Pandas, Bats, Goats, Cats... What a genomic zoo!

At the end of 2012 some interesting paper come out providing new insights on some well known animal species revealed by whole genome sequencing.

First of all, I report a curious genetic test offered by the Davis' feline genetics lab, at University of California. Provide them with a swab from your loved cat together with $120 and they will trace back the geographic and breed ancestry of your pet. However, if your cat is a true genetic mix, they may fail in identifying a breed makeup, since most mixed cats descend from populations of so-called "random bred cats". On the contrary, if you do get a match, the UC Davis lab currently estimates that the test's breed probability matches are over 90% accurate.

I'm going now to introduce a paper published on Science by Zhang et al. providing de novo assembly of two species of bats. The authors assembled a 100x draft sequence and performed comparative analyses of two distantly related bat species, fruit bat Pteropus alecto and insectivorous Myotis davidii.  Comparison of bat genomes with other mammalian species has provided new insights into bat biology and evolution. Indeed, bats are the only known mammals capable of sustained flight and they also present other peculiar biological feature such as echo-localization, hibernation and ability to host several highly infectious pathogens (such as Ebola and SARS viruses).

The authors found signs of positive selection on different DNA damage checkpoint genes that might have contributed to development of flying ability. Moreover, their results suggest that some of the genetic adaptations that provide support for flying, such as those implied in dealing with reactive oxygen species, could also have had secondary effects on bat immunity.

Indeed, positive selection for DNA damage response genes may also have helped bats in avoid some of the negative effects of viruses, as did selection for other components of innate and adaptive immune pathways, including genes that interact with the NF-kappa-beta transcription factor family.
Both new bat genomes are missing some of the genes responsible for sensing and responding to microbial pathogens in other mammals, supporting the idea that certain features of bat immunity are distinct from those found in other animals.

Another paper published on Nature Genetics by Zhao et al. reports the low-coverage genome sequencing on 34 giant pandas from different sites in central China, providing new information on both the history and current state of panda populations and revealing three geographically-related genetic clusters within existing wild panda communities in China. Using Illumina HiSeq 2000, the team sequenced each of the giant panda genomes to a 4.7-fold depth across 91.5 percent of the 2.25 billion base panda genome, on average.

Results suggest that humans may have contributed to some of the more recent divergence events. For example the MIN-QXL panda split seems to coincide with establishment of ancient human Shu populations on a river that separates the panda populations. Human activities may have widened this divide by cutting down trees representing the animals' forest habitat. The new NGS data also provide an opportunity for researchers to further look back at population expansions and bottlenecks, as well as genetic divergence and adaptation events.
The genetic diversity observed within the three existing panda populations appears to be quite high, suggesting that it will be important, from a conservative standpoint, to consider panda's genetic adaptations to specific habitats.

A paper by Dong et al. published on Nature Biotechnology applies NGS sequencing and automated whole-genome optical mapping to reconstruct the genome of the domestic goat (Capra hircus). To date, the goat lacks a reference genome, making breeding and genetic studies of this ruminant difficult and limiting our ability to select this species for productive QTLs.  

This article is the first example of a large genome assembled de novo using whole-genome mapping technology, without the aid of traditional genetic maps. The researchers first performed NGS sequencing (USING AN Illumina platform), generating 191.5 gigabases at about 65-fold coverage. The obtained reads were assembled into 542,145 contigs and 285,383 scaffolds longer than 100 bp. Sequencing fosmid ends, the researchers were able to further increase the size of their scaffolds,generating a goat genome sequence assembly of about 2.66 gigabases, close to the estimated goat genome size of about 2.92 gigabases. The next step implied whole-genome mapping to develop even longer scaffolds that were closer to the size of chromosomes. Authors used the 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 succeeded in joining 2,090 scaffolds into 315 super-scaffolds. Finally, with cattle genome assemblies as a guide, the researchers anchored the super scaffolds to presumptive goat chromosomes obtaining 2.52 gigabases mapped to 30 pseudo-chromosomes.

One of the main reasons for raising goats is for the production wool and cashmere. To get more information on how cashmere fibers are generated, the authors sequenced the transcriptome of the primary and secondary hair follicles of an Inner Mongolia cashmere-producing goat and then mapped those reads to the goat genome they had produced. The study identified 51 genes showing at least two-fold changes in expression between the two hair follicles, many of which were keratin genes.