Browsing by Author "Dittami, Simon M."

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    Genome and metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae
    (2014) Dittami, Simon M.; Barbeyron, Tristan; Boyen, Catherine; Cambefort, Jeanne; Collet, Guillaume; Delage, Ludovic; Gobet, Angelique; Groisillier, Agnes; Leblanc, Catherine; Michel, Gurvan; Scornet, Delphine; Siegel, Anne; Tapia, Javier E.; Tonon, Thierry
    Rhizobiales and related orders of Alphaproteobacteria comprise several genera of nodule-inducing symbiotic bacteria associated with plant roots. Here we describe the genome and the metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a member of a new candidate genus closely related to Rhizobiales and found in association with cultures of the filamentous brown algal model Ectocarpus. The "Ca. P. ectocarpi" genome encodes numerous metabolic pathways that may be relevant for this bacterium to interact with algae. Notably, it possesses a large set of glycoside hydrolases and transporters, which may serve to process and assimilate algal metabolites. It also harbors several proteins likely to be involved in the synthesis of algal hormones such as auxins and cytokinins, as well as the vitamins pyridoxine, biotin, and thiamine. As of today, "Ca. P. ectocarpi" has not been successfully cultured, and identical 16S rDNA sequences have been found exclusively associated with Ectocarpus. However, related sequences (>= 97% identity) have also been detected free-living and in a Fucus vesiculosus microbiome barcoding project, indicating that the candidate genus "Phaeomarinobacter" may comprise several species, which may colonize different niches.
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    The Ectocarpus genome and the independent evolution of multicellularity in brown algae
    (2010) Cock, J. Mark; Sterck, Lieven; Rouze, Pierre; Scornet, Delphine; Allen, Andrew E.; Amoutzias, Grigoris; Anthouard, Veronique; Artiguenave, Francois; Aury, Jean-Marc; Badger, Jonathan H.; Beszteri, Bank; Billiau, Kenny; Bonnet, Eric; Bothwell, John H.; Bowler, Chris; Boyen, Catherine; Brownlee, Colin; Carrano, Carl J.; Charrier, Benedicte; Cho, Ga Youn; Coelho, Susana M.; Collen, Jonas; Corre, Erwan; Da Silva, Corinne; Delage, Ludovic; Delaroque, Nicolas; Dittami, Simon M.; Doulbeau, Sylvie; Elias, Marek; Farnham, Garry; Gachon, Claire M. M.; Gschloessl, Bernhard; Heesch, Svenja; Jabbari, Kamel; Jubin, Claire; Kawai, Hiroshi; Kimura, Kei; Kloareg, Bernard; Kuepper, Frithjof C.; Lang, Daniel; Le Bail, Aude; Leblanc, Catherine; Lerouge, Patrice; Lohr, Martin; Lopez, Pascal J.; Martens, Cindy; Maumus, Florian; Michel, Gurvan; Miranda-Saavedra, Diego; Morales, Julia; Moreau, Herve; Motomura, Taizo; Nagasato, Chikako; Napoli, Carolyn A.; Nelson, David R.; Nyvall-Collen, Pi; Peters, Akira F.; Pommier, Cyril; Potin, Philippe; Poulain, Julie; Quesneville, Hadi; Read, Betsy; Rensing, Stefan A.; Ritter, Andres; Rousvoal, Sylvie; Samanta, Manoj; Samson, Gaelle; Schroeder, Declan C.; Segurens, Beatrice; Strittmatter, Martina; Tonon, Thierry; Tregear, James W.; Valentin, Klaus; von Dassow, Peter; Yamagishi, Takahiro; Van de Peer, Yves; Wincker, Patrick
    Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related(1). These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae(2-5), closely related to the kelps(6,7) (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic(2) approaches to explore these and other(4,5) aspects of brown algal biology further.
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    The Rhodoexplorer Platform for Red Algal Genomics and Whole-Genome Assemblies for Several Gracilaria Species
    (2023) Lipinska, Agnieszka P.; Krueger-Hadfield, Stacy A.; Godfroy, Olivier; Dittami, Simon M.; Ayres-Ostrock, Ligia; Bonthond, Guido; Brillet-Gueguen, Loraine; Coelho, Susana; Corre, Erwan; Cossard, Guillaume; Destombe, Christophe; Epperlein, Paul; Faugeron, Sylvain; Ficko-Blean, Elizabeth; Beltran, Jessica; Lavaut, Emma; Le Bars, Arthur; Marchi, Fabiana; Mauger, Stephane; Michel, Gurvan; Potin, Philippe; Scornet, Delphine; Sotka, Erik E.; Weinberger, Florian; de Oliveira, Mariana Cabral; Guillemin, Marie-Laure; Plastino, Estela M.; Valero, Myriam
    Macroalgal (seaweed) genomic resources are generally lacking as compared with other eukaryotic taxa, and this is particularly true in the red algae (Rhodophyta). Understanding red algal genomes is critical to understanding eukaryotic evolution given that red algal genes are spread across eukaryotic lineages from secondary endosymbiosis and red algae diverged early in the Archaeplastids. The Gracilariales is a highly diverse and widely distributed order including species that can serve as ecosystem engineers in intertidal habitats and several notorious introduced species. The genus Gracilaria is cultivated worldwide, in part for its production of agar and other bioactive compounds with downstream pharmaceutical and industrial applications. This genus is also emerging as a model for algal evolutionary ecology. Here, we report new whole-genome assemblies for two species (Gracilaria chilensis and Gracilaria gracilis), a draft genome assembly of Gracilaria caudata, and genome annotation of the previously published Gracilaria vermiculophylla genome. To facilitate accessibility and comparative analysis, we integrated these data in a newly created web-based portal dedicated to red algal genomics (https://rhodoexplorer.sb-roscoff.fr). These genomes will provide a resource for understanding algal biology and, more broadly, eukaryotic evolution.