Molecular evidence confirms the parasite Congracilaria babae (Gracilariaceae,Rhodophyta) from Malaysia

A phylogenetic study of two parasites found on the common host species Gracilaria salicornia from Japan and Malaysia based on nuclear, plastid, and mitochondrial molecular markers was conducted. The Japanese and Malaysian parasites were placed in the same cluster in the nuclear phylogenies inferred from the LSU rRNA gene and ITS region, supporting the monophyly of these parasites despite the slight anatomical variations observed. In addition to the molecular analyses, shared morphological and reproductive features including the lack of rhizoids, similar coloration to hosts, and the presence of deep spermatangial conceptacles supported the inclusion of both the Japanese and Malaysian parasites in Congracilaria babae. Phylogenetic analyses based on ITS sequences indicated that C. babae most likely evolved directly from its current host species, G. salicornia. C. babae was shown to be a member of Gracilaria sensu stricto along with its host. C. babae growing on G. salicornia is characterized by having plastid rbcL and mitochondrial cox1 gene sequences identical to those of its host, whereas the nuclear LSU rRNA gene and ITS region sequences are different from those of its host.     

Comparison of the photosynthetic efficiency,agar yield,and properties of <Emphasis Type="Italic">Gracilaria salicornia</Emphasis> (Gracilariales,Rhodophyta) with and without adelphoparasite

The red seaweed Gracilaria salicornia is widely distributed along the Gulf of Thailand and Andaman sea coast. In nature, the adelphoparasite Gracilaria babae is mostly found to grow on this alga, and it appears as a gall with dark green or yellowish orange color. This study was conducted to examine the photosynthetic efficiency, agar yield, and properties of G. salicornia in plants with (PGs) and without the adelphoparasite (Gs). The results showed that the photosynthetic efficiency of the PGs and Gs was influenced by environmental factors. The agar yield extracted from the Gs was mostly lower than that from the PGs. The gelling temperature of agar solution from the PGs was lower than in the Gs but was not significantly different (p > 0.05). The gel melting point and the viscosity of the agar solution of the PGs was significantly higher than those of the Gs (p < 0.05). The gel strength and total carbohydrate content of the PGs agar were higher than those obtained from the Gs agar, except for the sample collected in June. The content of 3,6-anhydrogalactose was higher in the PGs than in the Gs collected in February and August, when the PGs agar had greater gel strength. Similarly, the PGs agar had a higher sulfate content than did the Gs agar. This study showed that changes in the photosynthetic efficiency, yield, and properties of agar extracted from G. salicornia were influenced by the environmental factors in association with the presence of the adelphoparasite G. babae.     

Phylogeny of Gracilariaceae (Rhodophyta): evidence from plastid and mitochondrial nucleotide sequences

Gracilariaceae are mostly pantropical red algae and include ~230 species in seven genera. Infrafamilial classification of the group has long been based on reproductive characters, but previous phylogenies have shown that traditionally circumscribed groups are not monophyletic. We performed phylogenetic analyses using two plastid (universal plastid amplicon and rbcL) and one mitochondrial (cox1) loci from a greatly expanded number of taxa to better assess generic relationships and understand patterns of character distributions. Our analyses produce the most well‐supported phylogeny of the family to date, and indicate that key characteristics of spermatangia and cystocarp type do not delineate genera as commonly suggested. Our results further indicate that Hydropuntia is not monophyletic. Given their morphological overlap with closely related members of Gracilaria, we propose that Hydropuntia be synonymized with the former. Our results additionally expand the known ranges of several Gracilariaceae species to include Brazil. Lastly, we demonstrate that the recently described Gracilaria yoneshigueana should be synonymized as G. domingensis based on morphological and molecular characters. These results demonstrate the utility of DNA barcoding for understanding poorly known and fragmentary materials of cryptic red algae.     

SYSTEMATICS OF THE GRACILARIACEAE (GRACILARIALES,RHODOPHYTA): A CRITICAL ASSESSMENT BASED ON RBCL SEQUENCE ANALYSES1

Generic concepts in the economically important agarophyte red algal family Gracilariaceae were evaluated based on maximum parsimony, Bayesian likelihood, and minimum evolution analyses of the chloroplast‐encoded rbc L gene from 67 specimens worldwide. The results confirm the monophyly of the family and identify three large clades, one of which corresponds to the ancestral antiboreal genera Curdiea and Melanthalia, one to Gracilariopsis, and one to Gracilaria sensu lato, which contains nine distinct independent evolutionary lineages, including Hydropuntia. The species currently attributed to Hydropuntia comprise a single well‐supported clade composed of two distinct lineages. The two most basal clades within Gracilaria sensu lato deserve generic rank: a new genus centered around G. chilensis Bird, McLachlan et Oliveira and G. aff. tenuistipitata Chang et Xia and a resurrected Hydropuntia encompassing primarily Indo‐Pacific (G. urvillei [Montagne] Abbott, G. edulis [S. Gmelin] P. Silva, G. eucheumatoides Harvey, G. preissiana [Sonder] Womersley, and G. rangiferina [Kützing] Piccone) and western Atlantic species (G. cornea J. Agardh, G. crassissima P. et H. Crouan in Mazé et Schramm, G. usneoides [C. Agardh] J. Agardh, G. caudata J. Agardh, and G. secunda P. et H. Crouan in Mazé et Schramm). Cystocarpic features within the Gracilaria sensu lato clades appear to be more phylogenetically informative than male characters. The textorii‐type spermatangial configuration is represented in two distinct clusters of Gracilaria. The rbc L genetic divergence among the Gracilariaceae genera ranged between 8.46% and 16.41%, providing at least 2.5 times more genetic variation than does the 18S nuclear rDNA. rbc L also resolves intrageneric relationships, especially within Gracilaria sensu lato. The current number of gracilariacean species is underestimated in the western Atlantic because of convergence in habit and apparent homoplasy in vegetative and reproductive anatomy.     

Molecular identification of Grateloupia elliptica and G. lanceolata (Rhodophyta) inferred from plastid rbcL and mitochondrial COI genes sequence data

The marine red algae Grateloupia is the largest genus in the family Halymeniaceae and widely distributed from tropical to warm temperate regions of the world. In the genus Grateloupia, especially G. elliptica and G. lanceolata have common features of bladelike thalli with leather in texture and cruciately divided tetrasporangia. Due to this similar morphology, G. elliptica and G. lanceolata are frequently confused and resulted in considerable difficulty distinguishing these two taxa. We have reassessed the relationships between two species using molecular identification including plastid rbcL and mitochondrial COI genes to more accurately define their genetic diversity owing to the confusion of identification. As a result, the chloroplast-encoded rbcL sequence analyses support the distinction of two species, G. elliptica and G. lanceolata collected from Jeju Island, Korea and Japan at the species level, with interspecific divergence of 3.7-4.6 %. The genetic diversity of COI gene within species are estimated to be 0–0.3 % in G. elliptica and 0–1.0 % in G. lanceolata, respectively. The effectiveness of mtDNA COI barcoding in the identification for two species demonstrates in this study.     

57 Systematics of hydropuntia montagne (gracilariaceae,gracilariales, rhodophyta) based on comparative morphology and rbcL sequence analysis

The taxonomic validity of the genus Hydropuntia Montagne (1843) (including Polycavernosa) within the Gracilariaceae (Gracilariales, Rhodophyta) is controversial. Morphological characters that define species of Hydropuntia are said to be variable and to overlap with those of Gracilaria. Here we present a global phylogenetic study of the family based on a Bayesian analysis of a large rbcL DNA sequence dataset indicating that the genus Hydropuntia forms a well supported monophyletic clade within the family, and recognize Hydropuntia as a genus distinct from Gracilaria. We also conducted smaller phylogenetic analyses in which thirty four Hydropuntia rbcL sequences resulted in two major clades within the genus, comprising a Caribbean clade and an Indo‐Pacific clade. Diagnostic reproductive stages that separate these two clades will be illustrated.     

Plastid‐encoded rbcL phylogeny suggests widespread distribution of Galdieria phlegrea (Cyanidiophyceae,Rhodophyta)

The rare microscopic red alga Galdieria phlegrea (Cyanidiohyceae, Rhodophyta) has been discovered in the extremely acid Tinto River in Spain and this occurrence is here related to previous knowledge about the distribution and ecology of this enigmatic alga. The taxonomic affiliation of the new isolate of G. phlegrea was revealed by reconstructing the phylogeny of plastid‐encoded rbcL. According to this phylogeny, the Tinto River alga is closely related to other G. phlegrea strains originating from extreme habitats in Czechia, Italy and Turkey, suggesting a wider distribution and higher ecological versatility than previously thought. The results suggest that G. phlegrea, and then possibly also other cyanidiophycean algae, are not as restricted to strongly acidic and hot microhabitats as previously believed, which, in turn, may indicate that they may commonly have been overlooked and possibly are much more widespread than is currently believed.     

Evidence for a composite phylogenetic origin of the plastid genome of the brown alga Pylaiella littoralis (L.) Kjellm

The nucleotide sequence and the 5 flanking region of the rbcL gene coding for the large subunit of ribulose bisphosphate-1,5-carboxylase/oxygenase of Pylaiella littoralis, a brown alga, has been determined and the deduced amino-acid sequence has been compared to those of various photosynthetic and chemoautotrophic Eubacteria, of a red alga and of green plastids (Euglena gracilis, green algae and higher plants). Unlike the rbcL genes of green plastids which are more closely related to those of cyanobacteria the P. littoralis rbcL gene is more closely related to that of a -purple bacterium, as was found for the rbcS gene of another chromophytic alga [Boczar et al., Proc Natl Acad Sci USA 86: 4996–4999, 1989]. Matrix data of homology between the rbcL gene of P. littoralis and the same gene of other organisms are presented. Based on our previous report, the gene coding for the 16S rRNA from P. littoralis is closely related to that of E. gracilis (Markowicz et al., Curr Genet 14: 599–608, 1988). We suggest that the large plastid DNA molecule of P. littoralis is a phylogenetically composite genome which probably resulted from mixed endosymbiosis events, or from a horizontal transfer of DNA.     

The yield,physical and chemical properties of agar gel from Gracilaria species (Gracilariales,Rhodophyta) of the Kenya coast

Six species of Gracilaria, G. corticata J. Agardh, G. crassa Harvey, G. millardetii J. Agardh, G. salicornia (J. Ag.) Dawson, G. verrucosa (Huds.) Papenfuss and Gracilaria sp, collected from different stations along the Kenya coast were studied. The yield of hot water native agar extract ranges from 8.1–30% of dry weight, with G. verrucosa and G. salicornia having the greatest and the least yield, respectively. The gel-strength of 1.5% agar solution was highest in G. verrucosa (220 g cm^–2) and lowest in G. corticata (< 60 g cm – 2) whereas the highest gelling temperature was recorded for Gracilaria sp. (40.4 °C) and the lowest in G. verrucosa (28.9 °C). 3,6 anhydrogalactose content was the highest in G. verrucosa and the lowest in G. corticata while sulphate content was higher in the latter.     

Lineage-specific variations of congruent evolution among DNA sequences from three genomes,and relaxed selective constraints on <Emphasis Type="Italic">rbc</Emphasis>L in <Emphasis Type="Italic">Cryptomonas</Emphasis> (Cryptophyceae)

Background  

Plastid-bearing cryptophytes like Cryptomonas contain four genomes in a cell, the nucleus, the nucleomorph, the plastid genome and the mitochondrial genome. Comparative phylogenetic analyses encompassing DNA sequences from three different genomes were performed on nineteen photosynthetic and four colorless Cryptomonas strains. Twenty-three rbc L genes and fourteen nuclear SSU rDNA sequences were newly sequenced to examine the impact of photosynthesis loss on codon usage in the rbc L genes, and to compare the rbc L gene phylogeny in terms of tree topology and evolutionary rates with phylogenies inferred from nuclear ribosomal DNA (concatenated SSU rDNA, ITS2 and partial LSU rDNA), and nucleomorph SSU rDNA.     

Evidence of horizontal gene transfer between land plant plastids has surprising conservation implications

Background and AimsHorizontal gene transfer (HGT) is an important evolutionary mechanism because it transfers genetic material that may code for traits or functions between species or genomes. It is frequent in mitochondrial and nuclear genomes but has not been demonstrated between plastid genomes of different green land plant species.MethodsWe Sanger-sequenced the nuclear internal transcribed spacers (ITS1 and 2) and the plastid rpl16 G2 intron (rpl16). In five individuals with foreign rpl16 we also sequenced atpB-rbcL and trnL_UAA-trnF_GAA.Key ResultsWe discovered 14 individuals of a moss species with typical nuclear ITSs but foreign plastid rpl16 from a species of a distant lineage. None of the individuals with three plastid markers sequenced contained all foreign markers, demonstrating the transfer of plastid fragments rather than the entire plastid genome, i.e. entire plastids were not transferred. The two lineages diverged 165–185 Myr BP. The extended time interval since lineage divergence suggests that the foreign rpl16 is more likely explained by HGT than by hybridization or incomplete lineage sorting.ConclusionsWe provide the first conclusive evidence of interspecific plastid-to-plastid HGT among land plants. Two aspects are critical: it occurred at several localities during the massive colonization of recently disturbed open habitats that were created by large-scale liming as a freshwater biodiversity conservation measure; and it involved mosses whose unique life cycle includes spores that first develop a filamentous protonema phase. We hypothesize that gene transfer is facilitated when protonema filaments of different species intermix intimately when colonizing disturbed early succession habitats.     

Genetic differentiation and distribution of Pyropia acanthophora (Bangiales,Rhodophyta) in the Philippines

Pyropia acanthophora is a foliose Bangiales with widely known endemic populations in Indo-Pacific region. This alga has expanded its range recently as a consequence of introduction. In an attempt to explore the genetic diversity of Py. acanthophora within the Philippines and the impact of the introduction of the species from elsewhere, an examination of molecular differentiation and distribution was undertaken using the mitochondrial COI-5P and plastid rbcL gene sequences. The results revealed that the populations of Py. acanthophora in the Philippines exhibited high haplotypic and genetic diversities, and were found to be distinct from those previously reported as conspecific populations found in Taiwan, India, Japan, Hawaii, and from those introduced populations from Brazil. The network analyses as inferred from rbcL and from the combined COI-5P and rbcL genes showed evidence that the Philippine populations of Py. acanthophora exhibited a chaotic patchiness pattern characterized by a population with highly site-exclusive haplotypes, wide genetic variability and lack of local geographic patterns. The distribution of Py. acanthophora within the Philippines was also found to be greater than what was previously known, ranging from the extreme northwest to extreme northeast mainland Luzon coasts, including Camiguin Is., Cagayan. Understanding the genetic diversity and distribution of Py. acanthophora in the Philippines provides valuable information in relation to the conservation and effective resource management of native populations of Py. acanthophora in the tropical Asian region.     

Efficient expression of epidermal growth factor in <Emphasis Type="Italic">Chlamydomonas reinhardtii</Emphasis> CC400

The application of the green alga Chlamydomonas reinhardtii as a bioreactor is not adequate because of the difficulties caused by efficiency expressing foreign genes. To improve this efficiency a plasmid containing the epidermal growth factor (EGF) gene and a bleomycin resistance gene (ble) was constructed. We amplified the EGF gene according to the codon usage of C. reinhardtii. The vector carrying 2 expression cassettes for EGF gene and ble gene was constructed by adding rbc promoter and rbc terminator. Transformants, selected on Tris-acetate-phosphate medium containing 15 mg/L bleomycin, were screened by PCR and confirmed by Southern blotting, which showed that 3 transgenic C. reinhardtii cells contained only one copy of EGF gene integrated in different 3 sites of C. reinhardtii CC400 genome. Then EGF protein content of 3 transformants was determined by EGF precoated ELISA, indicating that EGF gene was first expressed, although at a low level, in algal cells. The presented study, as an example for expressing heterologous gene in green alga, provided feasibility to improve the efficiency of transformation of C. reinhardtii.     

The presence of exotic Hypnea flexicaulis (Rhodophyta) in the Mediterranean Sea as indicated by morphology, rbcL and cox1 analyses

Here we report the first finding of Hypnea flexicaulis Yamagishi and Masuda in the Mediterranean Sea (Lagoon of Venice, Italy), identified through molecular analyses using the plastid ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL) and the mitochondrial protein-coding cytochrome c oxidase subunit I (cox1) genes. The phylogenetic reconstruction, based on rbcL + cox1 multiple alignment, showed that all specimens of H. flexicaulis from Venice, Korea, Philippines and Taiwan were included in a monophyletic group supported by a bootstrap value of 100%.It is highly probable that H. flexicaulis has been introduced from Indo-Pacific populations, in particular the Korean one, probably via ship traffic or shellfish transfers.The use of DNA barcoding combined with morphological observations was, in this case, a rapid way to identify this allochthonous species.     

Morphological and phylogenetic study of algal partners associated with the lichen-forming fungus Porpidia crustulata from the Guancen Mountains, northern China

The algal photobiont of the lichen Porpidia crustulata from the Guancen Mountains was successfully cultivated under axenic conditions and tentatively designated as Chlorella sp. GC. The phylogenetic analysis of ribulose bisphosphate carboxylase (rbcL) and internal transcribed spacer (ITS) nucleotide sequence data revealed that this alga is closely related to C. sorokiniana. There are clear morphological differences between Chlorella sp. GC associated with Porpidia crustulata and the free-living C. sorokiniana, the former having a larger central pyrenoid. Based on our genetic and morphological characterization, the Chlorella photobiont of Porpidia crustulata is distinct from closely related Chlorella species.     

Investigation of a freshwater acrochaetioid alga (Rhodophyta) with molecular and morphological methods

An enigmatic acrochaetioid alga was collected from Niangziguan spring in Shanxi Province, northern China. Morphological data indicated that this alga reproduces exclusively asexually by monosporangia and its morphological characteristics suggested that it might be referred to Audouinella heterospora. To ascertain its phylogenetic position, phylogenetic trees were reconstructed using partial sequences of the plastid‐encoded gene (rbcL) and the nuclear‐encoded gene (SSU rDNA) applying Bayesian inference (BI), maximum parsimony (MP) and maximum likelihood (ML). However, phylogenetic reconstructions showed that this acrochaetioid alga does not belong in a clade with the genus Audouinella, but forms a clade with Thorea hispida (Thoreales). Based on this analysis it is concluded that A. heterospora represents the ‘chantransia’ stage of T. hispida.     

Effects of sulfate starvation on agar polysaccharides of Gracilaria species (Gracilariaceae,Rhodophyta) from Morib,Malaysia

The effects of sulfate starvation on the agar characteristics of Gracilaria species was investigated by culturing two red algae from Morib, Malaysia, Gracilaria changii and Gracilaria salicornia in sulfate-free artificial seawater for 5 days. The seaweed samples were collected in October 2012 and March 2013, periods which have significant variation in the amount of rainfall. The agar yields were shown to be independent of sulfate availability, with only 0.60–1.20 % increment in treated G. changii and 0.31–1.40 % increment in treated G. salicornia while their gel strengths did not increase significantly (approximately 5–7 %) after sulfate starvation for both species. The gelling and melting temperatures did not vary between control and treated samples from both species, except for the treated G. changii collected in March 2013. The gel syneresis index of G. salicornia collected in March 2013 increased significantly after sulfate deprivation. Sulfate starvation introduced some variations in the content of 3, 6-anhydrogalactose and total sulfate esters, but the changes did not have a pronounced effect on the physical properties of agar.     

SecA is plastid-encoded in a red alga: implications for the evolution of plastid genomes and the thylakoid protein import apparatus

Summary Partial sequence analysis of the plastid DNA (ptDNA) from a red alga, Antithamnion sp., revealed the presence of a homologue to the Escherichia coli SecA gene as well as two open reading frames (ORF 510, ORF 179). In addition a sec Y homologue has been detected on the plastid genome by heterologous hybridization. None of these genes has been found in completely sequenced chlorophytic plastid genomes. SecA and secY gene copies were also detected in the ptDNA of a chromophytic alga, indicating that secAY may be ubiquitous in rhodophytes and chromophytes. The significance of these findings for the evolution of plastid genomes and the thylakoid protein import mechanism is discussed.