Research Note: Simple molecular discrimination of cultivated Porphyra species (Porphyra yezoensis and Porphyra tenera) and related wild species (Bangiales,Rhodophyta)

To discriminate between cultivated Porphyra species (Porphyra yezoensis and Porphyra tenera) and closely related wild Porphyra species, we developed a polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) analysis of the rbcL gene using five restriction enzymes. Although our previous PCR‐RFLP analyses of internal transcribed spacer (ITS) rDNA and plastid RuBisCO spacer regions could not always discriminate wild P. yezoensis, wild P. tenera, and closely related wild species, the PCR‐RFLP profiles of the rbcL gene were useful in discriminating samples collected from natural habitats. Therefore, PCR‐RFLP analysis of the rbcL gene will help in the simple identification of a large number of samples, not only for the establishment of reliable cultures as breeding material, but also for the taxonomic investigations of species that are closely related to cultivated Porphyra.     

Cryptic diversity,biogeography and genetic variation in Northeast Pacific species of <Emphasis Type="Italic">Porphyra</Emphasis> sensu lato (Bangiales,Rhodophyta)

We sequenced the chloroplast rubisco large subunit (rbcL) gene in 236 samples of Porphyra sensu lato from the northeast Pacific. Comparisons of sequences within the study area as well as comparisons with published sequences revealed up to five cryptic species among the 22 named species: a species closely related to Porphyra abbottiae, a species previously identified as P. pseudolinearis, a species closely related to P. pseudolanceolata and previously identified as that species, a previously unknown species from the eastern Aleutian Islands, and a species closely related to P. schizophylla and previously identified as that species. All of these previously unrecognized species had high bootstrap values separating them from the other species. In addition, our wide geographic sampling allowed us to extend, curtail or clarify the geographic ranges of a number of the species. We also provide published sequences for P. gardneri and P. smithii for the first time. We compared amount of sequence divergence within species grouped on the basis of sexuality (monoecious, sectored into separate male and female “halves”, or dioecious), habitat (high, mid, or low intertidal/subtidal), and seasonality (winter, spring, or summer) using Tukey’s HSD t test, but we observed no significant differences between species grouped in this manner. Different species showed different levels of genetic variation in the rbcL gene apparently unrelated to these traits. Also, we observed no differences in the patterns of genetic variation in a species based on whether the specimens were collected from outside or from within the region covered by ice during Pleistocene glaciations.     

A simple and rapid technique to PCR amplify plastid genes from spores of <Emphasis Type="Italic">Porphyra</Emphasis> C. Agardh (Bangiales,Rhodophyta)

A user-friendly and fast protocol using PCR was developed to amplify the plastid rbcL gene of Porphyra, the most economically valuable genus of Rhodophyta. The technique involved the use of monospores, providing the advantage of a small and genetically homogeneous set of cells and thus reducing the risk of biological or chemical contamination. An additional factor in the choice of the rbcL gene was the huge amount of sequence data deposited in molecular biology databases and their utility as molecular markers in taxonomic studies.     

Molecular variation in Galdieria sulphuraria (Galdieri) Merola and its bearing on taxonomy

Cyanidium caldarium, Cyanidioschyzon merolae and Galdieria sulphuraria are three unicellular algae characteristic, of acid thermal environments. Recently, on the basis of morphological characters, three new species of Galdieria (G. partita, G. daedala, G. maxima ) isolated from acid-thermal springs in Russia have been instituted. A selected region of rbcL and the sequence of the intergenic spacer between the rbcL and rbcS have been amplified and sequenced from different Galdieria species and strains, in order to define molecular relationship among these interesting algae. The obtained cladogram shows that Cyanidium caldarium and Cyanidioschyzon merolae form a sister group which, in turn, is in a sister group relationship with Galdieria. This last genus is divided in two clades, one of which includes G. sulphuraria accessions from Naples (Italy), California, and Yellowstone and the other one includes G. sulphuraria accessions from Java (Indonesia) and from the Russian species. These results support the status of the genus Galdieria and suggest that G. daedala, G. maxima and G. partita are three very similar strains of G. sulphuraria; the rbcL variation within Galdieria accessions has a pattern which is broadly connected to the geographial distribution. The data obtained from the intergenic rbcL-rbcS spacer partly confirm those from the rbcL analysis.     

Conchospore production and seasonal occurrence of some Porphyra species (Bangiales,Rhodophyta) in Washington State

The leafy thalli of species of the marine red algal genus Porphyra grow rapidly but persist for a relatively short time on rocky intertidal or subtidal substrata or as epiphytes on other marine plants. In most species, the large, short-lived leafy thalli alternate with small, presumably perennial, filamentous conchocelis plants. Depending on the species of northeastern Pacific Porphyra, photoperiod and temperature are important regulators of conchospore formation and release. Data from laboratory studies of conchospore formation and release in five Washington species of Porphyra (P. abottae, P. nereocystis, P. perforata, P. pseudolanceolata and P. torta) indicate that conchospores are most likely to be released at a time that precedes the appearance of the leafy thalli in the field.     

An evaluation of species relationships in the Porphyra perforata complex (Bangiales,Rhodophyta) using starch gel electrophoresis

Traditional morphological features have formed the basis for distinguishing species of Porphyra. Among these features are number of cell layers, number of chloroplasts per cell, arrangement of reproductive structures on the thallus, and overall morphology. Chromosome number and chromosome morphology have helped corroborate some species identities. A survey of northeast Pacific species of Porphyra using starch gel electrophoresis of 15 soluble proteins has shown that electrophoretic banding patterns provide a reliable diagnostic tool for species identification. Data from starch gel electrophoresis are presented to confirm the identities of species formerly associated with the Porphyra perforata species-complex in British Columbia and northern Washington. Porphyra abbottae, P. fallax, P. kanakaensis, and P. torta are recognized as distinct species, and Porphyra sanjuanensis is synonymized with P. perforata.     

GENETIC DIVERSITY AND INTROGRESSION IN TWO CULTIVATED SPECIES (PORPHYRA YEZOENSIS AND PORPHYRA TENERA) AND CLOSELY RELATED WILD SPECIES OF PORPHYRA (BANGIALES,RHODOPHYTA)1

We investigated the genetic variations of the samples that were tentatively identified as two cultivated Porphyra species (Porphyra yezoensis Ueda and Porphyra tenera Kjellm.) from various natural populations in Japan using molecular analyses of plastid and nuclear DNA. From PCR‐RFLP analyses using nuclear internal transcribed spacer (ITS) rDNA and plastid RUBISCO spacer regions and phylogenetic analyses using plastid rbcL and nuclear ITS‐1 rDNA sequences, our samples from natural populations of P. yezoensis and P. tenera showed remarkably higher genetic variations than found in strains that are currently used for cultivation. In addition, it is inferred that our samples contain four wild Porphyra species, and that three of the four species, containing Porphyra kinositae, are closely related to cultivated Porphyra species. Furthermore, our PCR‐RFLP and molecular phylogenetic analyses using both the nuclear and plastid DNA demonstrated the occurrence of plastid introgression from P. yezoensis to P. tenera and suggested the possibility of plastid introgression from cultivated P. yezoensis to wild P. yezoensis. These results imply the importance of collecting and establishing more strains of cultivated Porphyra species and related wild species from natural populations as genetic resources for further improvement of cultivated Porphyra strains.     

Forecasting infections of the red rot disease on Porphyra yezoensis Ueda (Rhodophyta) cultivation farms

Pythium porphyrae is a fungal pathogen responsible for red rot disease of the seaweed Porphyra (Rhodophyta). Infection forecasts of Porphyra by P. porphyrae were estimated from the epidemiological observations of Porphyra thalli and numbers of zoospore of P. porphyrae in laboratory and cultivation areas. Four features of forecasting infections were determined by relating zoospore concentrations to the incidence of thallus infection; infection (in more than 1000 zoospores L⁻¹), microscopic infection [less than 2 mm in diameter of lesion (in from 2000 to 3000 zoospores L⁻¹)], macroscopic infection [more than 2 mm in diameter of lesion (in from 3000 to 4000 zoospores L⁻¹), and thallus disintegration (in more than 4000 zoospores L⁻¹). High zoospore concentrations led to more infection. The tendency that zoospore concentration of P. porphyrae increased with the rate of infection of Porphyra thalli was generally observed in forecasting infections in both the laboratory and in cultivation areas. Based on the Porphyra cultivation areas, the accuracy and consistency of forecasting infections suggest that this method could be employed to manage and control red rot disease.     

Sensory and fatty acid analyses of two Atlantic species of Porphyra (Rhodophyta)

Sensory analyses were conducted to determine levels of consumer acceptability of Porphyra yezoensis, P. umbilicalis, and P. amplissima to select appropriate species for aquaculture development in Maine (USA). The subjects included children (n = 67) and adults (n = 84); the children participated in study design by helping to select the 9 point hedonic scale used in the affective sensory tests. Two substrates were used; Porphyra was baked in crackers and also used as a coating for popcorn. No significant differences (p > 0.5) in acceptability of one species over another were observed in either trial, which suggests that native Atlantic species of Porphyra such as P. amplissima and P. umbilicalis have developmental potential in foods for North American consumers. Fatty acids were analyzed in the taste test material and in freshly collected P. umbilicalis; eicosapentaenoic acid [EPA; 20:5 (n-3)] and palmitic acid were the most common fatty acids. Quantitative analysis of EPA determined that freshly collected (January 2005) P. umbilicalis contained 3.2 mg EPA g dry wt⁻¹ (74 mg EPA 100 g fresh wt⁻¹). This concentration is not high enough to make P. umbilicalis a primary source of daily omega-3 fatty acids, but the favorable n-3/n-6 ratio (2-3:1) in these species contributes to their nutritional value.     

Porphyra and Bangia (Bangiaceae, Rhodophyta) in warm temperate waters of eastern Australia: Morphological and molecular analyses

Morphological observations confirm the presence of only three species of the Bangiaceae (Rhodophyta) in warm temperate waters of eastern Australia: Bangia atropurpurea, Porphyra columbina and Porphyra denti-culata. Analyses of DNA sequence data from the inter-generic spacer region between the large- and small-sub-unit ribulose-l,5-bisphosphate carboxylase/oxygenase gene (rbcL and rbcS, respectively) and portions of the flanking regions, confirm these taxonomic conclusions for the two Porphyra species: there is clear sequence divergence between the two species, and strong genetic similarity between P. columbina isolates over a wide geographical region. Sequence analyses also reveal a strong similarity between Bangia isolates over a wide geographical range, but the taxonomy of B. atropurpurea may need to be re-examined in light of sequence differences between these and northern hemisphere isolates of B. atropurpurea. Molecular analyses support the view that Bangia and Porphyra species are sufficiently closely related to be placed in a single genus.     

Inter- and intrapopulation genetic variation in species ofPorphyra (Rhodophyta: Bangiales) from British Columbia and adjacent waters

Starch gel electrophoresis of 17 proteins has provided data on inter- and intrapopulation genetic variation in 20 species ofPorphyra occurring in British Columbia and adjacent areas.P. cuneiformis andP. nereocystis showed no within species variation, even over ranges of more than 1000 km. Populations ofP. abbottae, P. fallax, P. fucicola, P. gardneri andP. schizophylla were characterized by fixation for certain alleles. The number of polymorphic loci in a population ranged from zero to nine, depending on the species. Six species had populations that were polymorphic at just a single locus. Only two species (P. mumfordii andP. pseudolanceolata) had populations that were polymorphic at more than three loci. These levels of genetic variation are lower than those reported for populations of JapanesePorphyra species. Eleven taxa were polymorphic for 6-phosphogluconate dehydrogenase, the most variable enzyme. No within species polymorphisms were detected for bromoperoxidase, lactate dehydrogenase, superoxide dismutase or phycoerythrin. Possible evidence for the chimeric nature of the thallus was observed only inP. mumfordii.     

Rapid DNA extraction from conchocelis and ITS-1 rDNA sequences of seven strains of cultivated Porphyra yezoensis (Bangiales, Rhodophyta)

In order to extract DNA rapidly from cultivated Porphyra, we extracted total DNA from conchocelis using the ISOPLANT II kit (Nippon Gene) without liquid nitrogen treatment or CsCl-gradient ultracentrifugation. By confirming the reproducibility of RAPD patterns, it is concluded that the quality of the extracted DNA is sufficient to use as a template for molecular investigation. Using this rapid method, the nuclear ribosomal DNA of the internal transcribed spacer (ITS) regions was amplified from seven strains of cultivated Porphyra, which had been maintained as free-living conchocelis by subculturing in the laboratory. From the amplified DNAs, the ITS-1 sequences were determined in order to identify the species and genetic relationship of the strains. The sequences were identical in the seven strains, and all the strains were identified as P. yezoensis. Furthermore, the gametophytic blades of these strains showed long linear or oblanceolate shapes in the laboratory culture. It was concluded that these strains are P. yezoensis form. narawaensis. This rapid DNA extraction method from conchocelis will be a powerful tool for phylogenetic analysis and for genetic improvement of cultivated Porphyra.     

Comparative study of wild and cultivated <Emphasis Type="Italic">Porphyra yezoensis</Emphasis> (Bangiales,Rhodophyta) based on molecular and morphological data

We compared the wild Porphyra strain OGATSU from northeastern Japan with cultivated Porphyra yezoensis f. narawaensis using the RuBisCO spacer, rbcL, and ITS-1 DNA sequences as well as early gametophyte development. Based on the molecular analyses and detailed morphological observations, OGATSU was identified as P. yezoensis, but also revealed important differences from the cultivated form. Under the same culture conditions, gametophytic blades of OGATSU produced more archeospores than P. yezoensis f. narawaensis strain HG-4. The length of blades and their length-to-width ratios were significantly lower in OGATSU than in HG-4, and the color of OGATSU blades was darker than that of HG-4. The first lateral cell division in conchospore germlings occurred significantly earlier in the OGATSU strain than in the HG-4 strain, resulting in the rounder shape of the OGATSU blade compared to that of P. yezoensis f. narawaensis. These results suggested that wild strains such as OGATSU can provide useful characters that could enhance cultivated varieties in a careful breeding program.     

Rapid detection of Pythium porphyrae in commercial samples of dried Porphyra yezoensis sheets by polymerase chain reaction

The fungal parasite Pythium porphyrae is the causative organism of red rot disease in Porphyra cultivation farms. The detection of P. porphyrae from dried Porphyra yezoensis sheets was achieved using the species-specific primers PP-1 (5′-TGTGTTCTGTGCT-CCTCTCG-3′) and PP-2 (5′-CCCAAATTGGTGTTGCCTCC-3′) with the polymerase chain reaction (PCR). The DNA sequence (707 bp) of PCR product was found to be identical to that amplified from ITS rDNA extracted from a type species of P. porphyrae (IFO 30800, The Institute of Fermentation, Osaka, Japan). Quantities of the product amplified varied with the time when samples were harvested after the occurrence of red rot disease in Porphyra farms. This simple, rapid, and inexpensive method should have great applications in furthering quality control and determination of quality ranking in the Porphyra processing industry.     

Effect of harvest method and timing on yield and regeneration of Karengo (Porphyra spp.) (Bangiales,Rhodophyta) in New Zealand

Commercial interest in harvesting wild stocks ofPorphyra and concern for this prized resource by the Maori community highlighted the need to investigate the impact of harvest method and timing onPorphyra beds. Harvesting trials were carried out at two locations near Kaikoura (South Island) and one in Wellington (southern North Island) between June 1987 and September 1987. At each of five sampling sites, ten replicate sets of four quadrats were used to test the effects of harvest method and timing on yield and regeneration. The method of harvest had a major effect on the extent of regeneration: in quadrats in which thePorphyra had been cut with basal portions left intact there were harvestable plants within two months, whereas in quadrats which were cleared of allPorphyra there was very little growth after the same period. Harvests in the latter half of thePorphyra growing season gave greater yields at all sites except Wellington. Several species ofPorphyra were found to exist at the Kaikoura sampling sites and a single, different, species at the Wellington site. There were site to site differences in the yields.     

Phylogeny and biosystematics ofPseudomonotes (Dipterocarpaceae) based on molecular and morphological data

The placement of a recently discovered South American monotypic genus,Pseudomonotes tropenbosii, in subfam.Monotoideae (Dipterocarpaceae) extends the geographical range of the subfamily from Africa to the Neotropics. Although morphological and anatomical evidence suggest similarities betweenPseudomonotes andMonotes, the close alliance of these two genera was questionable due to their disjunct distribution and a lack of phylogenetic analysis. In the present study, we reconstructed the phylogeny ofPseudomonotes and other putatively related taxa usingrbcL sequence data. The analysis ofrbcL sequences of 20 taxa belonging to 15 genera and eight families recovered a single most parsimonious tree. The genusSarcolaena (Sarcolaenaceae) formed a clade sister to the monophyleticDipterocarpaceae clade.Monotes andPseudomonotes formed a strongly supported group, sister to the monophyletic clade withPakaraimaea and the remaining Asiatic dipterocarp species studied. The study strongly supports the placement ofPseudomonotes within subfam.Monotoideae of theDipterocarpaceae.     

A molecular and morphological investigation of Batrachospermum arcuatum (Batrachospermales, Rhodophyta) in China

Batrachospermum arcuatum specimens were analysed from seven stream segments in North China. Morphological characteristics were observed and cluster analysis was used to evaluate the divergence among thalli from. Sequence data of the rbcL gene (chloroplast gene) and cox2-3 spacer region (mitochondrial gene) were also utilized to evaluate genetic variation in specimens among stream segments. The specimens from four of the streams were monoecious, while the individuals at the other three locations were dioecious. Cluster analysis showed that the monoecious specimens were not separated from the dioecious specimens, based on morphology, but rather the specimens were grouped by geographical closeness and habitat similarity. Likewise, the combined analyses of rbcL and the cox2-3 spacer data from provided more evidence that breeding system (monoecy vs. dioecy) is not a good morphological character to distinguish species.     

Making the links: towards a global taxonomy for the red algal genus <Emphasis Type="Italic">Porphyra</Emphasis> (Bangiales,Rhodophyta)

Species assigned to Porphyra sensu lato (Bangiales) make up one of the largest groups of red algae in the world. While the Bangiales are monophyletic, Porphyra is not, but the number of genera remains unresolved and a consensus needs to be reached on how to proceed. Here, it is proposed that a global taxonomy for the group would enable resolution and consensus. Using examples from our work on Porphyra in both the northern and southern hemispheres, including the North Atlantic, Mediterranean and Pacific, notably Chile, we have addressed the following questions: i) how many species are there, ii) how many species are there in different parts of the world, and iii) how do these species relate to those in different parts of the world? A cumulative total of species described in the North Atlantic and Mediterranean since 1800 indicates that there are still species to be added to the flora for these regions. Determination of intraspecific diversity or diversity within species complexes was examined using the mitochondrial cox1. The results split the species into two distinct groups, revealed differences between the British and Faroese floras and indicated a new species in the Faroes. Detection of species diversity in different geographical areas of the world and their relationship with the North Atlantic and southeast Pacific (Chile) was studied using the plastid Rubisco spacer and partial rDNA SSU data. While the Rubisco spacer was limited for global comparisons, it was useful for species identification adding five more species to the Atlantic flora. The partial rDNA SSU data, while its shortness made it unsuitable for generic interpretation, revealed the spread of taxa from different geographical areas throughout the tree. We have concluded that to achieve a global taxonomy standard molecular markers should be used and we propose that the rbcL and complete rDNA SSU would be suitable. We have also concluded that while a few regions of the world have been well studied, before a consensus on generic boundaries can be achieved detailed taxonomic studies are needed in many other parts of the world including circumpolar Arctic, mid and southwest Atlantic and southeast Asia.     

Random amplified polymorphic DNA (RAPD) identification of genetic variation in three species ofPorphyra (Bangiales,Rhodophyta)

The random amplified polymorphic DNA (RAPD) technique was used to characterize three species ofPorphyra from the western North Atlantic and adjacent Gulf of Mexico. Twenty 10-mer primers were screened for DNA amplification usingPorphyra template DNA. Nine of these oligonucleotide primers, all (G+C)-rich, were positive or band-producing, but yielded poor or variable band resolution. Subsequent use of the universal 20-mer M 13 primer resulted in both clear band resolution with a minimum of secondary bands and a high degree of reproducibility. Amplification products for DNA from six regional isolates ofPorphyra carolinensis Coll et Cox,P. leucosticta Thuret in Le Jolis andP. rosengurttii Coll et Cox were compared to each other and toBangia atropurpurea (Roth) C. Agardh. Results provide evidence of both genetically hetero- and homogeneous populations. Use of the RAPD method with the M 13 primer yields amplification products which can be used to fingerprint specific genotypes. This procedure could be used to discriminate between hetero- and homokaryotic fusion products from previously characterized donor strains.     

Effects of temperature and ammonium on growth,pigment production and nitrogen uptake by four species of <Emphasis Type="BoldItalic">Porphyra</Emphasis> (Bangiales,Rhodophyta) native to the New England coast

Porphyra is one of the world’s most valued maricultured seaweeds and has been cultivated for several hundred years in Asia. The objective of this study was to produce critical information as a guide for the selection of an appropriate Porphyra species from coastal New England for the development of a land-based aquaculture system. Four Northwest Atlantic Porphyra species: P. leucosticta, P. amplissima, P. linearis and P. umbilicalis, were cultivated for 1 and 2 weeks at saturated light intensities (100–150 μmol photons m⁻²s⁻¹) and six combinations of ammonium (25 and 250 μmoles L⁻¹) and temperature (10, 15 and 20°C). Specific growth rate (SGR) increased with decreasing temperature in P. leucosticta, P. linearis and P. umbilicalis and increased with increasing temperature in P. amplissima. The SGR of all species was greater at the higher ammonium concentration. Porphyra linearis had the highest SGR, increasing in biomass by approximately 16% day⁻¹. Phycoerythrin (PE) content was higher at 10°C and 250 μmoles L⁻¹ in all species except P. amplissima. The PE content, measured as fresh weight (FW), of P. linearis (29 mg g⁻¹ FW⁻¹) and P. umbilicalis (26 mg g⁻¹ FW⁻¹) was significantly higher than the other two species. Tissue nitrogen content of all species measured in dry weight was on average 1.45% higher at 250 μmoles L⁻¹ than at 25 μmoles L⁻¹ ammonium concentration. Porphyra umbilicalis had the highest tissue nitrogen contents (6.76%) at 10°C and 250 μmoles L⁻¹ ammonium. Based on these results, P. linearis and P. umbilicalis should be considered as potential candidates for bioremediation with finfish and shellfish mariculture.