The world of genomics is changing. It was initially about sequencing the genome a single representative individual from a particular species. Now, there's a large focus on polymorphism -- that is, sequencing multiple individuals from a single species to study the genomic variation in that species. That's well under way in humans, with HapMap and various other projects designed to generate DNA polymorphism data on a genome-wide scale.
That approach has made its way to Drosophila genomics with the publication of a paper describing polymorphism across the entire genome of D. simulans, a sibling species to D. melanogaster. The paper actually describes the genome sequences of two species: D. simulans and D. yakuba. The authors compared polymorphism in D. simulans with divergence from D. melanogaster (already sequenced), and used the D. yakuba genome sequence to polarize the differences along either the D. simulans lineage or the D. melanogaster lineage.
The D. simulans and D. yakuba genomes mark the third and fourth sequenced Drosophila genomes -- the second being the more distantly related D. pseudoobscura. If you're curious as to how long it takes to go from the initial proposal to the published sequence of a genome, check out the white papers proposing various Drosophila genome projects. The simulans/yakuba project was proposed in 2002 and then again in 2003. Over four years later, the paper has come out describing that research.
Around the same time as that white paper, another proposal was submitted to bring the total number of sequenced Drosophila genomes to twelve (making it the eukaryotic genus with the most species with completely sequenced genomes, although the diversity in this genus is equivalent to that of all eutherian mammals). See here for a list of all 12 species and their evolutionary relationships. The papers (yes, more than one -- in fact, many more than one) describing the comparisons of these 12 genomes are due out very soon.
Jonathan Eisen, who is in the same department as the two PIs who headed this project, offers a short take. Jonathan explains how this is a model for population genomics -- studying genome wide patterns of variation.
Adams MD, et al. 2000. The Genome Sequence of Drosophila melanogaster. Science 287: 2185-2195 doi:10.1126/science.287.5461.2185
Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, et al. 2007. Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans. PLoS Biol 5: e310 doi:10.1371/journal.pbio.0050310
Richards S, et al. 2005. Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution. Genome Res. 15: 1-18 doi:10.1101/gr.3059305
In fact the papers reporting the ten new Drosophila genomes are up as of 1 pm eastern time, at this link: http://www.nature.com/nature/focus/drosophila/index.html.
There's also a Plos Genetics paper from the same group that looks at evolution of gene expression in simulans, yakuba and melanogaster, compared to genomic evolution.
As I understand it, the UC Davis group assembled those three genomes using a slightly different approach to that in the "12 genomes" Nature paper. David Begun and Chuck Langley are authors on all three papers.
BioMed Central has published seven more open access articles that analyze these drosophilid genomes, you can see a summary of the articles here.