title: Potential impact of stress activated retrotransposons on genome evolution in a marine diatom.
abstract: BACKGROUND
  Transposable elements (TEs) are mobile DNA sequences present in the genomes of most organisms. They have been extensively studied in animals, fungi, and plants, and have been shown to have important functions in genome dynamics and species evolution. Recent genomic data can now enlarge the identification and study of TEs to other branches of the eukaryotic tree of life. Diatoms, which belong to the heterokont group, are unicellular eukaryotic algae responsible for around 40% of marine primary productivity. The genomes of a centric diatom, Thalassiosira pseudonana, and a pennate diatom, Phaeodactylum tricornutum, that likely diverged around 90 Mya, have recently become available.
  
  
  RESULTS
  In the present work, we establish that LTR retrotransposons (LTR-RTs) are the most abundant TEs inhabiting these genomes, with a much higher presence in the P. tricornutum genome. We show that the LTR-RTs found in diatoms form two new phylogenetic lineages that appear to be diatom specific and are also found in environmental samples taken from different oceans. Comparative expression analysis in P. tricornutum cells cultured under 16 different conditions demonstrate high levels of transcriptional activity of LTR retrotransposons in response to nitrate limitation and upon exposure to diatom-derived reactive aldehydes, which are known to induce stress responses and cell death. Regulatory aspects of P. tricornutum retrotransposon transcription also include the occurrence of nitrate limitation sensitive cis-regulatory components within LTR elements and cytosine methylation dynamics. Differential insertion patterns in different P. tricornutum accessions isolated from around the world infer the role of LTR-RTs in generating intraspecific genetic variability.
  
  
  CONCLUSIONS
  Based on these findings we propose that LTR-RTs may have been important for promoting genome rearrangements in diatoms.
authors.affiliation: CNRS UMR8186, Biologie Moléculaire des Organismes Photosynthétiques, Ecole Normale Supérieure, 75230 Paris cedex05, France. maumus@biologie.ens.fr
authors.forename: Florian
authors.initials: F
authors.lastname: Maumus
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Allen
authors.forename: Corinne
authors.initials: C
authors.lastname: Mhiri
authors.forename: Hanhua
authors.initials: H
authors.lastname: Hu
authors.forename: Kamel
authors.initials: K
authors.lastname: Jabbari
authors.forename: Assaf
authors.initials: A
authors.lastname: Vardi
authors.forename: Marie-Angèle
authors.initials: MA
authors.lastname: Grandbastien
authors.forename: Chris
authors.initials: C
authors.lastname: Bowler
mesh_terms: D000447:Aldehydes / Q000378:metabolism; D019175:DNA Methylation; D048028:DNA, Algal / Q000235:genetics; D017377:Diatoms / Q000235:genetics*; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D006239:Haplotypes; D054892:Metagenome; D009566:Nitrates / Q000378:metabolism; D010802:Phylogeny; D011110:Polymorphism, Genetic; D011995:Recombination, Genetic; D018626:Retroelements; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D013312:Stress, Physiological / Q000235:genetics*
chemical_list: D000447:Aldehydes; D048028:DNA, Algal; D009566:Nitrates; D018626:Retroelements