The Ectocarpus genome sequence: insights into brown algal biology and the evolutionary diversity of the eukaryotes

Authors

  • J. Mark Cock,

    1. UPMC Université Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France
    2. CNRS, UMR 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France
    3. (Author for correspondence: tel +33 (0)2 98 29 23 60; email cock@sb-roscoff.fr)
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  • Susana M. Coelho,

    1. UPMC Université Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France
    2. CNRS, UMR 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France
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  • Colin Brownlee,

    1. Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
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  • Alison R. Taylor

    1. Department of Biology and Marine Biology, The University of North Carolina, Wilmington, 601 South College Road, Wilmington, NC 28403, USA
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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 brown algae are one of only a small number of eukaryotic groups that exhibit complex multicellular development. Comparison of the Ectocarpus genome sequence with those of related unicellular eukaryotes (such as the diatoms) and with the genomes of other multicellular organisms has allowed the identification of a number of genome characteristics that may have been critical for the evolution of complex multicellularity in the brown algae (Cock et al., 2010). For example, many new protein-kinase families appear to have been acquired by the brown algae since they diverged from the diatoms, including a family of receptor kinases that are particularly interesting because analogous families evolved independently in both the green plant and animal groups and these signalling molecules are thought to have played a key role in the emergence of multicellularity in both of these groups.

The Ectocarpus genome has also provided clues about how brown algae cope with the highly variable environment of the intertidal zone. Evidence was found for a complex photosynthetic system, diverse enzymes involved in the metabolism of reactive oxygen species, a flavonoid pathway and halogen-metabolism enzymes, all of which are likely to contribute to combating the abiotic and biotic stresses encountered in the intertidal environment.

This issue of New Phytologist includes a special feature devoted to the analysis of the Ectocarpus genome sequence and the development of this brown alga as a model organism. In the first paper, Peters et al. (2010a; pp. 30–41) carried out an analysis of Ectocarpus strains isolated from the region of origin of the Peruvian strain that was used for genome sequencing. This study, which involved the isolation of >100 strains from the region, provided a solid basis for relating laboratory work on the sequenced strain to its ecology in the field. Until recently, Ectocarpus strains were classified into two species, E. siliculosus and E. fasiculatus, but it has become increasingly clear that this system underestimates the complexity of the genus. A third species, E. crouaniorum, has recently been reinstated (Peters et al., 2010b) and the new study suggests that additional species need to be defined, the sequenced strain itself probably representing a separate species.

Ectocarpus has long been studied as a model organism for the brown algae (Peters et al., 2004; Coelho et al., 2007; Charrier et al., 2008) and one of the objectives of the genome project was to provide support for the application of genetic and genomic approaches to this organism (Fig. 1). A number of additional tools have been developed recently, including, for example, an expressed sequence tag (EST)-based microarray (Dittami et al., 2009), classical genetic approaches (Peters et al., 2008), quantitative PCR (Le Bail et al., 2008) and proteomic techniques (Ritter et al., 2010). Tool development is an ongoing process, with current efforts focusing on the development of genetic transformation and the construction of a mutant population suitable for screening using the TILLING approach. In this issue, Heesch et al. (pp. 42–51) describe the construction of a high-density genetic map that will be an invaluable tool for future genetic analyses in Ectocarpus. The genetic map consists of 26 large linkage groups plus eight smaller ones, consistent with the estimation of c. 25 chromosomes reported by Müller (1966, 1967) based on cytogenetic analysis. In addition to being an important tool for future genetic analyses, the genetic map also allowed the individual supercontigs of the genome assembly to be organized into pseudochromosomes (concatenations of supercontigs based on the order in which they have been mapped onto linkage groups), providing a chromosome-scale view of the genome (Cock et al., 2010).

Figure 1.

 The brown algal model Ectocarpus siliculosus. (a) Gametophyte in culture. (b) Three-dimensional confocal reconstruction of a sporophyte filament with a plurilocular sporangium (asterisk). (c) Ribbon-shaped chloroplasts in gametophyte filament cells. (d) Partheno-sporophyte in culture. (e) Nonfused gametes and 24-h-old zygotes (arrowheads) from a genetic cross. Bars: 50 μm (a); 10 μm (b,e); 5 μm (c); 10 μm (d).

The availability of complete genome sequences, not just for Ectocarpus but also for other stramenopiles, now opens up the possibility of carrying out exhaustive inventories of gene families and comparing them across the stramenopiles and with the equivalents in other major eukaryotic groups. Rayko et al. (pp. 52–66) have carried out this type of analysis for the transcription factor families of a broad range of stramenopiles and have identified several stramenopile-specific characteristics, such as the abundance of Myb and C2H2 zinc-finger proteins. The study also identified lineage-specific events, such as the proteins with two tandem bZIP domains that appear to be present only in stramenopile genomes.

Similar approaches have revealed unique aspects of stramenopile carbohydrate metabolism. Michel et al. (2010a,b; pp. 67–81 and pp. 82–97) have carried out a comprehensive analysis of candidate genes underlying the biochemistry of metabolic, storage and cell-wall carbohydrates. Earlier biochemical and physiological studies have pointed to several unique aspects of carbohydrate metabolism in the stramenopiles. Key features are the use of d-mannitol rather than sucrose as a major product of photosynthetically produced d-fructose-6-phosphate, and the use of β-1,3-glucans (such as laminarin), rather than starch, as a primary storage carbohydrate. In several eukaryotes, enzymes involved in β-1,3-glucan synthesis are conserved but they have evolved to produce extracellular β-1,3-glucans. Bioinformatic analyses (Michel et al., 2010a) have revealed a complete set of enzymes involved in mannitol, laminarin and trehalose metabolism, and the complete absence of genes involved in sucrose, starch and glycogen metabolism. Phylogenetic analyses indicate that genes involved in trehalose synthesis were acquired from an ancestral red algal symbiont, whereas those underlying d-mannitol metabolism were acquired through horizontal gene transfer from Actinobacteria. The fundamental differences between the gene systems encoding metabolic proteins and storage carbohydrates between stramenopiles and alveolates has led Michel et al. (2010a) to speculate that they arose from distinct eukaryotic hosts, which is not consistent with the chromalveolate hypothesis (Cavalier-Smith, 1999) of a single ancient eukaryotic host. Interestingly, two recent articles converge towards a similar conclusion through independent approaches based on rigorous statistical testing of several explicit predictions of the chromalveolate hypothesis (Stiller et al., 2009; Baurain et al., 2010).

In a companion paper, Michel et al. (2010b) present an analysis of candidate genes involved in cell-wall biosynthesis and remodelling. Brown algal cell walls contain cellulose and certain unique polysaccharides, including alginates. Sulphated fucans are also a significant and unusual component of brown algal cell walls. Michel et al. (2010b) show the absence of genes encoding cellulase, expansins and alginate lyases. Phylogenetic analyses indicate the inheritance of cellulose-synthesis genes from the ancestral red algal symbiont. By contrast, genes involved in alginate and hemicellulose synthesis were acquired through horizontal gene transfer with an Actinobacterial origin. Further complexity in the evolution of stramenopile cell walls is indicated by the conservation of genes involved in sulphated fucan synthesis with those of animals, suggesting an origin with the eukaryotic host.

Other studies featured in this issue illustrate how genome information is being integrated with experimental data obtained using Ectocarpus as a model organism to investigate various aspects of brown algal biology. Gravot et al. (pp. 98–110) describe several aspects of primary metabolism in Ectocarpus during the diurnal cycle. Biochemical and transcriptional patterns are revealed that signify unique metabolic strategies. Intriguingly, Ectocarpus, like the stramenopile diatom Thallassiosira pseudonana (Armbrust et al., 2004), appears to have genes encoding enzymes characteristic of organic carbon-concentrating mechanisms. Moreover, the multicellular nature of the Ectocarpus thallus has the potential to provide the functional compartmentalization necessary for such pathways. Nevertheless, the metabolic data do not support active C4 or CAM (crassulacean acid metabolism) pathways under the conditions studied. Rather, inorganic carbon-concentrating mechanisms relying on bicarbonate transport and carbonic anhydrase activity are indicated. Given the challenges of photosynthesis in the upper intertidal zone, it will be interesting to determine whether or not Ectocarpus is restricted to C3 photosynthesis or if a combination of carbon-concentrating mechanisms may be utilized, as recently demonstrated in diatoms (Roberts et al., 2007).

Reproductive and developmental plasticity is characteristic of brown macroalgae, and Ectocarpus, a photoautotroph whose ecology demands alternative reproductive and developmental strategies, is no exception. With heteromorphic (but superficially similar) sporophyte and gametophyte generations, Ectocarpus can give rise to sporophyte clones, meiospores and gametes. This reproductive repertoire is expanded by parthenogenetic development of unfertilized gametes. What is remarkable about the resultant parthenosporophytes is that a proportion exhibit reproductive competence that is essentially identical to that of a diploid heterozygous sporophyte, implying DNA replication without cell division at some stage of parthenosporophyte development (Müller, 1967). Bothwell et al. (pp. 111–121) examine the cell ploidy of Ectocarpus during the parthenogenetic cycle and provide evidence that it is during the first cell cycle of the parthenosporophyte that endoreduplication events occur. While endoreduplication is a common developmental strategy in a range of sessile organisms, and especially in photoautotrophs (Sugimoto-Shirasu & Roberts, 2003), this is the first detailed description of how and when it occurs in a brown alga. The next challenge is to understand how the DNA of these parthenotes escapes the normal controls of ploidy during the cell cycle. The authors present the first step: a description of the genes that probably underpin the cell cycle and endoreduplication process. This genomic information, together with new genetic and genomic tools available in Ectocarpus, paves the way to new and important insights into the unique developmental strategies of multicellular heterokonts.

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.

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