Careful with understudied phyla: The case of chaetognath

Background: A recent study by Barthélémy et al. described a set of ribosomal protein (RP) genes extracted from a collection of expressed sequence tags (ESTs) of the chaetognath (arrow worm) Spadella cephaloptera. Three main conclusions were drawn in this paper. First, the authors stated that RP genes present paralogous copies, which have arisen through allopolyploidization. Second, they reported two alternate nucleotide stretches conserved within the 5' untranslated regions (UTR) of multiple ribosomal cDNAs and they suggested that these motifs are involved in the differential transcriptional regulation of paralogous RP genes. Third, they claimed that the phylogenetic position of chaetognaths could not be accurately inferred from a RP dataset because of the persistence of two problems: a long branch attraction (LBA) artefact and a compositional bias. / Results: We reconsider here the results described in Barthélémy et al. and question the evidence on which they are based. We find that their evidence for paralogous copies relies on faulty PCR experiments since they attempted to amplify DNA fragments absent from the genomic template. Our PCR experiments proved that the conserved motifs in 5'UTRs that they targeted in their amplifications are added post-transcriptionally by a trans-splicing mechanism. Then, we showed that the lack of phylogenetic resolution observed by these authors is due to limited taxon sampling and not to LBA or to compositional bias. A ribosomal protein dataset thus fully supports the position of chaetognaths as sister group of all other protostomes. This reinterpretation demonstrates that the statements of Barthélémy et al. should be taken with caution because they rely on inaccurate evidence. / Conclusion: The genomic study of an unconventional model organism is a meaningful approach to understand the evolution of animals. However, the previous study came to incorrect conclusions on the basis of experiments that omitted validation procedures

High Level of Structural Polymorphism Driven by Mobile Elements in the Hox Genomic Region of the Chaetognath Spadella cephaloptera

Little is known about the relationships between genome polymorphism, mobile element dynamics, and population size among animal populations. The chaetognath species Spadella cephaloptera offers a unique perspective to examine this issue because they display a high level of genetic polymorphism at the population level. Here, we have investigated in detail the extent of nucleotide and structural polymorphism in a region harboring Hox1 and several coding genes and presumptive functional elements. Sequencing of several bacterial artificial chromosome inserts representative of this nuclear region uncovered a high level of structural heterogeneity, which is mainly caused by the polymorphic insertion of a diversity of genetic mobile elements. By anchoring this variation through individual genotyping, we demonstrated that sequence diversity could be attributed to the allelic pool of a single population, which was confirmed by detection of extensive recombination within the genomic region studied. The high average level of nucleotide heterozygosity provides clues of selection in both coding and noncoding domains. This pattern stresses how selective processes remarkably cope with intense sequence turnover due to substitutions, mobile element insertions, and recombination to preserve the integrity of functional landscape. These findings suggest that genome polymorphism could provide pivotal information for future functional annotation of genomes

Chætognath transcriptome reveals ancestral and unique features among bilaterians

Background: The chætognaths (arrow worms) have puzzled zoologists for years because of their astonishing morphological and developmental characteristics. Despite their deuterostome-like development, phylogenomic studies recently positioned the chætognath phylum in protostomes, most likely in an early branching. This key phylogenetic position and the peculiar characteristics of chætognaths prompted further investigation of their genomic features. / Results: Transcriptomic and genomic data were collected from the chætognath Spadella cephaloptera through the sequencing of expressed sequence tags and genomic bacterial artificial chromosome clones. Transcript comparisons at various taxonomic scales emphasized the conservation of a core gene set and phylogenomic analysis confirmed the basal position of chætognaths among protostomes. A detailed survey of transcript diversity and individual genotyping revealed a past genome duplication event in the chætognath lineage, which was, surprisingly, followed by a high retention rate of duplicated genes. Moreover, striking genetic heterogeneity was detected within the sampled population at the nuclear and mitochondrial levels but cannot be explained by cryptic speciation. Finally, we found evidence for trans-splicing maturation of transcripts through splice-leader addition in the chætognath phylum and we further report that this processing is associated with operonic transcription. / Conclusion: These findings reveal both shared ancestral and unique derived characteristics of the chætognath genome, which suggests that this genome is likely the product of a very original evolutionary history. These features promote chætognaths as a pivotal model for comparative genomics, which could provide new clues for the investigation of the evolution of animal genomes

Restricted expression of a median Hox gene in the central nervous system of chaetognaths

Hox genes encode a set of evolutionarily conserved transcription factors that regulate anterior-posterior patterning. Here we report the first developmental expression of a Hox gene from Chaetognatha. These metazoans have been shown recently to be part of the protostome group of bilaterians. We describe the analysis of the SceMed4 gene (a Spadella cephaloptera Median Hox gene) including its expression from late stages of egg development to 7 days after hatching. In all of these stages, SceMed4 is expressed in two lateral stripes in a restricted region of the developing ventral ganglion

On the identity and origin of the Mediterranean invasive Caulerpa racemosa(Caulerpales, Chlorophyta)

Recent morphological and genetic studies on the Caulerpa racemosa (Forsskål) J. Agardh complex have demonstrated that three taxa occur in the Mediterranean Sea. One of them, the 'invasive variety', provisionally regarded as close to C. racemosa var. occidentalis J. Agardh, is currently spreading spectacularly throughout the Mediterranean. On the basis of new morphological and molecular studies (rDNA ITS1, 5.8S and ITS2 sequences), we confirm here that this invasion is the result of a recent introduction and we identify the invasive variety as Caulerpa cylindracea Sonder, endemic to south-west Australia, and currently known as C. racemosa var. laetevirens f. cylindracea (Sonder) Weber-van Bosse. C. cylindracea differs from the tropical north Australian C. laetevirens Montagne by its slender thallus, lack of large rhizoidal pillars, the slight inflation of the basal part of the upright axes immediately above the attachment to the stolon, by the range of morphological variations (branchlets clavate to cylindrical but never trumpet-like or shield-like) and by the rDNA ITS sequence data. The new combination C. racemosa var. cylindracea (Sonder) Verlaque, Huisman et Boudouresque is therefore proposed