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Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida
Collén, J.; Porcel, B.; Carre, W.; Ball, S.G.; Chaparro, C.; Tonon, T.; Barbeyron, T.; Michel, G.; Noel, B.; Valentin, K.; Elias, M.; Artiguenave, F.; Arun, A.; Aury, J.-M.; Barbosa-Neto, J.F.; Bothwell, J.H.; Bouget, F.-Y.; Brillet, L.; Cabello-Hurtado, F.; Capella-Gutiérrez, S.; Charrier, B.; Cladiere, L.; Cock, J.M.; Coelho, S.M.; Colleoni, C.; Czjzek, M.; Da Silva, C.; Delage, L.; Denoeud, F.; Deschamps, P.; Dittami, S.M.; Gabaldón, T.; Gachon, C.M.M.; Groisillier, A.; Hervé, C.; Jabbari, K.; Katinka, M.; Kloareg, B.; Kowalczyk, N.; Labadie, K.; Leblanc, C.; Lopez, P.J.; McLachlan, D.H.; Meslet-Cladière, L.; Moustafa, A.; Nehr, Z.; Collen, P.N.; Panaud, O.; Partensky, F.; Poulain, J.; Rensing, S.A.; Rousvoal, S.; Samson, G.; Symeonidi, A.; Weissenbach, J.; Zambounis, A.; Wincker, P.; Boyen, C. (2013). Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida. Proc. Natl. Acad. Sci. U.S.A. 110(13): 5247-5252. https://dx.doi.org/10.1073/pnas.1221259110
In: Proceedings of the National Academy of Sciences of the United States of America. The Academy: Washington, D.C.. ISSN 0027-8424; e-ISSN 1091-6490, more
Peer reviewed article  
Available in  Authors 
Keywords
    Marine Sciences
    Marine Sciences > Marine Genomics
    Scientific Community
    Scientific Publication
    Marine/Coastal
Project Top | Authors 
  • Association of European marine biological laboratories, more
Authors  Top 
  • Collén, J.
  • Porcel, B.
  • Carre, W.
  • Ball, S.G.
  • Chaparro, C.
  • Tonon, T.
  • Barbeyron, T.
  • Michel, G.
  • Noel, B.
  • Valentin, K.
  • Elias, M.
  • Artiguenave, F.
  • Arun, A.
  • Aury, J.-M.
  • Barbosa-Neto, J.F.
  • Bothwell, J.H.
  • Bouget, F.-Y.
  • Brillet, L.
  • Cabello-Hurtado, F.
  • Capella-Gutiérrez, S.
  • Charrier, B.
  • Cladiere, L.
  • Cock, J.M.
  • Coelho, S.M.
  • Colleoni, C.
  • Czjzek, M.
  • Da Silva, C.
  • Delage, L.
  • Denoeud, F.
  • Deschamps, P.
  • Dittami, S.M.
  • Gabaldón, T.
  • Gachon, C.M.M.
  • Groisillier, A.
  • Hervé, C.
  • Jabbari, K.
  • Katinka, M.
  • Kloareg, B., more
  • Kowalczyk, N.
  • Labadie, K.
  • Leblanc, C.
  • Lopez, P.J.
  • McLachlan, D.H.
  • Meslet-Cladière, L.
  • Moustafa, A.
  • Nehr, Z.
  • Collen, P.N.
  • Panaud, O.
  • Partensky, F.
  • Poulain, J.
  • Rensing, S.A.
  • Rousvoal, S.
  • Samson, G.
  • Symeonidi, A.
  • Weissenbach, J.
  • Zambounis, A.
  • Wincker, P.
  • Boyen, C., more
Abstract
    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.
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