Zoology: you aren't what you eat

A first glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus

Eulimnogammarus verrucosus is an amphipod endemic to the unique ecosystem of Lake Baikal and serves as an emerging model in ecotoxicological studies. We report here on a survey sequencing of its genome as a first step to establish sequence resources for this species. From a single lane of paired-end sequencing data, we estimated the genome size as nearly 10 Gb and we obtained an overview of the repeat content. At least two-thirds of the genome are non-unique DNA, and a third of the genomic DNA is composed of just five families of repetitive elements, including low-complexity sequences. Attempts to use off-the-shelf assembly tools failed on the available low-coverage data both before and after removal of highly repetitive components. Using a seed-based approach we nevertheless assembled short contigs covering 33 pre-microRNAs and the homeodomain-containing exon of nine Hox genes. The absence of clear evidence for paralogs implies that a genome duplication did not contribute to the large genome size. We furthermore report the assembly of the mitochondrial genome using a new, guided "crystallization" procedure. The initial results presented here set the stage for a more complete sequencing and analysis of this large genome.

Xenoturbellida: the fourth deuterostome phylum and the diet of worms

Since the discovery of the marine worm Xenoturbella bocki in 1915 by Sixten Bock and its first published description by Einar Westblad (Westblad,1949, Arkiv Zoologi 1:3-29), Xenoturbella was generally allied to the turbellarian flatworms, perhaps most closely to acoelomorphs. In 1997, however, analyses of ribosomal DNA (Norén and Jondelius, 1997, Nature 390:31-32) and developing oocytes (Israelsson, 1997, Nature 390:32) [and, subsequently, embryos (Israelsson, 1999, Proc R Soc Lond B 266:835-841)] recovered from Xenoturbella specimens led to the surprising conclusion that it was in fact a highly degenerate bivalve mollusc. Bourlat et al. showed in 2003 that this result was due to contamination from bivalves in its diet (Bourlat et al.,2003, Nature 424:925-928). Our analyses showed Xenoturbella is a deuterostome, related to the Ambulacraria (echinoderms and hemichordates). Subsequent work has shown that Xenoturbellida is a separate lineage from the Ambulacraria and therefore constitutes the fourth deuterostome phylum (Bourlat et al.,2006, Nature 444:85-88). I consider this phylogenetic position in the light of what is known of its genetics, morphology, and ontogeny. I examine what this phylogenetic position for Xenoturbella can tell us about its own evolution and what light this might shine on the common ancestor of the deuterostomes and hence on the origins of the chordates.

Basiepidermal nervous system in Nemertoderma westbladi (Nemertodermatida): GYIRFamide immunoreactivity

The Nemertodermatida are a small group of microscopic marine worms. Recent molecular studies have demonstrated that they are likely to be the earliest extant bilaterian animals. What was the nervous system (NS) of a bilaterian ancestor like? In order to answer that question, the NS of Nemertoderma westbladi was investigated by means of indirect immunofluorescence technique and confocal scanning laser microscopy. The antibodies to a flatworm neuropeptide GYIRFamide were used in combination with anti-serotonin antibodies and phalloidin-TRITC staining. The immunostaining revealed an entirely basiepidermal NS. A ring lying outside the body wall musculature at the level of the statocyst forms the only centralisation, the "brain". No stomatogastric NS has been observed. The GYIRFamide immunoreactive part of the "brain" is formed of loosely packed nerve fibres with multiple small neurones and a few large ones. The peptidergic and aminergic patterns of the NS do not correspond to each other: the former is more developed on the ventral side, the latter is more pronounced on the dorsal side. A pair of GYIRFamide immunoreactive nerve cords innervates the ventral side of the animal, the mouth and the male genital opening. The nemertodermatids studied to-date display no common NS pattern. Possible synapomorphies of the Acoelomorpha are discussed. The study demonstrates that the nemertodermatid NS possesses a number of plesiomorphic features and appears more primitive than the NS in other worms, except the Xenoturbellida. The bilaterian ancestor supposedly possessed only a basiepidermal nerve net and had no centralised brain-like structures and no stomatogastric NS.