2012
International Congress on Transposable Elements, Saint Malo, France
21 Apr 2012 Transposable Elements in DiatomsFlorian Maumus, Xin Lin, Alaguraj Veluchamy, Thomas Mock, Chris Bowler, Leïla Tirichine, Hadi Quesneville
Oceans contribute ~50% to net primary productivity (NPP) on Earth, which is essentially attributed to photosynthesis activity achieved by phytoplankton. Diatoms, which evolved after a secondary endosymbiosis event, are the most successful and diversified group of unicellular algae with possibly over 100,000 species. Their contribution to marine NPP has been estimated to be around 40%, playing a key role as a biological carbon pump as well as in other biogeochemical cycles. Diatom genomes can size up to several gigabases and transposable elements (TEs) are thought to be major contributors to genome size and dynamics in these species. The genome of three diatoms (Phaeodactylum tricornutum ~27 Mb, Thalassiosira pseudonana ~32 Mb, Fragilariopsis cylindrus ~80 Mb) have been sequenced.
We have analyzed the TE content in these genomes. We describe the panorama of TEs detected and their comparative contribution to diatom genomes. For example, we show that LTR-retrotransposons (LTR-RT), especially Ty1/Copia elements, are the most abundant TEs in diatom genomes. Phylogenetic reconstructions indicate that these constitute diatom-specific lineages called CoDis that belong to the recently postulated ‘Branch 1’ of Ty1/Copia-like LTR-RT. Similar sequences are also abundant in marine metagenomes.
Interestingly, the expression of some CoDis from P. tricornutum is activated in response to specific stresses such as nitrogen starvation, suggesting that CoDis generate genetic variability in response to challenging environmental conditions. This is ecologically relevant considering that nitrogen is the most common and widespread limiting nutrient for marine phytoplankton.
Furthermore, analysis of genome-wide DNA methylation profile in P. tricornutum shows that spreading from TEs appears to be a common mechanism resulting in the methylation of flanking genes. We also describe the presence in P. tricornutum of a family of non-autonomous Class II elements with internal captured gene which likely impacts the epigenetic regulation of the cognate host gene.
Creation date: 23 Dec 2012
eZ PublishPublication supervisor: A-F. Adam-Blondon
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