Meeting Abstract
In vertebrates and plants, transposon-derived content can exceed half of the whole genome. Comparatively, data on transposons is mostly limited to model organisms, and thus Lophotrochozoa, the major bilaterian clade with the greatest diversity of body plans, is poorly sampled for transposons. Here, we focus on the genome of an invertebrate to gain knowledge of transposons in marine setting. Specifically, we are searching the genome of the hydrocarbon seep-dwelling tube worm Lamellibrachia luymesi (which hosts a horizontally transmitted gamma-proteobacterial endosymbiont) for Long Terminal Repeat retrotransposons (LTR retrotransposon). We made use of “LTR harvest” and “LTR digest” software packages, amongst other bioinformatics tools, to aid automatic annotation of LTR’s in genome. LTR harvest finds repetitive structures of the LTR and LTR digest allows annotation of internal features and protein domains of putative LTR retrotransposons using local alignment and Hidden Markov Model based algorithm to detect retrotransposon. The identified elements were clustered and classified into families based on the 80-80-80 similarity rule. Our preliminary results suggest that Lamellibrachia luymesi hosts several known LTR retrotransposon families with putative GYPSY elements being one of the most common. We plan to further classify transposable elements in this non-model marine invertebrate and then extend our comparative analyses to other lophotrochozoan taxa.
