Expressed sequence tag analyses of the annelid Pomatoceros lamarckii, recently published in BMC Evolutionary Biology, are consistent with less extensive gene loss in the Lophotrochozoa than in the Ecdysozoa, but it would be premature to generalize about patterns of gene loss on the basis of the limited data available.
The pioneers of pyrosequencing have a lot to answer for. The availability of 'next generation' DNA sequencers has provided zoologists with unforeseen opportunities to address many basic evolutionary issues and, for those of us whose interests lie beyond the model organisms, these are indeed interesting times. Not so long ago the costs of large-scale expressed sequence tag (EST) analyses were prohibitive, but the recent development of the fast and (relatively) cheap 454, Illumina and SOLiD technologies is enabling large-scale transcriptome analysis, and potentially whole-genome analysis, to be applied to a wide range of animals, providing insights into evolutionary issues that were once considered essentially intractable.
One important and controversial issue that can now be addressed is the gene complement of Urbilateria. It is clear that this ancestor of all bilateral animals had a genome resembling that of a modern vertebrate, but which also contained some genes lost from modern vertebrates, raising the issue of just how many genes were present in the ancestor. In this respect, EST studies on lophotrochozoans, such as that reported in a recent paper in BMC Evolutionary Biology , are proving particularly informative. Of the three major divisions within Bilateria (the Ecdysozoa, the Lophotrochozoa and the Deuterostomia; Figure 1), Lophotrochozoa, which contains the annelids (worms) and mollusks (including snails) and various minor phyla, is still only poorly represented in terms of whole genome data.
Figure 1. A simplified view of animal phylogeny, showing the taxonomic position of groups and organisms mentioned in the text (genera are in italics). Taxa above the red line are animals. Relationships among the non-bilaterian phyla remain controversial, but the topology shown reflects the current consensus. Numbers in red are percentages of the total number (2,308) of Pomatoceros ESTs with matches against specific taxonomic groups. Numbers on the boundaries between taxonomic groups are shared exclusively between Pomatoceros and those groups, whereas in the cases of non-bilaterians and bacteria/protists the numbers reflect ESTs shared between Pomatoceros, lophotrochozoans and those taxonomic groups. For example, 7% of Pomatoceros ESTs are shared only with lophotrochozoans and deuterostomes, and less than 1% are shared only with lophotrochozoans and non-bilateral animals or with lophotrochozoans and bacteria or protists. Over half (1,205; 52%) of the total number of Pomatoceros ESTs had no matches in the databases.
One implication of work on the annelid Platynereis dumerilii is that lophotrochozoans may be less derived (are more representative of ancestral character states) than members of Ecdysozoa , but it is not yet clear how representative Platynereis is. Takahashi et al.  have now analyzed a set of ESTs from a second and only distantly related annelid, the serpulid Pomatoceros lamarckii, which differs from Platynereis both morphologically and in lifestyle. Platynereis is a free-living predator, whereas Pomatoceros lives within a tube that it constructs and captures food from the surrounding waters using a crown of feeding tentacles through which water is filtered. Nevertheless, data from the two species lead to the same conclusion, that annelids (and perhaps lophotrochozoans in general) are less derived than the insects and nematodes investigated so far. One focus of the paper  was patterns of gene sharing and gene loss between Pomatoceros and the other major groups of organisms. These figures are summarized in Figure 1: Pomatoceros shares a significant number of genes (158; 7% of the total) only with deuterostomes and other lophotrochozoans, but a much smaller number (23 genes; 1% of the total) only with e