small ruminant animals and may help to advance the understanding of distinct ruminants' genomic features from non-ruminant species, BGI said. This work also yields a valuable experience for facilitating the de novo assemblies of large, complex genomes in the future.
In many regions, goats are an important member of the livestock industry, providing milk, meat and fiber, and they have many unique biological features. They are an important economic resource in many developing countries around the world, especially in China and India.
However, despite their agricultural and biological importance, breeding and genetic studies of goats have been hampered by the lack of a high-quality reference genome sequence, BGI said.
The goat genome sequence will be useful for facilitating the identification of single-nucleotide polymorphism markers for marker-assisted breeding and improving the utility of the goat as a biomedical model and bioreactor, the announcement said.
With the availability of next-generation sequencing, draft assemblies are easy to generate now, but finishing a sequence on the chromosome level remains difficult, BGI explained.
In this study, the results show that a single next-generation sequencing platform, when combined with whole-genome mapping technology, could produce a finished assembly much faster and with higher quality than other currently available mapping strategies such as bacterial artificial chromosome or fluorescence in situ hybridization.
"This independent technology provides not only the validation of the genome sequencing but also provides the large-scale chromosome structure information that cannot be detected by sequencing," BGI-Shenzhen deputy director Xun Xu said. "The experience in these genome assembly projects shows that the physical whole genome map should be the standard for any reference genome to be assembled in the future."
BGI said transposable elements -- major components of a mammalian genome that contribute to gene evolution -- in the goat genome are similar to those of cattle and contain large numbers of ruminant-specific repeats, such as SINE-tRNA and SINE-BovA.
It has been reported that SINE-BovA repeats expanded primarily in the cattle genome. However, in this study, researchers found that the SINE-tRNA repeat expanded specifically in the goat genome.
Through constructing a phylogenetic tree among goats, cattle, horses, dogs, opossums and humans, researchers found that the goat shared a common ancestor with cattle about 23 million years ago, BGI said, adding that further comparison analysis revealed 44 rapidly evolving genes under positive selection, seven of which are immune-related genes and three pituitary hormone or related genes.
The immune-related genes identified also exist in cattle. The findings suggest that the rapid evolution of pituitary hormones may be related to the different features between goats and cattle in milk production, development rates of the fetus and/or hair variation.
"The goat reference genome is an important stepping stone in the molecular breeding of cashmere goats and will help to advance the comparative studies on ruminants," Xu concluded.