De novo transcriptome sequencing of a non-model polychaete species.

Transcriptome sequencing is a useful method for studying gene-sequences data, especially in non-model organisms whose genomic sequences are yet to be determined. Indeed, even without any genome reference, transcripts can be assembled de novo to produce a genome-scale transcription map. Here we describe a de novo transcriptome assembly for the polychaete worm Ophryotrocha diadema, generated from 454-sequencing (Roche GS-FLX Titanium Sequencing). We describe the sequencing, the assembly and functional annotation of EST sequences, and the level of transcriptome coverage provided by our sequence data. The sequences we assembled represent a wide depiction of expressed genes from throughout the lifespan of O. diadema. We found gene sequences to be part of a broad range of functions (i.e. biological and metabolic processes, immune system, reproductive processes, development and growth, signalling and response to stimuli) and we therefore built the first transcriptomic reference for Ophryotrocha polychaete worms. These results encourage us to focus our investigation on many aspects of O. diadema and to extend our research to co-generic species.

Insertional polymorphism of a non-LTR mobile element (NLRCth1) in European populations of Chironomus riparius (Diptera, Chironomidae) as detected by transposon insertion display.

The midge Chironomus riparius is distributed all over the Palearctic region and is well characterized both at the morphological and cytogenetic levels. Here we describe a population study based on the insertional polymorphism of the retroposon NLRCth1, by means of a S-SAP (sequence-specific amplification polymorphism) derived technique (transposon insertion display; TID). While a previous study of allozyme polymorphism in Russian samples showed little variability, all the amplicons we identified are polymorphic. Genetic distances between 6 natural populations were calculated according to Nei and did not show a positive correlation with geographic distances. The genetic diversity detected among individuals of a given population was one order of magnitude higher than that among populations. However, the value of phi(ST) was significant (p < 0.001) and indicates that natural populations are more genetically differentiated than random samples of individuals.