Thursday, January 21, 2010

More genomes than I know what to do with

OK, I give up. I've been going over the maize genome in my spare time, which is why I haven't blogged about it since I don't really have any spare time lately. Then I saw three parasitoid wasp genomes in Science, and I thought that'd be cool to talk about. Then the soybean genome was published in Nature, and this week, it's the panda genome also in Nature. So I give up. I'm still holding out hope that I'll be able to do something substantive for the maize genome, but for the others, I'm just going to give a brief rundown.

Parasitoid wasps lay their eggs on other critters, and when they hatch, the young gradually consume and eventually kill their hosts. If I recall correctly, this was one of the sticking points that Darwin mentioned: How could natural theologians argue for a loving God when such unpleasant things like parasitoids exist? Three species of the parasitoid wasp genus Nasonia now have their genomes published. What do we find? About 17,o00 genes (60% are homologous to humans) and abundant transposable elements. The authors also reported evidence of gene transfer from Pox viruses and the bacterial symbiont Wolbachia. Their discussion of the comparative genomics mostly focused on nucleotide substitutions.

The soybean (Glycine max) genome sequence is redundant. It's 950 Mb in 20 chromosomes and 46,000 genes, with whole genome duplications predicted to have happened twice in its history. That means that 75% of its genes are present in multiple copies, but they're mostly distributed in regions of high gene density on the ends of the chromosomes. The central parts of the chromosomes are dense with transposable elements and recombine at a lower rate than the gene-rich chromosome ends. Repetitive sequences make up almost 60% of the soybean genome. Not surprisingly, the chromosomes were significantly reorganized after the genome duplications, yet more evidence that genomes are highly fluid structures and probably not designed for perfect replication.

And then there's Ailuropoda, the giant panda. It's got a 2.25 Gb genome with about 36% repetitive sequences and a predicted set of 21,000 genes. Since this genome was sequenced using "next generation" technology, a lot of the paper is about the sequencing and validation techniques, which I'm not really going to talk about. What I found especially interesting was this little tidbit:
We did not find any homologues of digestive cellulase genes, including endoglucanase, exoglucanase and beta-glucosidase, indicating that the bamboo diet of the panda is unlikely to be dictated by its own genetic composition, and may instead be more dependent on its gut microbiome.
Joe Francis has been suggesting for years that microbes could significantly contribute to the diversification of life and the origin of biological novelties. So it's interesting that the panda might owe it's peculiar diet to microbes.

Nasonia Genome Working Group. 2010. Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species. Science 327:343-348.

Schmutz et al. 2010. Genome sequence of the palaeopolyploid soybean. Nature 463:178-183.

Li et al. 2010. The sequence and de novo assembly of the giant panda genome. Nature