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Lipinska AP, Krueger-Hadfield SA, Godfroy O, Dittami S, Ayres-Ostrock L, Bonthond G, Brillet-Guéguen L, Coelho S, Corre E, Cossard G, Destombe C, Epperlein P, Faugeron S, Ficko-Blean E, Beltrán J, Lavaut E, Le Bars A, Marchi F, Mauger S, Michel G, Potin P, Scornet D, Sotka EE, Weinberger F, de Oliveira MC, Guillemin ML, Plastino EM, Valero M. The Rhodoexplorer Platform for Red Algal Genomics and Whole Genome Assemblies for Several Gracilaria Species. Genome Biol Evol 2023:evad124. [PMID: 37481260 PMCID: PMC10388701 DOI: 10.1093/gbe/evad124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/24/2023] Open
Abstract
Macroalgal (seaweed) genomic resources are generally lacking as compared to 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 (G. chilensis and G. gracilis), a draft genome assembly of G. caudata, and genome annotation of the previously published G. 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.
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Affiliation(s)
- Agnieszka P Lipinska
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tubingen, Tubingen, Germany
- Sorbonne Université, CNRS, UMR 8227, Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Stacy A Krueger-Hadfield
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL, 35294, USA
| | - Olivier Godfroy
- Sorbonne Université, CNRS, UMR 8227, Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Simon Dittami
- Sorbonne Université, CNRS, UMR 8227, Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Lígia Ayres-Ostrock
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, Cidade Universitária 05508-090, São Paulo, SP, Brasil
- Hortimare - Breeding & Propagating Seaweed. Altonstraat 25A 1704 CC Heerhugowaard. The Netherlands
| | - Guido Bonthond
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Schleusenstrasse 1, 26382, Wilhelmshaven, Germany
| | - Loraine Brillet-Guéguen
- Sorbonne Université, CNRS, UMR 8227, Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
- CNRS, Sorbonne Université, FR2424, ABiMS-IFB, Station Biologique, 29680, Roscoff, France
| | - Susana Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tubingen, Tubingen, Germany
| | - Erwan Corre
- CNRS, Sorbonne Université, FR2424, ABiMS-IFB, Station Biologique, 29680, Roscoff, France
| | - Guillaume Cossard
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tubingen, Tubingen, Germany
| | - Christophe Destombe
- CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Paul Epperlein
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tubingen, Tubingen, Germany
| | - Sylvain Faugeron
- CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
- Núcleo Milenio MASH, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Elizabeth Ficko-Blean
- Sorbonne Université, CNRS, UMR 8227, Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Jessica Beltrán
- CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
- Núcleo Milenio MASH, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Emma Lavaut
- CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Arthur Le Bars
- CNRS, Sorbonne Université, FR2424, ABiMS-IFB, Station Biologique, 29680, Roscoff, France
- CNRS, Institut Français de Bioinformatique, IFB-core, UMS 3601, Évry, France
| | - Fabiana Marchi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, Cidade Universitária 05508-090, São Paulo, SP, Brasil
| | - Stéphane Mauger
- CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Gurvan Michel
- Sorbonne Université, CNRS, UMR 8227, Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Philippe Potin
- Sorbonne Université, CNRS, UMR 8227, Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Delphine Scornet
- Sorbonne Université, CNRS, UMR 8227, Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Erik E Sotka
- Department of Biology, College of Charleston, Charleston SC 29412
| | - Florian Weinberger
- GEOMAR Helmholtz-Zentrum für Ozeanforschung, Marine Ecology Division, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Mariana Cabral de Oliveira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, Cidade Universitária 05508-090, São Paulo, SP, Brasil
| | - Marie-Laure Guillemin
- CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
- Núcleo Milenio MASH, Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
- Centro FONDAP de Investigación de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
| | - Estela M Plastino
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, Cidade Universitária 05508-090, São Paulo, SP, Brasil
| | - Myriam Valero
- CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
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