2011
CNET, XVIIe edition 4th - 6th july 2011, Lyon France
06 Jul 2011 Transposable Elements in Marine Stramenopiles
F.Maumus , A. E. Allen , T. Mock , M. Cock , C. Bowler , H. Quesneville
Stramenopiles are a major line of eukaryotes that comprises autotrophic algae such as diatoms and brown algae, and heterotrophs such as oomycetes. Diatoms are among the most successful and diversified groups of photosynthetic eukaryotes, with possibly over 100,000 extant species. The contribution of diatoms to marine primary productivity has been estimated to be around 40% and they play a key role as a biological carbon pump as well as in other biogeochemical cycles. They also constitute a major resource at the base of the food chain. Brown algae, such as giant kelps, constitute a less ubiquitous group which is mostly restricted to near-shore lines and rocky areas where they represent an essential source of ecological habitats and food. The genome of three diatoms (Phaeodactylum tricornutum, Thalassiosira pseudonana, and Fragilariopsis cylindrus), and one brown algae (Ectocarpus silicuolsus) have been sequenced. Although sequencing data come from rather small genomes, those from diatoms and brown algae can size up to several gigabases. Thus, transposable elements (TEs) are thought to be major contributors to genome size and dynamics in marine stramenopiles.
We have analyzed manually and/or computationally the transposable element (TE) content in these genomes. We will describe the panorama of TEs detected and their comparative contribution to diatom genomes. For example, we will show that LTR-RT elements including Ty3/Gypsy, Ty1/Copia and DIRS-like elements are the most abundant TEs in diatom genomes. Phylogenetic reconstructions indicate the Ty1/Copia-like LTR retrotransposons (LTR-RT) from diatoms and brown algae constitute distinct lineages (called Codis and Brownies) 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 Ty1/Copia-like LTR-RT elements from P. tricornutum is activated under specific stresses such as nitrogen starvation, suggesting that they generate genetic variability in response to challenging environmental conditions. We will also describe some lineage-specific atypical TEs such as very large non LTR-RT elements from diatoms that are distantly related to LINEs, unclassified protein-coding LTR elements found in the E. siliculosus genome, and non-autonomous Class II elements with internal captured gene in P. tricornutum.
Creation date: 08 Jul 2011
eZ PublishPublication supervisor: A-F. Adam-Blondon
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