The Ectocarpus genome sequence by Wiley-Blackwell

Special Feature Articles: The Ectocarpus genome sequence: insights into brown algal biology and the evolutionary diversity of the eukaryotes J. Mark Cock, Susana M. Coelho, Colin Brownlee and Alison R. Taylor

Genetic diversity of Ectocarpus (Ectocarpales, Phaeophyceae) in Peru and northern Chile, the area of origin of the genome-sequenced strain Akira F. Peters, Aaron D. Mann, César A. Córdova, Juliet Brodie, Juan A. Correa, Declan C. Schroeder and J. Mark Cock

A sequence-tagged genetic map for the brown alga Ectocarpus siliculosus provides large-scale assembly of the genome sequence Svenja Heesch, Ga Youn Cho, Akira F. Peters, Gildas Le Corguillé, Cyril Falentin, Gilles Boutet, Solène Coëdel, Claire Jubin, Gaelle Samson, Erwan Corre, Susana M. Coelho and J. Mark Cock

Transcription factor families inferred from genome sequences of photosynthetic stramenopiles Edda Rayko, Florian Maumus, Uma Maheswari, Kamel Jabbari and Chris Bowler

Central and storage carbon metabolism of the brown alga Ectocarpus siliculosus: insights into the origin and evolution of storage carbohydrates in Eukaryotes Gurvan Michel, Thierry Tonon, Delphine Scornet, J. Mark Cock and Bernard Kloareg

The cell wall polysaccharide metabolism of the brown alga Ectocarpus siliculosus. Insights into the evolution of extracellular matrix polysaccharides in Eukaryotes Gurvan Michel, Thierry Tonon, Delphine Scornet, J. Mark Cock and Bernard Kloareg

Diurnal oscillations of metabolite abundances and gene analysis provide new insights into central metabolic processes of the brown alga Ectocarpus siliculosus Antoine Gravot, Simon M. Dittami, Sylvie Rousvoal, Raphael Lugan, Anja Eggert, Jonas Collén, Catherine Boyen, Alain Bouchereau and Thierry Tonon

Role of endoreduplication and apomeiosis during parthenogenetic reproduction in the model brown alga Ectocarpus John H. Bothwell, Dominique Marie, Akira F. Peters, J. Mark Cock and Susana M. Coelho

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Introduction Hidden beneath the ocean along many stretches of the coastline are luxuriant forests of brown seaweeds. These organisms have an atypical evolutionary history compared with the more commonly studied organisms in biology. The brown algae are members of the stramenopiles (or heterokonts), which diverged from other major eukaryotic groups, such as green plants, animals and fungi, well over a billion years ago (Yoon et al., 2004; Baldauf, 2008). As a result, the brown algae exhibit many unusual and interesting metabolic, developmental and cell-biological features. The recent analysis of the complete genome sequence of the filamentous brown alga Ectocarpus silicilosus has provided some important clues about how these features were acquired and the molecular mechanisms that underlie them (Cock et al., 2010). The seven feature papers presented in this issue illustrate how the Ectocarpus genome is being exploited to study many facets of brown algal biology and to investigate processes of fundamental importance to eukaryotes in general. The challenge now is to progress from analysis of the genome sequence to the application of approaches that will allow gene functions to be determined or confirmed experimentally. If this process is successful we can expect many new insights into the biology of these unusual and complex organisms in the coming years.

Summary Author for correspondence: Akira F. Peters Tel: +33 298193080 Email: akirapeters@gmail.com

New Phytologist (2010) 188: 30–41 doi: 10.1111/j.1469-8137.2010.03303.x

KEYWORDS: Chile; Ectocarpus; genetic diversity; Kuckuckia; Peru

The origin of the Ectocarpus strain used for genome sequencing (the ‘genome strain’) was Peru, where no Ectocarpus had been reported previously. To study the genetic diversity in the region and to increase the number of individuals from this area available for genetic experiments, 119 new Ectocarpus strains were isolated from eight localities along the 3000 km of coastline from central Peru to central Chile. Internal transcribed spacer 1 (ITS1) genotyping revealed nine different genotypes, five of which were endemic to the area studied and three of which were previously unknown. Individuals of the same genotype as the genome strain occurred from Peru to northernmost Chile, representing 61% of the samples in this area, from which five more genotypes were isolated. Further south, down to central Chile, most individuals belonged to Ectocarpus siliculosus, Ectocarpus fasciculatus and Ectocarpus crouaniorum. In sexual crosses, the genome strain and the new isolates of the same genotype were fully compatible. Sequences from four nuclear and cytoplasmic genetic markers (ITS1, ITS2, Rubisco spacer and Cytochrome-c oxidase subunit 3 (cox3)) separated the genome strain from the known species of Ectocarpus. It may in future be recognized as a separate species.

Summary Author for correspondence: J. Mark Cock Tel +33 (0)2 98 29 23 60 Email: cock@sb-roscoff.fr

Ectocarpus siliculosus has been proposed as a genetic and genomic model for the brown algae and the 214 Mbp genome of this organism has been sequenced. The aim of this project was to obtain a chromosome-scale view of the genome by constructing a genetic map using microsatellite markers that were designed based on the sequence supercontigs.

New Phytologist (2010) 188: 42–51 doi: 10.1111/j.1469-8137.2010.03273.x

To map genetic markers, a segregating F2 population was generated from a cross between the sequenced strain (Ec 32) and a compatible strain from northern Chile. Amplified fragment length polymorphism (AFLP) analysis indicated a significant degree of polymorphism (41%) between the genomes of these two parental strains. Of 1,152 microsatellite markers that were selected for analysis based on their location on long supercontigs, their potential as markers and their predicted ability to amplify a single genomic locus, 407 were found to be polymorphic.

KEYWORDS: chromosomes; Ectocarpus siliculosus; genetic linkage map; microsatellites; model organism; Phaeophyceae

A genetic map was constructed using 406 markers, resulting in 34 linkage groups. The 406 markers anchor 325 of the longest supercontigs on to the map, representing 70.1% of the genome sequence. The Ectocarpus genetic map described here not only provides a large-scale assembly of the genome sequence, but also represents an important tool for future genetic analysis using this organism.

Transcription factor families inferred from genome sequences of photosynthetic stramenopiles Edda Rayko, Florian Maumus, Uma Maheswari, Kamel Jabbari, Chris Bowler

Summary Author for correspondence: Chris Bowler Tel: + 0144323525 Email: cbowler@biologie.ens.fr

New Phytologist (2010) 188: 52â&#x20AC;&#x201C;66 doi: 10.1111/j.1469-8137.2010.03371.x

KEYWORDS: diatom; Ectocarpus; expression analysis; haptophyte; heat shock transcription factor; heterokont; Myb transcription factor; stramenopile; stress; transcription factor; transposable elements; zinc finger

By comparative analyses we identify lineage-specific diversity in transcription factors (TFs) from stramenopile (or heterokont) genome sequences. We compared a pennate (Phaeodactylum tricornutum) and a centric diatom (Thalassiosira pseudonana) with those of other stramenopiles (oomycetes, Pelagophyceae, and Phaeophyceae (Ectocarpus siliculosus)) as well as to that of Emiliania huxleyi, a haptophyte that is evolutionarily related to the stramenopiles. We provide a detailed description of diatom TF complements and report numerous peculiarities: in both diatoms, the heat shock factor (HSF) family is overamplified and constitutes the most abundant class of TFs; Myb and C2H2-type zinc finger TFs are the two most abundant TF families encoded in all the other stramenopile genomes investigated; the presence of diatom and lineage-specific gene fusions, in particular a class of putative photoreceptors with light-sensitive Per-Arnt-Sim (PAS) and DNA-binding (basic-leucine zipper, bZIP) domains and an HSF-AP2 domain fusion. Expression data analysis shows that many of the TFs studied are transcribed and may be involved in specific responses to environmental stimuli. Evolutionary and functional relevance of these observations are discussed.

Summary Author for correspondence: Gurvan Michel Tel: +33 298 29 23 30 Email: gurvan@sb-roscoff.fr

Brown algae exhibit a unique carbon (C) storage metabolism. The photoassimilate d -fructose 6-phosphate is not used to produce sucrose but is converted into dmannitol. These seaweeds also store C as β-1,3-glucan (laminarin), thus markedly departing from most living organisms, which use -1,4-glucans (glycogen or starch).

New Phytologist (2010) 188: 67–81 doi: 10.1111/j.1469-8137.2010.03345.x

Using a combination of bioinformatic and phylogenetic approaches, we identified the candidate genes for the enzymes involved in C storage in the genome of the brown alga Ectocarpus siliculosus and traced their evolutionary origins.

KEYWORDS: β-1,3-glucan, brown algae, Chromalveolate, Eukaryotic evolution, glycogen, mannitol, starch, trehalose.

Ectocarpus possesses a complete set of enzymes for synthesis of mannitol, laminarin and trehalose. By contrast, the pathways for sucrose, starch and glycogen are completely absent. The synthesis of β-1,3-glucans appears to be a very ancient eukaryotic pathway. Brown algae inherited the trehalose pathway from the red algal progenitor of phaeoplasts, while the mannitol pathway was acquired by lateral gene transfer from Actinobacteria. The starch metabolism of the red algal endosymbiont was entirely lost in the ancestor of Stramenopiles. In light of these novel findings we question the validity of the ‘Chromalveolate hypothesis’.

Summary Author for correspondence: Gurvan Michel Tel: +33 298 29 23 30 Email: gurvan@sb-roscoff.fr

Brown algal cell walls share some components with plants (cellulose) and animals (sulfated fucans), but they also contain some unique polysaccharides (alginates). Analysis of the Ectocarpus genome provides a unique opportunity to decipher the molecular bases of these crucial metabolisms.

New Phytologist (2010) 188: 82â&#x20AC;&#x201C;97 doi: 10.1111/j.1469-8137.2010.03374.x

An extensive bioinformatic census of the enzymes potentially involved in the biogenesis and remodeling of cellulose, alginate and fucans was performed, and completed by phylogenetic analyses of key enzymes.

KEYWORDS: adaptation to terrestrial environment, alginate, brown algae, cellulose, cell wall, Eukaryote evolution, multicellularity, sulfated fucans.

The routes for the biosynthesis of cellulose, alginates and sulfated fucans were reconstructed. Surprisingly, known families of cellulases, expansins and alginate lyases are absent in Ectocarpus, suggesting the existence of novel mechanisms and/or proteins for cell wall expansion in brown algae. Altogether, our data depict a complex evolutionary history for the main components of brown algal cell walls. Cellulose synthesis was inherited from the ancestral red algal endosymbiont, whereas the terminal steps for alginate biosynthesis were acquired by horizontal gene transfer from an Actinobacterium. This horizontal gene transfer event also contributed genes for hemicellulose biosynthesis. By contrast, the biosynthetic route for sulfated fucans is an ancestral pathway, conserved with animals. These findings shine a new light on the origin and evolution of cell wall polysaccharides in other Eukaryotes.

Diurnal oscillations of metabolite abundances and gene analysis provide new insights into central metabolic processes of the brown alga Ectocarpus siliculosus Antoine Gravot, Simon M. Dittami, Sylvie Rousvoal, Raphael Lugan, Anja Eggert, Jonas CollĂŠn, Catherine Boyen, Alain Bouchereau, Thierry Tonon

Summary Author for correspondence: Thierry Tonon Tel: +33 (0) 2 98 29 23 30 Email: tonon@sb-roscoff.fr

Knowledge about primary metabolic processes is essential for the understanding of the physiology and ecology of seaweeds. The Ectocarpus siliculosus genome now facilitates integrative studies of the molecular basis of primary metabolism in this brown alga.

New Phytologist (2010) 188: 98â&#x20AC;&#x201C;110 doi: 10.1111/j.1469-8137.2010.03400.x

Metabolite profiling was performed across two lightâ&#x20AC;&#x201C;dark cycles and under different CO2 and O2 concentrations, together with genome and targeted gene expression analysis.

KEYWORDS: brown algae (Phaeophyceae), carbon concentrating mechanisms, Ectocarpus siliculosus, metabolite profiling, nyctemeral cycle, photo-

Except for mannitol, E. siliculosus cells contain low levels of polyols, organic acids and carbohydrates. Amino acid profiles were similar to those of C3-type plants, including glycine/serine accumulation under photorespiration-enhancing conditions. Aminobutyric acid was only detected in traces. Changes in the concentrations of glycine and serine, genome annotation and targeted expression analysis together suggest the presence of a classical photorespiratory glycolate pathway in E. siliculosus rather than a malate synthase pathway as in diatoms. Several metabolic and transcriptional features do not clearly fit with the hypothesis of an alanine/aspartate-based inducible C4-like metabolism in E. siliculosus. We propose a model in which the accumulation of alanine could be used to store organic carbon and nitrogen during the light period. We finally discuss a possible link between low -aminobutyric acid contents and the absence of glutamate decarboxylase genes in the Ectocarpus genome.

Role of endoreduplication and apomeiosis during parthenogenetic reproduction in the model brown alga Ectocarpus John H. Bothwell, Dominique Marie, Akira F. Peters, J. Mark Cock and Susana M. Coelho

Summary Author for correspondence: Susana Coelho Tel: +33 (0)2 98 29 23 60 Email: coelho@sb-roscoff.fr

New Phytologist (2010) 188: 111–121 doi: 10.1111/j.1469-8137.2010.03357.x

KEYWORDS: apomeiosis, cell cycle, Ectocarpus, endoreduplication, haploid–diploid, life cycle.

The filamentous brown alga Ectocarpus has a complex life cycle, involving alternation between independent and morphologically distinct sporophyte and gametophyte generations. In addition to this basic haploid–diploid life cycle, gametes can germinate parthenogenetically to produce parthenosporophytes. This article addresses the question of how parthenosporophytes, which are derived from a haploid progenitor cell, are able to produce meiospores in unilocular sporangia, a process that normally involves a reductive meiotic division. We used flow cytometry, multiphoton imaging, culture studies and a bioinformatics survey of the recently sequenced Ectocarpus genome to describe its life cycle under laboratory conditions and the nuclear DNA changes which accompany key developmental transitions. Endoreduplication occurs during the first cell cycle in about one-third of parthenosporophytes. The production of meiospores by these diploid parthenosporophytes involves a meiotic division similar to that observed in zygote-derived sporophytes. By contrast, meiospore production in parthenosporophytes that fail to endoreduplicate occurs via a nonreductive apomeiotic event. Our results highlight Ectocarpus’s reproductive and developmental plasticity and are consistent with previous work showing that its life cycle transitions are controlled by genetic mechanisms and are independent of ploidy.

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