Genome biology

A transcriptomic analysis of the phylum Nematoda. Parkinson, J. et al. Nature Genet. 36, 1259–1267 (2004)

Although an incredible amount of information is available for Caenorhabditis elegans, little is known about the other members of the diverse phylum to which this worm belongs. Parkinson and colleagues have now created >250,000 ESTs and used them to type the transcriptional diversity of 30 nematode species, including many parasites. More than half the >90,000 genes studied were found only in nematodes, and the authors identified tens of thousands of potential targets for drug and vaccine development.

Evolution

Ciliary photoreceptors with a vertebrate-type opsin in an invertebrate brain. Arendt, D. et al. Science 306, 869–871 (2004)

Invertebrates predominantly use rhabdomeric photoreceptors (PRs) for vision, whereas vertebrates use ciliary receptors. The marine ragworm Platynereis dumerilii has rhabdomeric cells in its eyes but, as this work has found, has ciliary PRs in the brain. These 'deep brain' ciliary PRs express an opsin photopigment that is orthologous to vertebrate ciliary opsins. The authors suggest that deep brain PRs are involved in the control of photoperiodicity, and they reevaluate the evolution of PR cells since the last common ancestor of vertebrates and invertebrates.

Genome biology

Global identification of human transcribed sequences with genome tiling arrays. Bertone, P. et al. Science 11 November 2004 (doi:10.1125/science.1103388)

The large size of the mammalian genome presents a special obstacle to a comprehensive investigation of coding sequences, but Bertone et al. have now produced a draft expression map for the entire human genome using high-density microarrays that contain more than 51 million oligonucleotide probes and representing ∼1.5 Gb of non-repetitive genomic DNA. The authors identified more than 10,000 novel transcribed regions, revealing a more extensive and diverse set of expressed sequences than previously annotated, and were able to confirm that many of the genes predicted by sequencing projects are indeed transcribed.

Gene mapping

A single-nucleotide polymorphism tagging set for human drug metabolism and transport. Ahmadi, K. R. et al. Nature Genet. 19 December 2004 (doi:10.1038/ng1488)

David Goldstein and colleagues have genotyped 750 SNPs in European and Japanese populations to identify sets of SNPs — 'tagging' SNPs (tSNPs) — that are associated with variation in the metabolism and transport of medicines. The researchers have also used their dataset to investigate the use of tSNPs in linkage disequilibrium mapping studies, such as how many tSNPs are needed for sets to work in more than one population.