Nuclear genome characterization and carrageenan analysis ofGymnogongrus griffithsiae (Rhodophyta) from North Carolina

DNA reassociation kinetics were used to determine nuclear genome organization and complexity inGymnogongrus griffithsiae (Gigartinales, Rhodophyta). Results indicate the presence of three second order components corresponding to fast (3%), intermediate (8%) and slow (89%) fractions. Thus the genome consists mainly of unique sequences. Thermal denaturation (T _m) indicated a nuclear DNA base pair composition of 40 mol% G + C. Microspectrophotometry with the DNA-localizing fluorochrome DAPI was used to confirm ploidy level differences in the gametophytic and tetrasporoblastic phases. Comparisons of mean nuclear DNA (I _f) values to chicken erythrocytes (RBC) resulted in an estimate of 0.32 pg/2 C genome forGymnogongrus griffithsiae. Karyological studies using aceto-orcein revealed the presence of ca. 23 bivalents during diakinesis of tetrasporangial mother cells. Total carrageenan content in water extraction was 30% dry weight. Infrared spectroscopy confirmed the isolated carrageenan to be the iota-fraction.     

Nuclear genome characterization of the carrageenophyteAgardhiella subulata (Rhodophyta)

DNA reassociation kinetics were used to determine nuclear genome organization and complexity inAgardhiella subulata (Gigartinales, Rhodophyta). Results indicate the presence of three second-order components corresponding to fast (22%), intermediate (68%) and slow (10%) fractions. Thus, the genome consists of 90% repetitive sequences. Microspectrophotoometry with the DNA-localizing fluorochrome DAPI was used to confirm ploidy level differences in the gametophytic and tetrasporophytic phases. Results indicate that meiosis occurs during tetrasporogenesis. Comparison of mean nuclear DNA (I_f) values to chicken erythrocytes (RBC) resulted in an estimate of 0.9 pg/2C genome forAgardhiella. Karyological studies using aceto-orcein revealed a chromosome complement of 2N = 44 in carposporangia and the presence of 22 bivalents during diakinesis of tetraspore mother cells.     

Nuclear genome characterization of the carrageenophyteHypnea musciformis (Rhodophyta)

DNA reassociation kinetics were used to determine nuclear genome organization and complexity in the carrageenophyteHypnea musciformis (Gigartinales, Rhodophyta). Results indicate the presence of three second order components corresponding to fast (2%), intermediate (33%) and slow (65%) fractions. Microspectrophotometry with the DNA-localizing fluorochrome DAPI confirmed ploidy level differences in the gametophytic and tetrasporophytic phases. Elevated (endopolyploid) nuclear DNA levels were observed in both gametophytic and cystocarpic tissue. Comparison of mean nuclear DNA (If) values to chicken erthrocytes (RBC) resulted in an estimate of 0.22 pg/2 C genome forHypnea musciformis. Karyological studies using aceto-orcein revealed a chromosome complement of five bivalents during diakinesis of tetraspore mother cells.     

Agar Analysis,nuclear genome quantification and characterization of four agarophytes (Gracilaria) from the Mexican Gulf Coast

DNA reassociation kinetics were used to determine nuclear genome organization and complexity in four species of Gracilaria (Gracilariales, Rhodophyta). In Gracilaria tikvahiae, G. caudata, G. cervicornis and G. divaricata, results indicate the presence of three second order components corresponding to fast, intermediate and slow fractions. Repetitive sequences varied from 13–46% and unique DNA ranged from 45–78%, Thermal denaturation (T _m) indicated guanine + cytosine (G + C) levels of 41.9–46.0 mol % G + C. Microspectrophotometry with the DNA-localizing fluorochrome DAPI was used to quantify nuclear DNA content. Comparisons of mean nuclear DNA (I _f) values to chicken erythrocytes (RBC) resulted in an estimate of 0.37–0.40 pg/2C genomes for the four Gracilaria species. Total agar content following alkaline pretreatment ranged from 7–15% dry weight. Gel strengths were generally below commercial levels, ranging from 40–260 g cm⁻² Nuclear genome profiles developed from information for genome size, organization and complexity are compared with data for agar quantity and quality. Gel quality and quantity do not appear to be correlated with either large repetitive fraction DNA or a high degree of genome complexity as previously speculated.     

Relationships among Eucheuma denticulatum,Eucheuma isiforme and Kappaphycus alvarezii (Gigartinales,Rhodophyta) based on nuclear ssu-rRNA gene sequences

The nuclear genes encoding small-subunit ribosomal RNAs (ssu-rDNAs) of the carrageenophytes Eucheuma denticulatum, E. isiforme and Kappaphycus alvarezii were amplified by the polymerase chain reaction, cloned and sequenced. The sequences range from 1767 (K. alvarezii) to 1781 (E. isiforme) nucleotides in length, and have guanine+cytosine contents between 51.2% (E. isiforme) and 51.5% (E. denticulatum). Pairwise sequence identities among these sequences ranged from 97.6% to 98.5%, levels comparable to some intergeneric identities within Gracilariales. In phylogenetic analyses, the two Eucheuma ssu-rDNAs group stably together vis-a-vis the ssu-rDNA of K. alvarezii, and these three ssu-rDNAs form a monophyletic group within a larger grouping of other carrageenophytes. The results demonstrate quantitatively that analysis of nuclear-encoded ssu-rDNA sequences is likely to be useful in resolving taxonomic, phylogenetic and biogeographic questions among tribe Eucheumatoideae Doty.     

The farmed Eucheuma species (Gigartinales,Rhodophyta) in Danajon Reef,Philippines: carrageenan properties

Six cultured strains of Eucheuma denticulatum and E. alvarezii, from which stocks can be selected for the development of a Eucheuma seedling bank, were tested for their carrageenan quality from June to November 1988. Percent yield of all the varieties taken together was apparently higher in June, becoming lower in November (regression, r –0.785, probability, p 0.001). Stepwise regression analysis was done to determine the existence of any relationship between any of the following parameters: gel strength, viscosity, sulfate content, month of sampling, and yield, whether taken individually or in combination. Results show variations of the yield with the month of sampling. ANOVA was performed to test whether there are differences in sulfate levels, gel strength, and viscosity between the Eucheuma alvarezii morphotypes. There was no significant difference between the green and the brown types.     

Laboratory and field growth studies of commercial strains ofEucheuma denticulatum andKappaphycus alvarezii in the Philippines

Daily growth rates of 0.1 to 8.4% d^-1 for the brown form and 0.2 to 6.3% d^-1 of the green form were measured for 3 to 5-cm long branches of the tropical red seaweedKappaphycus alvarezii cultured in the laboratory. Highest growth rates were found using inexpensive enrichments such as soil water and coconut water supplemented with 0.7 mM N and 13 µM P and with a liquid fertilizer, Algafer, produced from seaweeds in the Philippines. Laboratory grown branches of bothK. alvarezii andEucheuma denticulatum transplanted to rafts in the field showed daily growth rates of 4.4 to 8.9% d^-1, as high or higher than other reported growth rates. The studies, carried out in the Philippines, demonstrate the viability and high yield of laboratory cultivars and methods to keep laboratory culture costs low.     

Quantification and characterization of nuclear genomes in commercial red seaweeds (Gracilariales) from the Philippines

Eight species of Gracilariaceae from the Philippines, representing the generaGracilaria, Gracilariopsis andHydropuntia, were investigated to quantify and characterize their nuclear genomes. DNA reassociation kinetics were used to determine nuclear genome organization and complexity in six of these species. Results indicate the presence of three second order components corresponding to fast, intermediate and slow fractions. Repetitive sequences varied from 13–74% and unique DNA ranged from 26–84%. Microspectrophotometry with the DNA-localizing fluorochrome DAPI was used to quantify nuclear DNA contents. Comparisons of mean nuclear DNA (I _f ) values to chicken erythrocytes (RBC) resulted in an estimate of 0.38–0.43 pg/2 C genomes for seven of the species investigated. Preliminary analyses of agar content and quality confirm the economic potential ofGracilaria firma, Gracilaria sp. 2 from Sorsogon andGracilariopsis bailinae. Nuclear genome profiles developed from data for genome size, organization and complexity are compared with data for agar quantity and quality. Gel quality and quantity do not appear to be correlated with either large repetitive fraction DNA or a high degree of genome complexity.Author for correspondence     

Recent developments in manufacturing and marketing carrageenan

Carrageenan has annual sales of over US$ 200 million, about 15% of the world use of food hydrocolloids. The market for carrageenan has grown exponentially at 5% per year for at least 25 years: 5 500 metric tons in 1970, and over 20 000 metric tons expected in 1995. The industry has become dominated by very large, multi-product companies with carrageenan factories in Europe and the US, but factories are now springing up in the Philippines and Chile, where red seaweeds grow in abundance. About 80 000 tons of dry red seaweeds are needed to produce 20 000 tons of carrageenan. About 40 000 tons comes from the Philippines, 15 000 tons from Indonesia, 15 000 tons from Chile, and 10 000 tons from elsewhere. Carrageenan growth depends on food fads like the McLean hamburger and food winners like processed pork and turkey. Carrageenan is a regulated food additive, and current health concerns focus on the minimum safe molecular weight for carrageenan when eaten. The most innovative development in carrageenans in recent years has been the introduction of a food grade version of lower cost natural grade carrageenan. Its acceptance, however, has been hampered by strong resistance from conventional carrageenan producers.     

Cage culture ofKappaphycus alvarezii var.tambalang (Gigartinales,Rhodophyceae)

Kappaphycus alvarezii var.tambalang was cultured in a 3 × 3 m bamboo raft installed inside a 4 × 4 m floating net cage ofLates calcarifer (sea bass) broodstock at SEAFDEC Sub-station Igang, Guimaras, Philippines, from December 1989 to May 1990. Growth and production ofK. alvarezii var.tambalang was influenced by the culture months. The highest growth rate and production were recorded in January and May, respectively, while the lowest growth rate and production were observed in March. Average growth rate (wet weight) ranged from 3.72 to 7.17% day^-1, while production ranged from 575.5 to 2377 g m^-1 line^-1. A total production of approximately 123 t (fresh) or 37 t (dried) ha^-1 in the 5-month harvest season was produced from this culture system. Cultivation ofK. alvarezii var.tambalang in cages is possible, which indicates that seaweeds can be grown with carnivorous finfish, a practice which is still untapped.     

Quantification and characterization of nuclear genomes in commercial red seaweeds: Gracilariales and Gelidiales

Nuclear genome profiles were developed for representative species of the Gelidiales and Gracilariales using information from present and previous studies of cytogenetics, cytophotometry and DNA reassociation kinetics. Results indicate that species of Gracilaria and Gracilariopsis are characterized by distinct chromosome complements of n = 24 and n = 32, respectively, a narrow range of small genome sizes (2C = 0.35–0.45 pg) and a wide range of values for repeated and unique genome sequences. In contrast, the Gelidiales investigated are characterized by a wide range of chromosome complements, n = 6–29, a wider range of genome sizes (2C = 0.42–0.68 pg) and a large proportion of unique genome sequences. Nuclear genome sizes for species of the Gelidiales and Gracilariales are compared with estimates of other red algal orders including the Bangiales, Ceramiales and Gigartinales.     

Brominated sesquiterpene metabolites of Hypnea pannosa (Gigartinales,Rhodophyta)

A chloroform extract of freeze-dried Hypnea pannosa J. Ag., collected from the intertidal region near Karachi, Pakistan, furnished three bromine-containing secondary metabolites. These were characterised, using spectroscopic techniques, as 10-bromo-7, 12-dihydroxy-Δ^{3, 4}-laurene, filiformin and filiforminol. This is the first report of halogenated terpenoids from the genus Hypnea. author for correspondence     

Laboratory-induced development of the ice-ice disease of the farmed red algae Kappaphycus alvarezii and Eucheuma denticulatum (Solieriaceae,Gigartinales, Rhodophyta)

The most common perception of unfavorable environmental factors causing the ice-ice disease in the farmed seaweeds, Kappaphycus and Eucheuma, was demonstrated in this study for the first time using stressful conditions of abiotic factors in a continuous culture system. Light intensity of less than 50 mol photon m^–2 s^–1 and salinity of 20% or less induced ice-ice whitening characterized by short segments at midbranches which were similar to those observed in the Philippine seaweed farms, while temperatures of up to 33–35 °C resulted in wide-scale whitening leading to complete damage of the branches. These effects were preceded by slow growth rates from an optimum of 3.7% d^–1 to almost –2.0% d^–1. Mechanical stress by wound injury did not result to ice-ice whitening similar to the above. Environmental factors observed to trigger ice-ice in the laboratory, although may not necessarily parallel those in the field, may act synergestically to produce similar effects.     

Seasonal variation in growth and carrageenan content ofCalliblepharis jubata (Rhodophyceae,Gigartinales) from the Normandy coast,France

Study of the seasonal variation in the quality and content of iota carrageenan inCalliblepharis jubata from the Normandy coast of France shows that seasonal fluctuation of the environment affects the growth and chemical composition of this red alga. Growth increases during winter, when there is little synthesis of carrageenan and floridean starch is accumulated. When inorganic nitrogen content decreases, growth also decreases and stops (May to August); with high light intensity, the metabolism is oriented towards a synthesis of parietal carrageenans to the detriment of the reserve products such as floridean starch.Author for correspondence     

A discrete-time logistic model of frond dynamics for Mazzaella parksii (Rhodophyta, Gigartinales)

Mathematical modelling is useful in population ecology and resource management. Logistic models have traditionally been applied to unitary organisms, but it is unclear whether they could be used at the frond (ramet) level for clonal seaweeds. This study shows that frond dynamics for the clonal seaweed Mazzaella parksii (=M. cornucopiae) can be described by a discrete-time logistic model. The model is realistic in that it includes density-dependence, which was previously demonstrated experimentally for this species, and only necessitates data on frond density measured at discrete time intervals. This may constitute a useful tool for the management of clonal seaweeds of economic importance that occur in dense stands. This revised version was published online in August 2006 with corrections to the Cover Date.     

Effects of environmental factors on carrageenan fromGymnogongrus griffithsiae (Gigartinales,Rhodophyta)

The effects of environmental factors on substratum coverage, thallus length, production of iota carrageenan and gelling behavior were investigated in field populations of the red algaGymnogongrus griffithsiae (Turner) Martius. Irradiance and water temperature affected thallus substratum coverage and water gel strength of the carrageenan. The significant monthly differences in thallus length, carrageenan content and carrageenan gelling properties were not attributable to seasonal variations in irradiance and water temperature. The effect of temperature and N loading on biomass productivity, carrageenan yield and gelling characteristics were also investigated using cultures. N-enriched cultures showed decreased gel yields, higher viscosities and higher water gel strengths in the carrageenans extracted from these cultures. Milk reactivity tests were correlated with thallus nitrogen and water dessert gel strength, but neither culture temperature nor N loading showed a significant effect. The field and culture studies indicate how temperature, irradiance and N availability affect growth and hydrocolloid production.Author for correspondence     

A transposon-like sequence with short terminal inverted repeats in the nuclear genome of Chlamydomonas reinhardtii

A 1.2 kb DNA sequence, flanked by a potential seven base target-site duplication, was found inserted into a TOC1 transposable element from Chlamydomonas reinhardtii. The insertion sequence, named TOC2, is a member of a family of repeated DNA sequences that is present in all the C. reinhardtii strains tested. It resembles class II transposable elements: it possesses short 14 bp imperfect terminal repeats that begin AGGAGGGT, and sub-terminal direct repeats located within 250 bp of the termini. No large open reading frames were found. The terminal bases and length of target-site duplication are important in classifying transposable elements. On this basis TOC2 does not fall readily into existing families of class II transposable elements found in plants.     

Management of natural beds and standing stock evaluation of Hypnea musciformis (Gigartinales, Rhodophyta) in south-eastern Brazil

Hypnea musciformis, a source of-carrageenan, is abundant along the coast ofBrazil. Although the species has been exploitedsporadically on the north-east coast, this has beendone in the absence of data on seasonal fluctuationsin stock and on management of the natural beds. Thispaper evaluates the stock of a population from theUbatuba Bay, S-E Brazilian Coast, and how thepopulation recovers from monthly harvests. Dry monthlyyield ranged from 4.9 to 201.2 g m^-2 and showedno obvious seasonal pattern. The mean recovery rateafter harvesting is estimated as 35 days, and thestanding stock in the Bay (1.5 km) is approximately3.68 t y^-1 dry wt.     

Size and complexity of the nuclear genome of the ectomycorrhizal fungus Paxillus involutus

The basidiomycete Paxillus involutus is forming ectomycorrhizal symbiosis with a broad range of forest trees. Reassociation kinetics on P. involutus nuclear DNA indicated a haploid genome size of 23 Mb including 11% of repetitive DNA. A similar genome size (20 Mb) was estimated by genomic reconstruction analysis using three single copy genes. To assess the gene density in the P. involutus genome, a cosmid containing a 33-kb fragment of genomic DNA was sequenced and used to identify putative open reading frames (ORFs). Twelve potential ORFs were predicted, eight displayed significant sequence similarities to known proteins found in other organisms and notably, several homologues to the Podospora anserina vegetative incompatibility protein (HetE1) were found. By extrapolation, we estimate the total number of genes in the P. involutus haploid genome to approximately 7700.