Genomic data is accumulating in public database at an unprecedented rate. Although presently dominated by the sequences of metazoan, plant, parasitic, and picoeukaryotic taxa, both expressed sequence tag (EST) and complete genomes of free-living algae are also slowly appearing. This wealth of information offers the opportunity to clarify many long-standing issues in algal and plant evolution such as the contribution of the plastid endosymbiont to nuclear genome evolution using the tools of comparative genomics and multi-gene phylogenetics. A particularly powerful approach for the automated analysis of genome data from multiple taxa is termed phylogenomics. Phylogenomics is the convergence of genomics science (the study of the function and structure of genes and genomes) and molecular phylogenetics (the study of the hierarchical evolutionary relationships among organisms, their genes and genomes). The use of phylogenetics to drive comparative genome analyses has facilitated the reconstruction of the evolutionary history of genes, gene families, and organisms. Here we survey the available genome data, introduce phylogenomic pipelines, and review some initial results of phylogenomic analyses of algal genome data.

In this work we report the occurrence of Scytosiphon gracilis Kogame (Scytosiphonaceae, Phaeophyceae) on the Pacific coast of Mexico. This is the first report of S. gracilis outside its previously known distribution in the western North Pacific (Korea and Japan). The identification was based on a morphological revision and a comparison of the plastid-encoded RuBisCO spacer sequences determined for Korean and Mexican algal material. Thalli were collected from the intertidal zone of Saldamando Beach, Baja California, in January 2003. The vegetative structure, as well as habitat and geographic distribution of the species are described. Reproductive structures were not found in our specimens. The poor presence/absence of S. gracilis in previous floristic studies of the area could be due to its small size and low frequency.

The genus Martensia (Delesseriaceae, Rhodophyta) is characterized by thalli composed of one to several blades that consist of proximal membranous sections and distal latticework. Nerves or veins are absent in the membranous sections. The life cycle of Martensia is accomplished by isomorphic alternation of generations. The gametophytes of Martensia are dioecious, and the male and female gametangial plants are morphologically similar. The type species of Martensia is M. elegans Hering. In this study, nine species were confirmed to occur in the subtidal regions of Jeju Island, Korea: M. albida sp. nov., M. australis Harvey, M. bibarii Y. Lee, M. elegans Hering, M. flammifolia sp. nov, M. fragilis Harvey, M. jejuensis Y. Lee, M. palmata Y. Lee, and M. projecta Y. Lee. Three of these, M. australis, M. fragilis, and M. elegans, are new records in the flora of Korea. The results of molecular analyses of the internal transcribed spacer (ITS) 1 region in the nrDNA showed that M. elegans is identical to M. australis, and M. fragilis coincides with M. bibarii. It may be a less effective tool for the species discrimination in Martensia.

A total of twenty one species of marine macro-algae were reported from 460 kms long Orissa coast in the east coast of India. Of these 9 species belongs to Chlorophyta, 2 to Phaeophyta and 10 to Rhodophyta. The low species richness compared with southern and western coasts of India was due to lack of rocky and/or coral substratum. Enteromorpha usneoides and Gelidium divaricatum were reported first from India. Enteromorpha linza, E. clathrata, Colpomenia sinuosa, Dictyota dichotoma, Catenella impudica, Compsopogon aeruginosus and Grateloupia lithophila were the new records for Orissa coast.

Sixty taxa of Euglenaceae belonging to 19 species of Euglena, 1 species of Colacium, 8 species of Lepocinclis, 22 species of Phacus and 10 species of Trachelomonas were reported from different habitats of Orissa state in the east cost of India. All the taxa were recorded for the first time from this region.

Cyanobacteria regulate their buoyancy in response to changing environmental conditions. This process is essential for cyanobacterial development and can account for their dominance in eutrophic waters in summer. The present investigation was conducted to understand the 24-hour vertical distribution of cyanobacteria and water quality characteristics in Lake Daecheong. Water samples were collected and analyzed at depth intervals of 2 or 3 m and at an interval of three hours for a day on August 28, 2001 and September 24, 2002. In 2001 the accumulated standing crop of Microcystis spp. from surface to a depth of 6 m was 94.9%. Microcystis spp. showed no vertical migration below the thermocline. Microcystis spp. had maximum density near the surface, but shifted to 2 m depth at 2 p.m. A dense population of Anabaena spp. accumulated near the surface from 2 to 5 p.m. in 2002.

Phytoplankton community in the coastal waters off the northeastern Korean Peninsula were characterized from May 2002 to August 2003. Taxonomic composition, abundance and biomass were determined at two water depths at 10 sample sites. A total of 153 phytoplankton species including 121 diatoms, 28 dinoflagellates, 7 green algae and 7 other species were identified. The mean abundance of phytoplankton varied from 15 to 430 cells mL–1 in the surface layer and from 11 to 545 cells mL–1 in the bottom layer, respectively. Phytoplankton was more abundant in coastal stations relative to those in more open ocean. The most dominant species were marine diatoms such as Thalassionema nitzschioides, Licmorphora abbreviata, Chaetoceros affinis and Chaetoceros socialis. In addition, a few limnotic diatoms including Fragilaria capucina v. rumpens, the green alga Scenedesmus dimorphus, some marine dinoflagellates and Cryptomonas sp. appeared as dominant species. Mean concentration of total chlorophyll-a varied from 0.22 to 7.87 μg chl-a L–1 and from 0.45 to 6.79 μg chl-a L–1 in the surface and bottom layers, respectively. The contribution of phytoplankton each size-fractionated varied highly with season. The contribution of microphytoplankton to total biomass of phytoplankton in the surface and bottom layer was high in February and August 2003, and that of nano-phytoplankton was high in May 2002 in both surface and bottom layers.

Despite continued studies on red algal flora in Korea, the taxonomy of the tiny ceramiaceous algae has received little attention. We report for the first time Griffithsia okiensis from Korea on the basis of morphology and molecular data. The species is small in thalli height (0.3-1.5 cm), and in diameter of vegetative cells (50-500 μm), and the ratio of cell length/breadth is 2-3 times. It has two carpogonial branches from the supporting cell of procarp. We generated psbA and rbcL sequences from ten specimens of G. okiensis isolated from Korea and Japan and from one G. japonica species isolated Japan. Eight specimens of G. okiensis from Korea were almost identical in both psbA and rbcL regions, nevertheless they differed from Japanese specimens by 4 ucleotides in psbA and 7 in rbcL. In all analyses of psbA, rbcL, and psbA + rbcL data sets, G. okiensis was determined to be a different species from G. japonica isolated from Japan, although both species showed a sister relationship. For all that extensive collection trips, we found no evidence for the occurrence of G. japonica in Korea.

Rhodochorton purpureum 4187 from Jeju Island, Korea may have a sexual life history similar to that seen by other investigators working on other strains around the world. In culture short days (8:16, 11:13, 12:12 LD) at 10-15°C induced tetrasporogenesis. Discharged spores were observed with time lapse videomicroscopy. They showed a slight amoeboid movement for 2-3 minutes before rounding up and settling. Tetrasporelings develop into male and female gametophytes. No fertilisation was observed. Tetrasporangia often were borne on carpogonial clusters of females but no discharged spores were seen. Isolate 4241 from San Juan I., Washington, USA grew well in most conditions tested but did not reproduce in short days (8:16, 11:13, 12:12 LD) at 10-15°C.

Responses to various types of mechanically induced wounding were followed in the giant-celled Caulerpalean species, Derbesia tenuissima, using time-lapse video-microscopy. Gametophyte vesicle cells. Puncture wounding: the gametophyte cell seals the puncture in 5 min. This is followed by cycles of ruptures and sealing, ending with full recovery in 24 hrs. Cut wounding: the protoplast immediately retracts away from the wall and reforms an intact, deflated protoplast that expands to fill the original cell within 21 hrs. Crush wounding (internal). When retained within the cell wall many protoplast fragments condense, round up, and coalesce; the reconstituted protoplast expands until it attains complete recovery, filling the original cell shape in 12 hrs. Crush wounding (external). Protoplast fragments extruded from the crushed cell are more numerous and smaller taking longer to recover. Most fragments become spherical, transforming into small viable cells capable of reproduction in several days. Sporophyte filaments. Crush wounding creates many small fragments that initially condense, coalesce and then expand within the wall to restore a complete filament with normal cytoplasmic streaming within 5 hrs. Reproduction: gametophyte. Our culture isolates produce more females than males (30:1). Gametangia develop one day before discharge that occurs explosively (1/6 sec) at first morning light. The vesicle cell forms successive gametangia every 14 days. Sporophyte. Each sporangium develops on a lateral branch that becomes isolated by the creation of successive basal plugs. After cytoplasmic cleavage and differentiation the stephanokont spores are discharged. The spores settle quickly and germinate forming gametophyte cells.

Long-term preservation of bloom-forming cyanobacteria was evaluated using cryopreservation and freeze-drying of nine strains belonging to four genera and seven species. All test strains, except Aphanizomenon flos-aquae NIER- 10028, showed partial or complete survival following cryopreservation and freeze-drying. Frozen and freeze-dried strains were preserved for more than two years and were revived monthly. Most strains showed higher post-thaw viability after cryopreservation, especially without cryoprotectant compared to freeze-drying. Microcystis aeruginosa NIER-10010, M. viridis NIER-10020, M. ichthyoblabe NIER-10023, M. novacekii NIER-10029 and Oscillatoria sancta NIER-10027 were revived after 2.5 years of cryopreservation. These results suggest that cryopreservation may be an easy and timesaving long-term preservation method for bloom-forming cyanobacteria.

Outdoor cultivation of cyanobacterium Spirulina platensis was carried out for 40 days in a batch mode. A half concentration of the SOT based on the underground water was used as culture medium. Working volume was 5.7 tons with 0.2 m depth. During cultivation, mean water temperature, DO and light intensity were all in proper conditions for the S. platensis growth. The adjustment of pH to over 10 with Na2CO3 and addition of the 1.5% natural salt were very effective to delete contaminant organisms, Chlamydomonas moewusii and Chlorella minutissima occurred one after the other in the culture. The mean productivity of the biomass based on the dry cell weight from 14 to 25 days, after the contaminants were deleted, was 7.8 g ·m–2· d–1, which was relatively high productivity in that a half concentration of the SOT was used for the culture. Underground water used in the culture minimized contaminants invasion and addition of the 1.5% natural salt was effective to delete contaminants as well as acted as mineral supplement in outdoor cultivation of S. platensis. Harvesting using the floating activity of S. platensis was effective from mass floating in day time after overnight without agitation and illumination.

Benthic diatoms are known as a good food for shellfish in nature and in commercial hatchery of Jeju Island, Korea. Grammatophora marina is commonly found as dominant benthic micro-algae in Jeju coastal waters throughout the year. To know the best growth conditions of this species, culture was done in terms of three parameters; water temperature, salinity and nutrients. Each parameter was controlled by temperature of 15, 20 and 25°C; salinity of 25, 30 and 35 psu; and nutrient concentrations of 50, 100 and 200%. F/2 media was used with artificial seawater for the culture, which was continued for two weeks with L:D cycle 12:12 by using fluorescent light. Maximum specific growth rate was recorded 1.68 d–1 at temperature of 25°C with salinity of 35 psu and nutrient concentration of 200% on 6th day during the culture period. Maximum biomass was also observed 4.9 × 105 cells mL–1 in the same condition. This species may belong to the euryhaline and eutrophic habitat with warm condition. For nutritional aspects of this species, protein, lipid and carbohydrate were measured. The value of protein, lipid and carbohydrate was 4.96%, 15.82% and 5.65%, respectively. The antioxidant activities of 80% methanolic extract were 46.7%, 23.7% and 23.8% on DPPH (1,1-Diphenyl-2-picrylydrazy) radical, superoxide anion radical and hydrogen peroxide scavenging, respectively. Percentage metal chelating activity was 81.2%. Enzymatic extracts of Alcalase and Ultraflow showed remarkable scavenging activities on DPPH radical (86.5% and 57.2%, respectively), and superoxide anion scavenging activities were 45.3% and 41.4% from Kojizyme and Viscozyme extracts, respectively. Extract of Protomex revealed 24.8% activity on hydrogen peroxide and Neutase showed 30.8% on hydroxyl radical scavenging effects. Celluclast and Viscozyme extracts showed 33.2% and 32.1% activities on nitric oxide scavenging, respectively, while Alcalase showed 61.5% on metal chelating. This species contains higher lipids among the biochemical compounds and higher metal chelating activities from both 80% methanolic and enzymatic extracts.

The aim of the present study was to evaluate the antioxidant activity of red algae in Jeju Island. The algal extracts were obtained with MeOH and fresh water at 20 and 70°C, and screened for antioxidant activities using hydroxyl radical (HO·), superoxide anion (O2–), hydrogen peroxide (H2O2) and DPPH free radical scavenging assays. Among them, Gracilaria verrucosa methanolic extract at 20°C (20ME, 96.85%), G. textorii aqueous extract at 20°C (20AE, 88.01%), Grateloupia filicina 20AE (85.35%), and Polysiphonia japonica 20ME (94.92%) exhibited the highest scavenging activities against HO·, O2–, H2O2, and DPPH free radicals, respectively. Moreover, P. japonica (20ME and 70ME) is correlated between DPPH free radical scavenging activity and polyphenolic contents. These results indicate that some red algae in Jeju Island could be potential candidates for development of antioxidants.

Three different forms of Undaria pinnatifida, the southern form (U. pinnatifida f. typica), the northern form (U. pinnatifida f. distans), and Samcheok form (recently cultivated strain), were examined for the contents and compositions of fucoidans. Fucoidans were extracted from the dried edible portions of three forms of U. pinnatifida in low pH condition, mainly by ethanol precipitation and CaCl2 treatment. It was shown that Samcheok form contains 1.8 and 3.5 times more fucoidans than the northern and the southern forms, respectively. The monosaccharide compositions of individual fucoidans were also varied. The fucoidans from the southern and the northern forms were shown to be composed of mainly fucose and galactose with the molar percentage ratios of 83.5%:16.5% and 87.4%:12.6%, respectively, indicating that these are F-type fucoidans. The fucoidan from Samcheok form, however, consisted of fucose (62.7%), galactose (32.9%), and small amount of glucose (4.4%). The results of this study showed that both amount and monosaccharide compositions of fucoidans are variable depending on U. pinnatifida forms.