%0 Journal Article %J Molecular Ecology %D 2018 %T Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network %A Meng, Arnaud %A Corre, Erwan %A Probert, Ian %A Gutierrez-Rodriguez, Andres %A Siano, Raffaele %A Annamale, Anita %A Alberti, Adriana %A Da Silva, Corinne %A Wincker, Patrick %A Le Crom, Stéphane %A Not, Fabrice %A Bittner, Lucie %K Genomics/Proteomics %K Microbial Biology %K Molecular Evolution %K Protists %K rcc1491 %K RCC1516 %K RCC3387 %K rcc3468 %K rcc3507 %K transcriptomics %X Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core predicted proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated to functional traits. With respect to toxicity, sequences homologous to those of proteins found in species with toxicity potential (e.g. sxtA4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of respectively the toxic and symbiotic species represented in our analyses. Of these, 56% and 57% respectively (i.e. 25,393 and 52,193 pCDs) completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization. This article is protected by copyright. All rights reserved. %B Molecular Ecology %P 0–2 %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/29624751%0Ahttp://doi.wiley.com/10.1111/mec.14579 %R 10.1111/mec.14579 %0 Journal Article %J Frontiers in Microbiology %D 2018 %T Comparative time-scale gene expression analysis highlights the infection processes of two amoebophrya strains %A Farhat, Sarah %A Florent, Isabelle %A Noel, Benjamin %A Kayal, Ehsan %A Da Silva, Corinne %A Bigeard, Estelle %A Alberti, Adriana %A Labadie, Karine %A Corre, Erwan %A Aury, Jean-Marc %A Rombauts, Stephane %A Wincker, Patrick %A Guillou, Laure %A Porcel, Betina M. %K amoebophrya %K Dinoflagellates %K Gene Expression %K infection %K oxidative stress response %K parasite %K plankton %K RCC1627 %K RCC3596 %K RCC4383 %K RCC4398 %K syndiniales %B Frontiers in Microbiology %V 9 %P 1–19 %8 oct %G eng %U https://www.frontiersin.org/article/10.3389/fmicb.2018.02251/full %R 10.3389/fmicb.2018.02251 %0 Journal Article %J Proceedings of the National Academy of Sciences %D 2013 %T Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida %A Collen, Jonas %A Porcel, Betina %A Carré, Wilfrid %A Ball, Steven G %A Chaparro, Cristian %A Tonon, Thierry %A Barbeyron, Tristan %A Michel, Gurvan %A Noel, Benjamin %A Valentin, Klaus %A Elias, Marek %A Artiguenave, François %A Arun, Alok %A Aury, Jean-Marc %A Barbosa-Neto, José F %A Bothwell, John H %A Bouget, François-Yves %A Brillet, Loraine %A Cabello-Hurtado, Francisco %A Capella-Gutiérrez, Salvador %A Charrier, Bénédicte %A Cladière, Lionel %A Cock, J Mark %A Coelho, Susana M %A Colleoni, Christophe %A Czjzek, Mirjam %A Da Silva, Corinne %A Delage, Ludovic %A Denoeud, France %A Deschamps, Philippe %A Dittami, Simon M %A Gabaldón, Toni %A Gachon, Claire M M %A Groisillier, Agnès %A Hervé, Cécile %A Jabbari, Kamel %A Katinka, Michael %A Kloareg, Bernard %A Kowalczyk, Nathalie %A Labadie, Karine %A Leblanc, Catherine %A Lopez, Pascal J %A McLachlan, Deirdre H %A Meslet-Cladiere, Laurence %A Moustafa, Ahmed %A Nehr, Zofia %A Nyvall Collén, Pi %A Panaud, Olivier %A Partensky, Frédéric %A Poulain, Julie %A Rensing, Stefan A %A Rousvoal, Sylvie %A Samson, Gaelle %A Symeonidi, Aikaterini %A Weissenbach, Jean %A Zambounis, Antonios %A Wincker, Patrick %A Boyen, Catherine %K RCC299 %X Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements. %B Proceedings of the National Academy of Sciences %V 110 %P 5247–5252 %G eng %U http://www.pnas.org/content/110/13/5247.abstract %R 10.1073/pnas.1221259110 %0 Journal Article %J Genome Biology %D 2009 %T Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell %A von Dassow, Peter %A Ogata, Hiroyuki %A Probert, Ian %A Wincker, Patrick %A Da Silva, Corinne %A Audic, Stéphane %A Claverie, Jean-Michel %A de Vargas, Colomban %K 2009 %K rcc %K RCC1216 %K rcc1217 %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto?ppo %X BACKGROUND:Eukaryotes are classified as either haplontic, diplontic, or haplo-diplontic, depending on which ploidy levels undergo mitotic cell division in the life cycle. Emiliania huxleyi is one of the most abundant phytoplankton species in the ocean, playing an important role in global carbon fluxes, and represents haptophytes, an enigmatic group of unicellular organisms that diverged early in eukaryotic evolution. This species is haplo-diplontic. Little is known about the haploid cells, but they have been hypothesized to allow persistence of the species between the yearly blooms of diploid cells. We sequenced over 38000 Expressed Sequence Tags (ESTs) from haploid and diploid E. huxleyi normalized cDNA libraries to identify genes involved in important processes specific to each life phase (2N calcification or 1N motility), and to better understand the haploid phase of this prominent haplo-diplontic organism.RESULTS:The haploid and diploid transcriptomes showed a dramatic differentiation, with [almost equal to]20% greater transcriptome richness in diploid cells than in haploid cells and only [less than or equal to]50% of transcripts estimated to be common between the two phases. The major functional category of transcripts differentiating haploids included signal transduction and motility genes. Diploid-specific transcripts included Ca2+, H+, and HCO3- pumps. Potential factors differentiating the transcriptomes included haploid-specific Myb transcription factor homologs and an unusual diploid-specific histone H4 homolog.CONCLUSIONS:This study permitted the identification of genes likely involved in diploid-specific biomineralization, haploid-specific motility, and transcriptional control. Greater transcriptome richness in diploid cells suggests they may be more versatile for exploiting a diversity of rich environments whereas haploid cells are intrinsically more streamlined. %B Genome Biology %V 10 %P R114 %G eng %U http://genomebiology.com/2009/10/10/R114 %R 10.1186/gb-2009-10-10-r114