The genome of Ectocarpus subulatus highlights unique mechanisms for stress tolerance in brown algae

Simon M. Dittami, Erwan Corre, Loraine Brillet-Guéguen, Noé Pontoizeau, Meziane Aite, 5 Komlan Avia, Christophe Caron, Chung Hyun Cho, Jonas Collén, Alexandre Cormier, Ludovic 6 Delage, Sylvie Doubleau, Clémence Frioux, Angélique Gobet, Irene González-Navarrete, Agnès 7 Groisillier, Cécile Hervé, Didier Jollivet, Hetty KleinJan, Catherine Leblanc, Agnieszka P. Lipinska, 8 Xi Liu, Dominique Marie, Gabriel V. Markov, André E. Minoche, Misharl Monsoor, Pierre 9 Pericard, Marie-Mathilde Perrineau, Akira F. Peters, Anne Siegel, Amandine Siméon, Camille 10 Trottier, Hwan Su Yoon, Heinz Himmelbauer, Catherine Boyen, Thierry Tonon 11

[1]  K. Mikami,et al.  Parthenosporophytes of the brown alga Ectocarpus siliculosus exhibit sex-dependent differences in thermotolerance as well as fatty acid and sterol composition. , 2018, Marine environmental research.

[2]  Olivier Dameron,et al.  Traceability, reproducibility and wiki-exploration for “à-la-carte” reconstructions of genome-scale metabolic models , 2018, PLoS Comput. Biol..

[3]  C. Boyen,et al.  Exploring the Cultivable Ectocarpus Microbiome , 2017, Front. Microbiol..

[4]  E. Corre,et al.  Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast , 2017, PeerJ.

[5]  Susana M. Coelho,et al.  Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus. , 2017, The New phytologist.

[6]  T. Tonon,et al.  Mannitol biosynthesis in algae: more widespread and diverse than previously thought. , 2017, The New phytologist.

[7]  Jérémie Bourdon,et al.  Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks , 2017, PLoS Comput. Biol..

[8]  M. Long,et al.  LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans , 2016, Genome research.

[9]  J. West,et al.  Parallel evolution of highly conserved plastid genome architecture in red seaweeds and seed plants , 2016, BMC Biology.

[10]  N. Satoh,et al.  A draft genome of the brown alga, Cladosiphon okamuranus, S-strain: a platform for future studies of ‘mozuku’ biology , 2016, DNA research : an international journal for rapid publication of reports on genes and genomes.

[11]  I. Nasir,et al.  Genomics of Salinity Tolerance in Plants , 2016 .

[12]  Sudhir Kumar,et al.  MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. , 2016, Molecular biology and evolution.

[13]  Monika S. Doblin,et al.  Arabinogalactan proteins have deep roots in eukaryotes: identification of genes and epitopes in brown algae and their role in Fucus serratus embryo development. , 2016, The New phytologist.

[14]  Dennis J. McHugh,et al.  A guide to the seaweed industry , 2016 .

[15]  O. De Clerck,et al.  Molecular evolution of candidate male reproductive genes in the brown algal model Ectocarpus , 2016, BMC Evolutionary Biology.

[16]  V. Volkov Salinity tolerance in plants. Quantitative approach to ion transport starting from halophytes and stepping to genetic and protein engineering for manipulating ion fluxes , 2015, Front. Plant Sci..

[17]  S. Kelly,et al.  OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy , 2015, Genome Biology.

[18]  Anat Kreimer,et al.  NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation , 2015, BMC Bioinformatics.

[19]  J. Qi,et al.  Saccharina genomes provide novel insight into kelp biology , 2015, Nature Communications.

[20]  David James Sherman,et al.  Pantograph: A template-based method for genome-scale metabolic model reconstruction , 2015, J. Bioinform. Comput. Biol..

[21]  T. Tonon,et al.  Monoclonal Antibodies Directed to Fucoidan Preparations from Brown Algae , 2015, PloS one.

[22]  Jun Wang,et al.  The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau , 2015, Proceedings of the National Academy of Sciences.

[23]  A. Roychoudhury,et al.  Reactive oxygen species (ROS) and response of antioxidants as ROS-scavengers during environmental stress in plants , 2014, Front. Environ. Sci..

[24]  Zhi-Guo Liu,et al.  The complex jujube genome provides insights into fruit tree biology , 2014, Nature Communications.

[25]  L. Delage,et al.  The Vanadium Iodoperoxidase from the Marine Flavobacteriaceae Species Zobellia galactanivorans Reveals Novel Molecular and Evolutionary Features of Halide Specificity in the Vanadium Haloperoxidase Enzyme Family , 2014, Applied and Environmental Microbiology.

[26]  T. Tonon,et al.  A metabolic approach to study algal–bacterial interactions in changing environments , 2014, Molecular ecology.

[27]  S. Pan,et al.  Genomic insights into salt adaptation in a desert poplar , 2013, Nature Communications.

[28]  Monica C Munoz-Torres,et al.  Web Apollo: a web-based genomic annotation editing platform , 2013, Genome Biology.

[29]  H. Lokstein,et al.  Chlorophyll-binding Proteins , 2013 .

[30]  Marc Lohse,et al.  OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets , 2013, Nucleic Acids Res..

[31]  David W. Cheung,et al.  SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.

[32]  Simon M Dittami,et al.  Genomes of extremophile crucifers: new platforms for comparative genomics and beyond , 2012, Genome Biology.

[33]  Jun Wang,et al.  Insights into salt tolerance from the genome of Thellungiella salsuginea , 2012, Proceedings of the National Academy of Sciences.

[34]  T. Tonon,et al.  Towards deciphering dynamic changes and evolutionary mechanisms involved in the adaptation to low salinities in Ectocarpus (brown algae). , 2012, The Plant journal : for cell and molecular biology.

[35]  H. Bohnert,et al.  The genome of the extremophile crucifer Thellungiella parvula , 2011, Nature Genetics.

[36]  D. Tautz,et al.  The evolutionary origin of orphan genes , 2011, Nature Reviews Genetics.

[37]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[38]  B. S. Manjunath,et al.  The iPlant Collaborative: Cyberinfrastructure for Plant Biology , 2011, Front. Plant Sci..

[39]  J. Poulain,et al.  In Silico Survey of the Mitochondrial Protein Uptake and Maturation Systems in the Brown Alga Ectocarpus siliculosus , 2011, PloS one.

[40]  B. Kloareg,et al.  Evolution and diversity of plant cell walls: from algae to flowering plants. , 2011, Annual review of plant biology.

[41]  Richard M. Clark,et al.  The Arabidopsis lyrata genome sequence and the basis of rapid genome size change , 2011, Nature Genetics.

[42]  W. Pirovano,et al.  Scaffolding pre-assembled contigs using SSPACE , 2011, Bioinform..

[43]  T. Flutre,et al.  Considering Transposable Element Diversification in De Novo Annotation Approaches , 2011, PloS one.

[44]  T. Tonon,et al.  The cell wall polysaccharide metabolism of the brown alga Ectocarpus siliculosus. Insights into the evolution of extracellular matrix polysaccharides in Eukaryotes. , 2010, The New phytologist.

[45]  Susana M. Coelho,et al.  A sequence-tagged genetic map for the brown alga Ectocarpus siliculosus provides large-scale assembly of the genome sequence. , 2010, The New phytologist.

[46]  B. Green,et al.  Photoprotection in the diatom Thalassiosira pseudonana: role of LI818-like proteins in response to high light stress. , 2010, Biochimica et biophysica acta.

[47]  Corinne Da Silva,et al.  The Ectocarpus genome and the independent evolution of multicellularity in brown algae , 2010, Nature.

[48]  Federico Abascal,et al.  TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations , 2010, Nucleic Acids Res..

[49]  C. Jubin,et al.  Plastid genomes of two brown algae, Ectocarpus siliculosus and Fucus vesiculosus: further insights on the evolution of red-algal derived plastids , 2009, BMC Evolutionary Biology.

[50]  Dominique Lavenier,et al.  PLAST: parallel local alignment search tool for database comparison , 2009, BMC Bioinformatics.

[51]  S. Gribaldo,et al.  Phylogenomics of Sterol Synthesis: Insights into the Origin, Evolution, and Diversity of a Key Eukaryotic Feature , 2009, Genome biology and evolution.

[52]  T. Bosch,et al.  More than just orphans: are taxonomically-restricted genes important in evolution? , 2009, Trends in genetics : TIG.

[53]  P. Rouzé,et al.  Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress , 2009, Genome Biology.

[54]  J. Archibald The Puzzle of Plastid Evolution , 2009, Current Biology.

[55]  Geoffrey J. Barton,et al.  Jalview Version 2—a multiple sequence alignment editor and analysis workbench , 2009, Bioinform..

[56]  Brandi L. Cantarel,et al.  The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics , 2008, Nucleic Acids Res..

[57]  T. Tonon,et al.  Normalisation genes for expression analyses in the brown alga model Ectocarpus siliculosus , 2008, BMC Molecular Biology.

[58]  Thomas Schiex,et al.  Genome Annotation in Plants and Fungi: EuGene as a Model Platform , 2008 .

[59]  Stefan Kurtz,et al.  LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons , 2008, BMC Bioinformatics.

[60]  Susana M. Coelho,et al.  Development and physiology of the brown alga Ectocarpus siliculosus: two centuries of research. , 2007, The New phytologist.

[61]  B. Koop,et al.  Bursts and horizontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids , 2007, BMC Genomics.

[62]  Ziheng Yang PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[63]  U. Fascio,et al.  The cell wall sensor Wsc1p is involved in reorganization of actin cytoskeleton in response to hypo‐osmotic shock in Saccharomyces cerevisiae , 2004, Yeast.

[64]  F. Blattner,et al.  Mauve: multiple alignment of conserved genomic sequence with rearrangements. , 2004, Genome research.

[65]  Daniel C. Desrosiers,et al.  The ankyrin repeat as molecular architecture for protein recognition , 2004, Protein science : a publication of the Protein Society.

[66]  Debashish Bhattacharya,et al.  A molecular timeline for the origin of photosynthetic eukaryotes. , 2004, Molecular biology and evolution.

[67]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[68]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[69]  K. Katoh,et al.  MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.

[70]  W. Swanson,et al.  The rapid evolution of reproductive proteins , 2002, Nature Reviews Genetics.

[71]  S. Franzblau,et al.  Inhibition of Mycobacterium tuberculosis growth by saringosterol from Lessonia nigrescens. , 2001, Journal of natural products.

[72]  W. Peters Some don't like it hot , 2001 .

[73]  J. Collén,et al.  REACTIVE OXYGEN METABOLISM IN INTERTIDAL FUCUS SPP. (PHAEOPHYCEAE) , 1999 .

[74]  R. Ballester,et al.  A family of genes required for maintenance of cell wall integrity and for the stress response in Saccharomyces cerevisiae. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[75]  J. West,et al.  Ectocarpus siliculosus (Dillwyn) Lyngb. from Hopkins River Falls, Victoria- the first record of a freshwater brown alga in Australia , 1996, Muelleria: An Australian Journal of Botany.

[76]  I. Davison,et al.  STRESS TOLERANCE IN INTERTIDAL SEAWEEDS , 1996 .

[77]  A. Bacic,et al.  Analysis of the structural heterogeneity of laminarin by electrospray-ionisation-mass spectrometry. , 1996, Carbohydrate research.

[78]  Richard C. Starr,et al.  UTEX—THE CULTURE COLLECTION OF ALGAE AT THE UNIVERSITY OF TEXAS AT AUSTIN 1993 LIST OF CULTURES 1 , 1993 .

[79]  R. Quatrano,et al.  Structure of the cell walls of marine algae and ecophysiological functions of the matrix polysaccharides. , 1988 .

[80]  J. Bolton Ecoclinal variation in Ectocarpus siliculosus (Phaeophyceae) with respect to temperature growth optima and survival limits , 1983 .

[81]  P. Robbins,et al.  alpha-D-Mannosidases of rat liver Golgi membranes. Mannosidase II is the GlcNAcMAN5-cleaving enzyme in glycoprotein biosynthesis and mannosidases Ia and IB are the enzymes converting Man9 precursors to Man5 intermediates. , 1982, The Journal of biological chemistry.

[82]  Peter D. Karp,et al.  Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology , 2016, Briefings Bioinform..

[83]  A. Amtmann Learning from evolution: Thellungiella generates new knowledge on essential and critical components of abiotic stress tolerance in plants. , 2009, Molecular plant.

[84]  R. Knippers,et al.  Viruses in marine brown algae. , 1998, Advances in virus research.

[85]  M. Robles,et al.  University of Birmingham High throughput functional annotation and data mining with the Blast2GO suite , 2022 .

[86]  Andreas Wilke,et al.  phylogenetic and functional analysis of metagenomes , 2022 .