Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida.
Jonas Collén
(1, 2)
,
Betina Porcel
(3)
,
Wilfrid Carré
(4)
,
Steven G Ball
(5)
,
Cristian Chaparro
(6)
,
Thierry Tonon
(1, 2)
,
Tristan Barbeyron
(1, 2)
,
Gurvan Michel
(1, 2)
,
Benjamin Noel
(3, 7)
,
Klaus Valentin
(8)
,
Marek Elias
(9)
,
François Artiguenave
(3)
,
Alok Arun
(1, 2)
,
Jean-Marc Aury
(3, 7)
,
José F Barbosa-Neto
(6)
,
John H Bothwell
(10)
,
François-Yves Bouget
(11)
,
Loraine Brillet
(4)
,
Francisco Cabello-Hurtado
(12)
,
Salvador Capella-Gutiérrez
(13, 14)
,
Bénédicte Charrier
(1, 2)
,
Lionel Cladière
(1, 2)
,
J Mark Cock
(1, 2)
,
Susana M Coelho
(1, 2)
,
Christophe Colleoni
(5)
,
Mirjam Czjzek
(1, 2)
,
Corinne da Silva
(3, 7)
,
Ludovic Delage
(1, 2)
,
France Denoeud
(3, 7)
,
Philippe Deschamps
(5)
,
Simon M Dittami
(15, 1)
,
Toni Gabaldón
(16, 13)
,
Claire M M Gachon
(17)
,
Agnès Groisillier
(1, 2)
,
Cécile Hervé
(1, 2)
,
Kamel Jabbari
(3, 18)
,
Michael Katinka
(3)
,
Bernard Kloareg
(1, 2)
,
Nathalie Kowalczyk
(1, 2)
,
Karine Labadie
(3)
,
Catherine Leblanc
(1, 2)
,
Pascal-Jean Lopez
(19)
,
Deirdre H Mclachlan
(10)
,
Laurence Meslet-Cladiere
(1, 20, 2)
,
Ahmed Moustafa
(21)
,
Zofia Nehr
(1, 2)
,
Pi Nyvall Collén
(1, 2)
,
Olivier Panaud
(6)
,
Frédéric Partensky
(2)
,
Julie Poulain
(22)
,
Stefan A Rensing
(23)
,
Sylvie Rousvoal
(15)
,
Gaelle Samson
(22)
,
Aikaterini Symeonidi
(24)
,
Jean Weissenbach
(22)
,
Antonios Zambounis
(25)
,
Patrick Wincker
(3)
,
Catherine Boyen
(1, 2)
1
Végétaux marins et biomolécules
2 MAPP - Procaryotes Phototrophes Marins = MArine Phototrophic Prokaryotes
3 UMR 8030 - Génomique métabolique
4 SBR - Station biologique de Roscoff [Roscoff]
5 UGSF - Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576
6 LGDP - Laboratoire Génome et développement des plantes
7 LBGB - Laboratoire de Bioinformatique pour la Génomique et la Biodiversité
8 AWI - Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung = Alfred Wegener Institute for Polar and Marine Research = Institut Alfred-Wegener pour la recherche polaire et marine
9 Department of Plant Physiology, Faculty of Sciences
10 BESC - Belfast e-Science Centre [Belfast]
11 LOMIC - Laboratoire d'Océanographie Microbienne
12 ECOBIO - Ecosystèmes, biodiversité, évolution [Rennes]
13 UPF - Universitat Pompeu Fabra [Barcelona]
14 CRG-UPF - Center for Genomic Regulation
15 LBI2M - Laboratoire de Biologie Intégrative des Modèles Marins
16 Bioinformatics and Genomics Programme
17 SAMS - Scottish Association for Marine Science
18 IBENS - Institut de biologie de l'ENS Paris
19 BOREA - Biologie des Organismes et Ecosystèmes Aquatiques
20 LEMAR - Laboratoire des Sciences de l'Environnement Marin (LEMAR)
21 American University in Cairo
22 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
23 Albert-Ludwigs-Universität Freiburg = University of Freiburg
24 Freiburg Initiative in Systems Biology
25 CERTH - Centre for Research and Technology Hellas
2 MAPP - Procaryotes Phototrophes Marins = MArine Phototrophic Prokaryotes
3 UMR 8030 - Génomique métabolique
4 SBR - Station biologique de Roscoff [Roscoff]
5 UGSF - Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576
6 LGDP - Laboratoire Génome et développement des plantes
7 LBGB - Laboratoire de Bioinformatique pour la Génomique et la Biodiversité
8 AWI - Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung = Alfred Wegener Institute for Polar and Marine Research = Institut Alfred-Wegener pour la recherche polaire et marine
9 Department of Plant Physiology, Faculty of Sciences
10 BESC - Belfast e-Science Centre [Belfast]
11 LOMIC - Laboratoire d'Océanographie Microbienne
12 ECOBIO - Ecosystèmes, biodiversité, évolution [Rennes]
13 UPF - Universitat Pompeu Fabra [Barcelona]
14 CRG-UPF - Center for Genomic Regulation
15 LBI2M - Laboratoire de Biologie Intégrative des Modèles Marins
16 Bioinformatics and Genomics Programme
17 SAMS - Scottish Association for Marine Science
18 IBENS - Institut de biologie de l'ENS Paris
19 BOREA - Biologie des Organismes et Ecosystèmes Aquatiques
20 LEMAR - Laboratoire des Sciences de l'Environnement Marin (LEMAR)
21 American University in Cairo
22 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
23 Albert-Ludwigs-Universität Freiburg = University of Freiburg
24 Freiburg Initiative in Systems Biology
25 CERTH - Centre for Research and Technology Hellas
Jonas Collén
Connectez-vous pour contacter l'auteur
- Function : Correspondent author
- PersonId : 957194
Connectez-vous pour contacter l'auteur
Betina Porcel
- Function : Author
- PersonId : 1058697
- IdHAL : betina-porcel
- ORCID : 0000-0003-0169-5302
Cristian Chaparro
- Function : Author
- PersonId : 172039
- IdHAL : cristian-chaparro
- ORCID : 0000-0002-5162-349X
- IdRef : 253122988
Thierry Tonon
- Function : Author
- PersonId : 2649
- IdHAL : thierry-tonon
- ORCID : 0000-0002-1454-6018
- IdRef : 132275414
Tristan Barbeyron
- Function : Author
- PersonId : 762576
- ORCID : 0000-0002-5504-5236
- IdRef : 178771899
Gurvan Michel
- Function : Author
- PersonId : 1176853
- IdHAL : gurvan-michel
- ORCID : 0000-0002-3009-6205
Benjamin Noel
- Function : Author
- PersonId : 1168862
- ORCID : 0000-0002-5830-3253
Jean-Marc Aury
- Function : Author
- PersonId : 756899
- IdHAL : jean-marc-aury
- ORCID : 0000-0003-1718-3010
Loraine Brillet
- Function : Author
- PersonId : 1233847
- IdHAL : loraine-brillet-gueguen
- ORCID : 0000-0002-8640-4190
Francisco Cabello-Hurtado
- Function : Author
- PersonId : 989893
- ORCID : 0000-0002-3212-9429
- IdRef : 226741346
Bénédicte Charrier
- Function : Author
- PersonId : 965505
- IdHAL : benedicte-charrier
- ORCID : 0000-0001-5721-1640
Lionel Cladière
- Function : Author
- PersonId : 3417
- IdHAL : lionel-cladiere
- IdRef : 084111550
J Mark Cock
- Function : Author
- PersonId : 184497
- IdHAL : j-mark-cock
- ORCID : 0000-0002-2650-0383
- IdRef : 113742665
Susana M Coelho
- Function : Author
- PersonId : 777675
- ORCID : 0000-0002-9171-2550
- IdRef : 185862780
Mirjam Czjzek
- Function : Author
- PersonId : 3511
- IdHAL : mirjam-czjzek
- ORCID : 0000-0002-7483-2841
- IdRef : 145158225
Corinne da Silva
- Function : Author
- PersonId : 908690
- IdHAL : corinne-da-silva
France Denoeud
- Function : Author
- PersonId : 908628
- IdHAL : france-denoeud
- ORCID : 0000-0001-8819-7634
- IdRef : 078754917
Philippe Deschamps
- Function : Author
- PersonId : 174557
- IdHAL : philippe-deschamps
- ORCID : 0000-0001-6497-913X
- IdRef : 111483972
Simon M Dittami
- Function : Author
- PersonId : 2339
- IdHAL : simon-dittami
- ORCID : 0000-0001-7987-7523
- IdRef : 142926493
Claire M M Gachon
- Function : Author
- PersonId : 183171
- IdHAL : claire-gachon
- ORCID : 0000-0002-3702-7472
- IdRef : 091976901
Agnès Groisillier
- Function : Author
- PersonId : 1364742
- IdHAL : agnes-groisillier
- ORCID : 0000-0002-5358-923X
- IdRef : 13193886X
Cécile Hervé
- Function : Author
- PersonId : 2698
- IdHAL : cecile-herve
- ORCID : 0000-0001-6649-8137
- IdRef : 101613873
Kamel Jabbari
- Function : Author
- PersonId : 911237
Nathalie Kowalczyk
- Function : Author
- PersonId : 7363
- IdHAL : nathalie-kowalczyk
- IdRef : 17738929X
Karine Labadie
- Function : Author
- PersonId : 757912
- ORCID : 0000-0001-7467-8509
- IdRef : 089020235
Catherine Leblanc
- Function : Author
- PersonId : 3421
- IdHAL : catherineleblanc
- ORCID : 0000-0001-7149-0332
- IdRef : 178655279
Pascal-Jean Lopez
- Function : Author
- PersonId : 180735
- IdHAL : pascal-jean-lopez
- ORCID : 0000-0002-9914-4252
- IdRef : 16826692X
Olivier Panaud
- Function : Author
- PersonId : 758336
- ORCID : 0000-0002-9292-503X
- IdRef : 089360982
Frédéric Partensky
- Function : Author
- PersonId : 19787
- IdHAL : frederic-partensky
- ORCID : 0000-0003-1274-4050
- IdRef : 08555006X
Julie Poulain
- Function : Author
- PersonId : 756903
- IdHAL : julie-poulain
- ORCID : 0000-0002-8744-3116
- IdRef : 061407232
Jean Weissenbach
- Function : Author
- PersonId : 911249
Patrick Wincker
- Function : Author
- PersonId : 757160
- IdHAL : patrick-wincker
- ORCID : 0000-0001-7562-3454
Catherine Boyen
- Function : Author
- PersonId : 1353
- IdHAL : catherine-boyen
- IdRef : 032106335
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.
Domains
Life Sciences [q-bio]Origin | Publisher files allowed on an open archive |
---|
Loading...