Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida. - Sorbonne Université Access content directly
Journal Articles Proceedings of the National Academy of Sciences of the United States of America Year : 2013

Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida.

1 Végétaux marins et biomolécules
2 MAPP - Procaryotes Phototrophes Marins = MArine Phototrophic Prokaryotes
3 Commissariat à l'Energie Atomique
4 UMR 8030 - Génomique métabolique
5 SBR - Station biologique de Roscoff [Roscoff]
6 UGSF - Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576
7 LGDP - Laboratoire Génome et développement des plantes
8 LBGB - Laboratoire de Bioinformatique pour la Génomique et la Biodiversité
9 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
10 Department of Plant Physiology, Faculty of Sciences
11 BESC - Belfast e-Science Centre [Belfast]
12 LOMIC - Laboratoire d'Océanographie Microbienne
13 ECOBIO - Ecosystèmes, biodiversité, évolution [Rennes]
14 UPF - Universitat Pompeu Fabra [Barcelona]
15 CRG-UPF - Center for Genomic Regulation
16 LBI2M - Laboratoire de Biologie Intégrative des Modèles Marins
17 Bioinformatics and Genomics Programme
18 SAMS - Scottish Association for Marine Science
19 IBENS - Institut de biologie de l'ENS Paris
20 BOREA - Biologie des Organismes et Ecosystèmes Aquatiques
21 LEMAR - Laboratoire des Sciences de l'Environnement Marin (LEMAR)
22 Department of Biology and Biotechnology Graduate Program, American University in Cairo
23 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
24 University of Freiburg [Freiburg]
25 Freiburg Initiative in Systems Biology
26 CERTH - Centre for Research and Technology Hellas
Wilfrid Carré
  • Function : Author
  • PersonId : 834354
François Artiguenave
  • Function : Author
  • PersonId : 908642
Claire M M Gachon
Michael Katinka
  • Function : Author
  • PersonId : 911250
Karine Labadie
Patrick Wincker

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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Dates and versions

hal-01073830 , version 1 (10-10-2014)

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Jonas Collén, Betina Porcel, Wilfrid Carré, Steven G Ball, Cristian Chaparro, et al.. Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida.. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110 (13), pp.5247-52. ⟨10.1073/pnas.1221259110⟩. ⟨hal-01073830⟩
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