Ga Youn Cho

The Ectocarpus genome and the independent evolution of multicellularity in brown algae

Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further.

Reinstatement of Ectocarpus crouaniorum Thuret in Le Jolis as a third common species of Ectocarpus (Ectocarpales, Phaeophyceae) in Western Europe, and its phenology at Roscoff, Brittany

Based on morphological characters, cross‐fertility and molecular systematics, two species are currently recognized in the ubiquitous temperate brown algal genus Ectocarpus: the type species E. siliculosus (Dillwyn) Lyngbye and E. fasciculatus Harvey. We studied diversity, cross‐fertility and ecology of Ectocarpus in megatidal areas in northwest France (Western Europe) and propose to reinstate a third species, E. crouaniorum Thuret in Le Jolis. Genotyping of 67 individuals from five localities, including the type locality of E. crouaniorum, using internal transcribed spacer 1 (ITS1) length as a marker, showed that the three species co‐occurred whenever the habitat was suitable. Our survey also revealed a single putative field hybrid between E. crouaniorum and E. siliculosus, and a single individual of a further Ectocarpus genotype. In laboratory experiments, E. crouaniorum was crossed with E. siliculosus and E. fasciculatus. In 12 of 13 crosses, the zygotes did not develop (postzygotic sterility); in one experiment a viable hybrid was produced after crossing a female E. crouaniorum with a male E. siliculosus, but this hybrid was unable to form meiospores. Phylogenetic analysis of five molecular markers from the nuclear, mitochondrial and plastid genomes (in total 1818 bp) confirmed genetic separation of the three species. Ecologically, E. crouaniorum was confined to high intertidal pools and run‐offs, where the gametophyte was common from spring to summer. Another characteristic was that it usually occurred as an epiphyte of up to 12 cm in length on erect thalli of Scytosiphon lomentaria. Sporophytes of E. crouaniorum were found all year long; they were <3 cm in size or microscopic and were epilithic in the same habitat. The presence of a third species of Ectocarpus in Western Europe suggests that species diversity in this genus is larger than recognized during the last 40 years.

Genetic diversity of Scytosiphon lomentaria (Scytosiphonaceae, Phaeophyceae) from the Pacific and Europe based on RuBisCO large subunit and spacer, and ITS nrDNA sequences

G.Y. Cho, K. Kogame, H. Kawai and S.M. Boo 2007. Genetic diversity of Scytosiphon lomentaria (Scytosiphonaceae, Phaeophyceae) from the Pacific and Europe based on RuBisCO large subunit and spacer, and ITS nrDNA sequences. Phycologia 46: 657–665. DOI: 10.2216/06-70.1 Sequence variations of the internal transcribed spacers (ITS) 1 and 2 of the nrDNA and the partial RuBisCO large subunit gene-spacer-partial RuBisCO small subunit gene (rbcL-sp-S) region were investigated in samples of Scytosiphon lomentaria (Lyngbye) Link from 50 localities in the Pacific (Australia, Japan, Korea, New Zealand, Russia and United States) and the North Atlantic. ITS1 and ITS2 sequences were determined for 83 samples, the rbcL-sp-S region for 43 samples, and complete rbcL sequences for two European and three Japanese samples. Molecular phylogenetic analyses using rbcL sequences were performed including S. lomentaria and 15 other scytosiphonacean species. In the rbcL analyses the S. lomentaria samples made a clade consisting of a Pacific and a European subclade. These two subclades also were supported by the ITS and rbcL-sp-S analyses. The nucleotide differences in rbcL were 1.8–2.3% (27–33 bp/1,467 bp) between the two subclades. Such differences are so large that they are considered as indicating different, although cryptic, species. In the ITS analyses the Pacific clade was further divided into two well-supported subclades. In the Pacific clade sample localities were not geographically related to the molecular phylogeny: both subclades included samples from Korea, Japan, Oregon and New Zealand. Artificial translocations are suggested to have occurred because identical sequences were found from localities far from each other, for example, Korea and the United States, the United States and New Zealand. The two Pacific groups are possibly two distinct but cryptic species.

Colpomenia claytonii sp. nov. (Scytosiphonaceae, Phaeophyceae) based on morphology and mitochondrial cox3 sequences

Abstract Colpomenia, a small genus with 11 species of globular to bullate form, occurs in temperate to tropical waters worldwide. Because morphology is highly diverse, the species-level taxonomy requires re-evaluation. We analyzed the mitochondrial cox3 gene from 50 samples of the genus. A new species, Colpomenia claytonii sp. nov., is described based on samples collected from Korea, Japan, Hong Kong, Australia, New Zealand, South Africa, and the USA and compared with similar congeners. Compared to others, the new species is larger, and has a more irregular thallus often with a deeply infolded surface. It is usually epilithic in tide pools and in the lower intertidal and subtidal zones. In all phylogenetic analyses of cox3 sequences, C. claytonii was consistently distinct from congeners. Colpomenia expansa is closely related to C. claytonii, and the clade containing these two species is closely related to C. peregrina. A total of 14 cox3 haplotypes was found in C. claytonii, indicating high haplotype diversity and a recent dispersal pattern. The present study shows that C. claytonii is a widely distributed species across the Pacific Ocean to South Africa; it was previously misidentified as a variant of C. peregrina.

The Ectocarpus Genome and Brown Algal Genomics

Brown algae are important organisms both because of their key ecological roles in coastal ecosystems and because of the remarkable biological features that they have acquired during their unusual evolutionary history. The recent sequencing of the complete genome of the filamentous brown alga Ectocarpus has provided unprecedented access to the molecular processes that underlie brown algal biology. Analysis of the genome sequence, which exhibits several unusual structural features, identified genes that are predicted to play key roles in several aspects of brown algal metabolism, in the construction of the multicellular bodyplan and in resistance to biotic and abiotic stresses. Information from the genome sequence is currently being used in combination with other genomic, genetic and biochemical tools to further investigate these and other aspects of brown algal biology at the molecular level. Here, we review some of the major discoveries that emerged from the analysis of the Ectocarpus genome sequence, with a particular focus on the unusual genome structure, inferences about brown algal evolution and novel aspects of brown algal metabolism.

Petalonia tatewakii sp. nov. (Scytosiphonaceae, Phaeophyceae) from the Hawaiian Islands

Kogame K., Kurihara A., Cho G.Y., Lee K.M., Sherwood A.R. and Boo S.M. 2011. Petalonia tatewakii sp. nov. (Scytosiphonaceae, Phaeophyceae) from the Hawaiian Islands. Phycologia 50: 563–573. DOI: 10.2216/10-75.1 A new brown alga Petalonia tatewakii sp. nov. (Scytosiphonaceae) is described from the Hawaiian Islands based on morphological observations and phylogenetic analyses of DNA sequences of the chloroplast-encoded rbcL gene and the ITS1-5.8S-ITS2 region of the nuclear ribosomal cistron. The thalli are linear and complanate, up to 15 cm in length and 0.8 cm in width with rhizoidal filaments in the medulla. This species is morphologically distinguishable from other Petalonia species by having ascocysts among plurilocular zoidangia. Molecular phylogenetic analyses revealed that samples of P. tatewakii form a distinct clade that is sister to the clade of P. binghamiae (J. Agardh) Vinogradova. All our collections of Hawaiian Petalonia from the main Hawaiian Islands were assigned to P. tatewakii.

The Ectocarpus Genome and Brown Algal Genomics: The Ectocarpus Genome Consortium

Brown algae are important organisms both because of their key ecological roles in coastal ecosystems and because of the remarkable biological features that they have acquired during their unusual evolutionary history. The recent sequencing of the complete genome of the filamentous brown alga Ectocarpus has provided unprecedented access to the molecular processes that underlie brown algal biology. Analysis of the genome sequence, which exhibits several unusual structural features, identified genes that are predicted to play key roles in several aspects of brown algal metabolism, in the construction of the multicellular bodyplan and in resistance to biotic and abiotic stresses. Information from the genome sequence is currently being used in combination with other genomic, genetic and biochemical tools to further investigate these and other aspects of brown algal biology at the molecular level. Here, we review some of the major discoveries that emerged from the analysis of the Ectocarpus genome sequence, with a particular focus on the unusual genome structure, inferences about brown algal evolution and novel aspects of brown algal metabolism.

RuBisCO cistron sequence variation and phylogeography of Ceramium kondoi (Ceramiaceae, Rhodophyta)

Ceramium kondoi is a morphologically variable ceramiaceous red alga that occurs commonly in the northwest Pacific Ocean region and has recently been reported in the United States. Forty-five specimens of C. kondoi from 29 locations in Korea, Japan, Russia, and the USA were examined for DNA sequence variation along the whole plastid-encoded RuBisCO cistron: 1406 bp for rbcL, 103 bp for the spacer, and 387 bp for rbcS. C. kondoi specimens were variable, having up to nine haplotypes, with six found in Korea, southern Japan, far-eastern Russia, and the USA, and three found in northern Japan and far-eastern Russia. The occurrence of the same haplotype on both sides of the North Pacific Ocean provides evidence of recent introduction of the species from the west to the east. Phylogenetic reconstructions revealed the monophyly of C. kondoi and two well-supported lineages: a ‘southern lineage’ that contained specimens from Korea, southern Japan, far-eastern Russia and the USA, and a ‘northern lineage’ that included specimens from northern Japan and far-eastern Russia. The two genetic lineages are morphologically indistinguishable and referred to as cryptic species. The boundary between the two cryptic species is at the Tsugaru Strait, Japan.

Taxonomic reassessment of the Indo-Pacific Scytosiphonaceae (Phaeophyceae): Hydroclathrus rapanuii sp. nov. and Chnoospora minima from Easter Island, with proposal of Dactylosiphon gen. nov. and Pseudochnoospora gen. nov.

Abstract A new and putatively endemic species of Hydroclathrus, Hydroclathrus rapanuii, is described from the geographically isolated Easter Island in the southeastern Pacific based on morphological and molecular phylogenetic data. It is distinguished from other Hydroclathrus by thalli of unevenly furrowed thin membranes, and angular, block-like plurangial sori. Our phylogenetic analyses indicated that H. rapanuii is closely related to the generitype Hydroclathrus clathratus. We also report on the morphology and phylogeny of Chnoospora minima from Easter I. and elsewhere in the Indo-Pacific Ocean, noting the previously unreported presence of hollow portions in its medulla. Although not collected from Easter I., we herein propose the recognition of two new genera, Dactylosiphon gen. nov. and Pseudochnoospora gen. nov., based on our three-gene phylogeny and their known morphologies and anatomies. Dactylosiphon is based on the three species currently assigned to Colpomenia (C. bullosa, C. durvillei, and C. wynnei) that are genetically and morphologically (i.e. thalli with erect and finger-like tubes arising from a common saccate base) distinct from other members of Colpomenia. The monotypic genus Pseudochnoospora is represented by the decumbent, branching, and inter-adhesive species currently known as Chnoospora implexa. With the above proposals, we further increase the genus-level diversity of Scytosiphonaceae in the Indo-Pacific Ocean.

Phylogeny and distribution of the genus Pikea (Gigartinales, Rhodophyta) with special reference to P. yoshizakii from Korea

Abstract: Four species have been described in the genus Pikea (Dumontiaceae, Gigartinales): three species from North America and one species from Japan. However, the phylogeny and species delimitation in Pikea remain poorly resolved. Here we provide both rbcL and cox1 sequences for all species of Pikea, including the type of P. pinnata and a paratype of P. robusta. Our data reveal that P. californica, P. pinnata and P. yoshizakii are distinct in both data sets, but P. robusta is synonymous with the earlier-described P. pinnata. Morphological and molecular data show that Pikea from Korea is identical to P. yoshizakii and that the previous report of P. californica in Korea is a misidentification. The genus Pikea is well resolved in the main clade of the Dumontiaceae. This is the first study on the phylogeny of Pikea using rbcL and cox1 sequence data.