NEW YORK (GenomeWeb News) – A team of researchers led by Wen Wang from the Chinese Academy of Sciences has generated a de novo genome sequence of the domestic goat, Capra hircus, by combining next-generation sequencing with whole-genome mapping.
As the researchers noted in a Nature Biotechnology article posted online last night, the goat lacked a reference genome, making breeding and genetic studies of the ruminant difficult.
Further, optical mapping had previously been limited to mainly bacterial genome assembly or to sequence finishing as mapping methods include manual steps and are relatively low-throughput. Here, though, the researchers said that they were able to quickly get to an assembled genome that could then be annotated and analyzed to learn more about, for example, hair follicles in cashmere-producing goats.
"The goat genome is, to our knowledge, the first large genome to be sequenced and assembled de novo using whole-genome mapping technology, demonstrating that this approach can be used to obtain a highly contiguous assembly for a large genome without the aid of traditional genetic maps," Wang and his colleagues wrote.
To develop the goat genome, the researchers first performed Illumina sequencing on genomic DNA obtained from a female Yunnan black goat, generating 191.5 gigabases of reads at about 65-fold coverage. Those reads were then assembled using SOAPdenovo software into 542,145 contigs and 285,383 scaffolds longer than 100 basepairs. Then, by sequencing fosmid ends, the researchers further refined their scaffolds, increasing their size, and generated a goat genome sequence assembly of about 2.66 gigabases — close to the estimated goat genome size of about 2.92 gigabases.
The researchers next turned to whole-genome mapping to develop even longer scaffolds that were closer to the size of chromosomes. To do this, they used OpGen's Argus system to develop a single-molecule restriction map using genomic DNA from the same goat.
Then using the company's GenomeBuilder hybrid assembly software to bring together the short-read generated scaffolds with the single-molecule restriction maps, the researchers then joined 2,090 scaffolds into 315 super-scaffolds. And with cattle genome assemblies as a guide, the researchers anchored the super scaffolds to presumptive goat chromosomes. They were able to anchor 2.52 gigabases to 30 pseudo-chromosomes. The domestic goat, they noted, has 29 pairs of autosomes and a pair of sex chromosomes.
Diving into the goat genome, the researchers pointed out that it contains transposable elements similar to those of cattle, though also a few transposable element classes that diverged recently from cattle. Additionally, regions of the goat genome appear to have undergone expansions and contractions. In particular, they reported an expansion in the ferritin heavy chain gene family, which they postulated might help the goat detoxify iron it ingests while foraging.
Many of the approximately 22,175 protein-coding genes the researchers found in the goat genome are orthologous to those found in cattle and 16,771 are orthologous between humans and goats. By constructing a phylogenetic tree including goats, cattle, horses, dogs, opossums, and humans, they estimated that goats and cattle shared a common ancestor about 23 million years ago.
Forty-four genes, some of which are related to the immune system or to pituitary hormones, appeared to be under positive selection and were evolving rapidly in goat. Cattle, too, have immune system genes that appear to be under selection.
"Rapid evolution of pituitary hormones may be related to differences between goats and cattle in milk production, development rates of the fetus and/or hair variation, which are traits associated with pituitary hormomes," Wang and his colleagues wrote.
To get a firmer grasp of how cashmere fibers are generated by goats, the researchers sequenced the transcriptome of the primary and secondary hair follicles — cashmere comes from hair produced by secondary hair follicles — of an Inner Mongolia cashmere-producing goat. They then mapped those reads to the goat genome they had produced, finding 51 genes that showed at least two-fold changes in expression between the two hair follicles, many of which were keratin genes.
"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," Xun Xu, the deputy director of BGI and a co-author of the paper, said in a statement. "The transcriptomic analysis on the primary and secondary follicles will open a new way for better improving the quality cashmere wool."