FN Archimer Export Format PT J TI Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems BT AF Denoeud, France Godfroy, Olivier Cruaud, Corinne Heesch, Svenja Nehr, Zofia Tadrent, Nachida Couloux, Arnaud Brillet-Guéguen, Loraine Delage, Ludovic Mckeown, Dean Motomura, Taizo Sussfeld, Duncan Fan, Xiao Mazéas, Lisa Terrapon, Nicolas Barrera-Redondo, Josué Petroll, Romy Reynes, Lauric Choi, Seok-Wan Jo, Jihoon Uthanumallian, Kavitha Bogaert, Kenny Duc, Céline Ratchinski, Pélagie Lipinska, Agnieszka Noel, Benjamin Murphy, Eleanor A. Lohr, Martin Khatei, Ananya Hamon-Giraud, Pauline Vieira, Christophe Akerfors, Svea Sanja Akita, Shingo Avia, Komlan Badis, Yacine Barbeyron, Tristan Belcour, Arnaud Berrabah, Wahiba Blanquart, Samuel Bouguerba-Collin, Ahlem Bringloe, Trevor Cattolico, Rose Ann Cormier, Alexandre Cruz de Carvalho, Helena Dallet, Romain De Clerck, Olivier Debit, Ahmed Denis, Erwan Destombe, Christophe Dinatale, Erica Dittami, Simon Drula, Elodie Faugeron, Sylvain Got, Jeanne Graf, Louis Groisillier, Agnès Guillemin, Marie-Laure Harms, Lars Hatchett, William John Henrissat, Bernard Hoarau, Galice Jollivet, Chloé Jueterbock, Alexander Kayal, Ehsan Kogame, Kazuhiro Le Bars, Arthur Leblanc, Catherine Ley, Ronja Liu, Xi Lopez, Pascal Jean Lopez, Philippe Manirakiza, Eric Massau, Karine Mauger, Stéphane Mest, Laetitia Michel, Gurvan Monteiro, Catia Nagasato, Chikako Nègre, Delphine Pelletier, Eric Phillips, Naomi Potin, Philippe Rensing, Stefan A. Rousselot, Ellyn Rousvoal, Sylvie Schroeder, Declan Scornet, Delphine Siegel, Anne Tirichine, Leila Tonon, Thierry Valentin, Klaus Verbruggen, Heroen Weinberger, Florian Wheeler, Glen Kawai, Hiroshi Peters, Akira F. Yoon, Hwan Su Hervé, Cecile Ye, Naihao Bapteste, Eric Valero, Myriam Markov, Gabriel V. Corre, Erwan Coelho, Susana M. Wincker, Patrick Aury, Jean-Marc Cock, J. Mark AS 1:1;2:2;3:3;4:4;5:4;6:1;7:1;8:5,6;9:7;10:6;11:8;12:1,9;13:10,11;14:2;15:12,13;16:14;17:14;18:15;19:16;20:16;21:17;22:18;23:19;24:4;25:4,14;26:1;27:20,21;28:22;29:23;30:24;31:25;32:22;33:26;34:27;35:4;36:2;37:24;38:1;39:24;40:2;41:28;42:29;43:30;44:31,32;45:6;46:18;47:31;48:1;49:15;50:14;51:7;52:12,13;53:33;54:24;55:16;56:19;57:15,34;58:35;59:36;60:37,38;61:36;62:2;63:23;64:6;65:39;66:6,40;67:7;68:22;69:6;70:41;71:9;72:19;73:6;74:15;75:4;76:2;77:7;78:8;79:6;80:1;81:42;82:7;83:43;84:19;85:7;86:44;87:4;88:24;89:19;90:45;91:35;92:28;93:46;94:21;95:47;96:48;97:16;98:2;99:10,11;100:9;101:15;102:7;103:6;104:14;105:1;106:1;107:4; FF 1:;2:;3:;4:;5:;6:;7:;8:;9:;10:;11:;12:;13:;14:;15:;16:;17:;18:;19:;20:;21:;22:;23:;24:;25:;26:;27:;28:;29:;30:;31:;32:;33:;34:;35:;36:;37:;38:;39:;40:;41:;42:;43:PDG-IRSI-SEBIMER;44:;45:;46:;47:;48:;49:;50:;51:;52:;53:;54:;55:;56:;57:;58:;59:;60:;61:;62:;63:;64:;65:;66:;67:;68:;69:;70:;71:;72:;73:;74:;75:;76:;77:;78:;79:;80:;81:;82:;83:;84:;85:;86:;87:;88:;89:;90:;91:;92:;93:;94:;95:;96:;97:;98:;99:;100:;101:;102:;103:;104:;105:;106:;107:; C1 Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, 91057, France Sorbonne Université, CNRS, Integrative Biology of Marine Models Laboratory, Station Biologique de Roscoff, Roscoff, France Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France Sorbonne Université, CNRS, Algal Genetics Group, Integrative Biology of Marine Models Laboratory, Station Biologique de Roscoff, Roscoff, France CNRS, UMR 8227, Laboratory of Integrative Biology of Marine Models, Sorbonne Université, Station Biologique de Roscoff, Roscoff, France CNRS, Sorbonne Université, FR2424, ABiMS-IFB, Station Biologique, Roscoff, France Sorbonne Université, CNRS, UMR 8227, ABIE Team, Integrative Biology of Marine Models Laboratory, Station Biologique de Roscoff, Roscoff, France Muroran Marine Station, Hokkaido University, Muroran, Japan Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR 7205, Sorbonne Université, CNRS, Museum State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China Aix Marseille Univ, CNRS, UMR 7257 AFMB, Marseille, France INRAE, USC 1408 AFMB, Marseille, France Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany IRL 3614, UMR 7144, DISEEM, CNRS, Sorbonne Université, Station Biologique de Roscoff, Roscoff, 29688, France Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea University of Melbourne, Australia Phycology Research Group, Ghent University, Krijgslaan 281 S8, 9000 Ghent, Belgium Nantes Université, CNRS, US2B, UMR 6286, F-44000 Nantes, France University of Bristol, UK Marine Biological Association, Plymouth, UK Johannes Gutenberg University, Mainz, Germany Algal and Microbial Biotechnology Division, Nord University, Norway Univ Rennes, Inria, CNRS, IRISA, Equipe Dyliss, Rennes, France Research Institute for Basic Sciences, Jeju National University, Jeju 63243, Korea Faculty of Fisheries Sciences, Hokkaido University, Minato-cho 3-1-1, Hakodate, Hokkaido, 041- 8611, Japan INRAE, Université de Strasbourg, UMR SVQV, 68000 Colmar, France University of Melbourne, Australia University of Washington, USA Ifremer, IRSI, SeBiMER Service de Bioinformatique de l'Ifremer, F-29280 Plouzané, France Institut de Biologie de l'ENS (IBENS), Département de Biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France Université Paris Est-Créteil (UPEC), Faculté des Sciences et Technologie, 61, avenue du Général De Gaulle 94000 Créteil, France Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile Núcleo Milenio MASH, Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile Alfred Wegener Institute (AWI), Bremenhaven Nord University, Norway Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs Lyngby, Denmar Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan CNRS, Institut Français de Bioinformatique, IFB-core, Évry, France Centre National de la Recherche Scientifique, UMR BOREA MNHN/CNRS-8067/SU/IRD/Univ. Caen Normandie/Univ. Antilles, France Biology Department, Arcadia University, USA University of Freiburg, Germany Minneapolis-St Paul University, USA Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany Kobe University Research Center for Inland Seas, Kobe, Japan Bezhin Rosko, 29250 Santeg, France C2 UNIV PARIS SACLAY, FRANCE UNIV SORBONNE, FRANCE UNIV PARIS SACLAY, FRANCE UNIV SORBONNE, FRANCE CNRS, FRANCE CNRS, FRANCE UNIV SORBONNE, FRANCE UNIV HOKKAIDO, JAPAN UNIV SORBONNE, MUSEUM CHINESE ACAD SCI, CHINA QNLM, CHINA UNIV AIX MARSEILLE, FRANCE INRAE, FRANCE MAX PLANCK INST, GERMANY UNIV SORBONNE, FRANCE UNIV SUNGKYUNKWAN, SOUTH KOREA UNIV MELBOURNE, AUSTRALIA UNIV GHENT, BELGIUM UNIV NANTES, FRANCE UNIV BRISTOL, UK MBA, UK UNIV MAINZ, GERMANY UNIV NORD, NORWAY UNIV RENNES, FRANCE UNIV JEJU NATL, SOUTH KOREA UNIV HOKKAIDO, JAPAN INRAE, FRANCE UNIV MELBOURNE, AUSTRALIA UNIV WASHINGTON, USA IFREMER, FRANCE ENS, FRANCE UNIV PARIS EST, FRANCE UNIV PONTIFICIA CATOLICA CHILE, CHILE UNIV AUSTRAL CHILE, CHILE INST A WEGENER, GERMANY UNIV NORD, NORWAY UNIV TECH DENMARK, DENMAR KAUST, SAUDI ARABIA UNIV HOKKAIDO, JAPAN CNRS, FRANCE CNRS, FRANCE UNIV ARCADIA, USA UNIV FREIBURG, GERMANY UNIV MINNESOTA, USA UNIV YORK, UK IFM GEOMAR, GERMANY UNIV KOBE, JAPAN BEZHIN ROSKO, FRANCE SI BREST CEDRE SE PDG-IRSI-SEBIMER CEDRE-ADMIN IN DOAJ TC 0 UR https://archimer.ifremer.fr/doc/00879/99116/108963.pdf LA English DT Article AB  Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, that are under considerable threat from climate change. Despite their ecological and evolutionary importance, this phylogenetic group, which is very distantly related to animals and land plants, is still poorly characterised at the genome level. Here we analyse 60 new genomes that include species from all the major brown algal orders. Comparative analysis of these genomes indicated the occurrence of several major events coinciding approximately with the emergence of the brown algal lineage. These included marked gain of new orthologous gene families, enhanced protein domain rearrangement, horizontal gene transfer events and the acquisition of novel signalling molecules and metabolic pathways. The latter include enzymes implicated in processes emblematic of the brown algae such as biosynthesis of the alginate-based extracellular matrix, and halogen and phlorotannin biosynthesis. These early genomic innovations enabled the adaptation of brown algae to their intertidal habitats. The subsequent diversification of the brown algal orders tended to involve loss of gene families, and genomic features were identified that correlated with the emergence of differences in life cycle strategy, flagellar structure and halogen metabolism. We show that integration of large viral genomes has had a significant impact on brown algal genome content and propose that this process has persisted throughout the evolutionary history of the lineage. Finally, analysis of microevolutionary patterns within the genusEctocarpusindicated that deep gene flow between species may be an important factor in genome evolution on more recent timescales. PY 2024 PD FEB SO bioRxiv PU Cold Spring Harbor Laboratory DI 10.1101/2024.02.19.579948 ID 99116 ER EF