Phylogeny of the Bangia flora of New Zealand suggests a southern origin for Porphyra and Bangia (Bangiales, Rhodophyta)

Life cycle and reproduction dynamics of Bangiales in response to environmental stresses

Red algae of the order Bangiales are notable for exhibiting flexible promotion of sexual and asexual reproductive processes by environmental stresses. This flexibility indicates that a trade-off between vegetative growth and reproduction occurs in response to environmental stresses that influence the timing of phase transition within the life cycle. Despite their high phylogenetic divergence, both filamentous and foliose red alga in the order Bangiales exhibit a haploid-diploid life cycle, with a haploid leafy or filamentous gametophyte (thallus) and a diploid filamentous sporophyte (conchocelis). Unlike haploid-diploid life cycles in other orders, the gametophyte in Bangiales is generated independently of meiosis; the regulation of this generation transition is not fully understood. Based on transcriptome and gene expression analyses, the originally proposed biphasic model for alternation of generations in Bangiales was recently updated to include a third stage. Along with the haploid gametophyte and diploid sporophyte, the triphasic framework recognizes a diploid conchosporophyte-a conchosporangium generated on the conchocelis-phase and previously considered to be part of the sporophyte. In addition to this sexual life cycle, some Bangiales species have an asexual life cycle in which vegetative cells of the thallus develop into haploid asexual spores, which are then released from the thallus to produce clonal thalli. Here, we summarize the current knowledge of the triphasic life cycle and life cycle trade-off in Neopyropia yezoensis and 'Bangia' sp. as model organisms for the Bangiales.

Molecular phylogeny of Plagiothecium and similar hypnalean mosses, with a revised sectional classification of Plagiothecium

We investigated the systematic relationships within the pleurocarpous moss genus Plagiothecium, based on cladistic analyses of sequence data from one nuclear (ITS) and two plastid (trnK-psbA (matK) and rpl16 intron) DNA regions for 110 specimens of Plagiothecium and similar hypnalean mosses. Plastid and nuclear trees were mostly similar, but differed in the placement of several species of Plagiothecium, and in the relationships among other genera. The phylogenetic hypotheses based on plastid markers were well resolved; in contrast, nuclear data were insufficient to resolve some of the lowest-level relationships within the genus. In the main Plagiothecium is natural, includes more taxa than are often recognized, and is most closely related to Isopterygiopsis and Herzogiella. Nine sections are recognized within Plagiothecium, four new: Section Pseudo-Neckera to accommodate P. neckeroideum and its allies, Section Ortholimnobium for P. handelii and P. paleaceum, Section Struckia for P. argentatum and P. enerve, and Section Rectithecium for P. piliferum. The geographical distribution of the sections suggests that Plagiothecium originated in Asia. The derived, mainly autoicous sections Plagiothecium and Leptophyllum may have spread to the Southern Hemisphere through long distance dispersal. Three new species in section Leptophyllum (P. funale, P. pacificum and P. rhizolucidum) and two new taxa in section Pseudo-Neckera (P. decoratum and P. neckeroideum fo. exile) are described. A limited phylogenetic hypothesis for the superficially similar hypnalean genus Taxiphyllum, which was used as outgroup, is included. A related genus (Longiella) is described, with a single species (L. plagiothecioides). The aquarium species T. barbieri is transferred to Ectropothecium.

A molecular phylogeny of the bladed Bangiales (Rhodophyta) in China provides insights into biodiversity and biogeography of the genus Pyropia

A molecular taxonomic study was undertaken for the first time of the bladed Bangiales of the mainland coast of China (Northwest Pacific) based on sequence data of 201 plastid rbcL and 148 nuclear 18S sequences of historical and contemporary specimens. The results revealed that only one genus of bladed Bangiales, Pyropia, was present along Chinese coast. Species delimitation was determined using two empirical methods: the Automatic Barcode Gap Discovery (ABGD) and General Mixed Yule Coalescence (GMYC) coupled with detection of monophyly in tree reconstruction. At least fourteen species of Pyropia were recovered. Six species were confirmed that had been recorded previously based on morphology (Py. suborbiculata, Py. yezoensis, Py. haitanensis, Py. katadae, Py. tenera and Py. acanthophora), three species were recorded from China for the first time (Py. kinositae, Py. pseudolinearis and Py. tanegashimensis), and five cryptic species that did not match any molecular sequences were also discovered. The phylogeny of the concatenated rbcL and 18S dataset resolved three singletons and four clades. Each clades has a strong trend towards occupying a biogeographic region, but they are not confined to them. A transoceanic and antitropical pattern of distribution was found for Pyropia at both the subgeneric and species level. This together with high biodiversity (ca. 30% of all known Pyropia species) indicates that the Northwest Pacific might act as a centre of origin for modern distribution of Pyropia since the early Cenozoic.

The bladed Bangiales (Rhodophyta) of the South Eastern Pacific: Molecular species delimitation reveals extensive diversity

A molecular taxonomic study of the bladed Bangiales of the South Eastern Pacific (coast of Chile) was undertaken based on sequence data of the mitochondrial COI and chloroplast rbcL for 193 specimens collected from Arica (18°S) in the north to South Patagonia (53°S) in the south. The results revealed for the first time that four genera, Porphyra, Pyropia, Fuscifolium and Wildemania were present in the region. Species delimitation was determined based on a combination of a General Mixed Yule Coalescence model (GMYC) and Automatic Barcode Gap Discovery (ABGD) coupled with detection of monophyly in tree reconstruction. The overall incongruence between the species delimitation methods within each gene was 29%. The GMYC method led to over-splitting groups, whereas the ABGD method had a tendency to lump groups. Taking a conservative approach to the number of putative species, at least 18 were recognized and, with the exception of the recently described Pyropia orbicularis, all were new to the Chilean flora. Porphyra and Pyropia were the most diverse genera with eight 'species' each, whereas only a 'single' species each was found for Fuscifolium and Wildemania. There was also evidence of recently diverging groups: Wildemania sp. was distinct but very closely related to W. amplissima from the Northern Hemisphere and raises questions in relation to such disjunct distributions. Pyropia orbicularis was very closely related to two other species, making species delimitation very difficult but provides evidence of an incipient speciation. The difference between the 'species' discovered and those previously reported for the region is discussed in relation to the difficulty of distinguishing species based on morphological identification.

Multi-gene phylogenetic analyses of New Zealand coralline algae: Corallinapetra Novaezelandiae gen. et sp. nov. and recognition of the Hapalidiales ord. nov

Coralline red algae from the New Zealand region were investigated in a study focused on documenting regional diversity. We present a multi-gene analysis using sequence data obtained for four genes (nSSU, psaA, psbA, rbcL) from 68 samples. The study revealed cryptic diversity at both genus and species levels, confirming and providing further evidence of problems with current taxonomic concepts in the Corallinophycidae. In addition, a new genus Corallinapetra novaezelandiae gen. et sp. nov. is erected for material from northern New Zealand. Corallinapetra is excluded from all currently recognized families and orders within the Corallinophycidae and thus represents a previously unrecognized lineage within this subclass. We discuss rank in the Corallinophycidae and propose the order Hapalidiales.

Diversity of bladed Bangiales (Rhodophyta) in western Mediterranean: recognition of the genus Themis and descriptions of T. ballesterosii sp. nov., T. iberica sp. nov., and Pyropia parva sp. nov

The diversity of the bladed species of the red algal order Bangiales from the Iberian Mediterranean shores has been reassessed after a detailed study of this region. Prior to this study, 11 bladed species of Bangiales had been reported from Mediterranean waters: Porphyra atropurpurea, P. cordata, P. coriacea, P. dioica, P. linearis, P. purpurea, P. umbilicalis, Pyropia leucosticta, Pyropia koreana (as P. olivii), Py. elongata (as P. rosengurttii) and Py. suborbiculata. A combined analysis of the nuclear nSSU and the plastid rbcL genes together with detailed morphological studies has confirmed the presence of species within the genera Porphyra and Pyropia and also revealed a third, undescribed genus, Themis gen. nov. Porphyra linearis, Pyropia elongata and the introduced Pyropia koreana had been previously listed for the Mediterranean and were recorded in this study. An additional four species, including the introduced Pyropia suborbiculata and three new species: Pyropia parva sp. nov., Themis ballesterosii sp. nov., and Themis iberica sp. nov. were also observed. Hence, most of the Porphyra species traditionally reported along these shores were not reported in this survey. This new floristic Bangiales composition confirms the importance of the Mediterranean basin as a hotspot for biodiversity, possible endemics of ancient origin and high proportion of introductions. Our data also continue to confirm the extent of Bangiales diversity at regional and worldwide levels.

Insights from natural history collections: analysing the New Zealand macroalgal flora using herbarium data

Herbaria and natural history collections (NHC) are critical to the practice of taxonomy and have potential to serve as sources of data for biodiversity and conservation. They are the repositories of vital reference specimens, enabling species to be studied and their distribution in space and time to be documented and analysed, as well as enabling the development of hypotheses about species relationships. The herbarium of the Museum of New Zealand Te Papa Tongarewa (WELT) contains scientifically and historically significant marine macroalgal collections, including type specimens, primarily of New Zealand species, as well as valuable exsiccatae from New Zealand and Australia. The herbarium was initiated in 1865 with the establishment of the Colonial Museum and is the only herbarium in New Zealand where there has been consistent expert taxonomic attention to the macroalgae over the past 50 years. We examined 19,422 records of marine macroalgae from around New Zealand collected over the past 164 years housed in WELT, assessing the records in terms of their spatial and temporal coverage as well as their uniqueness and abundance. The data provided an opportunity to review the state of knowledge of the New Zealand macroalgal flora reflected in the collections at WELT, to examine how knowledge of the macroalgal flora has been built over time in terms of the number of collections and the number of species recognised, and identify where there are gaps in the current collections as far as numbers of specimens per taxon, as well as with respect to geographical and seasonal coverage.

Pyropia plicata sp. nov. (Bangiales, Rhodophyta): naming a common intertidal alga from New Zealand

A commonly found red alga of the upper intertidal zone of New Zealand rocky coasts is described for the first time as Pyropia plicata sp. nov. This species has been incorrectly known as Porphyra columbina Mont. (now Pyropia columbina (Mont.) W.A.Nelson) for many years. Pyropia plicata is widespread and common, and it is readily distinguished from other species of bladed Bangiales in New Zealand by its distinctive morphology, with pleated blades attached by a central rhizoidal holdfast.

A SURVEY OF BANGIALES (RHODOPHYTA) BASED ON MULTIPLE MOLECULAR MARKERS REVEALS CRYPTIC DIVERSITY(1)

The Bangiales is a diverse order consisting of 28 species in Canada. Morphological simplicity and similarity among species has led to taxonomic confusion and the need for molecular techniques for species identification. This study is the first to employ the standardized DNA barcode marker COI-5P in a broad floristic survey of the Bangiales in Canadian marine waters. A total of 37 species were ultimately sequenced, 29 of which occurred in Canada. Molecular results led to the synonymization of Wildemania cuneiformis with W. amplissima, as well as the description of two new species: Porphyra corallicola sp. nov. and Pyropia peggicovensis sp. nov., and discovery of another five putative new species. Comparison of the performance of COI-5P as a species identification tool relative to rbcL (large subunit of ribulose-1,5-bisphosphate carboxylase oxygenase) and the UPA (universal plastid amplicon) revealed that, although each marker had strengths and weaknesses, the COI-5P showed the highest species-discriminatory power due to its high level of interspecific variation. The rbcL was further used to place the new species into a phylogenetic context, whereas UPA was not recommended for species identification in the Bangiales owing to within-individual heterogeneity between the two copies present in the plastid genomes in some lineages.

SELECTION OF INTERNAL CONTROL GENE FOR EXPRESSION STUDIES IN PORPHYRA HAITANENSIS (RHODOPHYTA) AT DIFFERENT LIFE-HISTORY STAGES(1)

Accurate gene quantification depends on the use of an appropriate internal control gene, which should be verified before its use for normalizing data. Housekeeping genes, which are expressed at relatively constant levels, are generally regarded as candidate internal control genes. To determine the ideal internal control for gene expression profiles for Porphyra haitanensis T. J. Chang et B. F. Zheng (Bangiales, Rhodophyta) at different life-history stages, we used absolute quantification to assess the expression levels of six housekeeping genes (18S ribosomal RNA, 30S ribosomal protein, glyceraldehyde-3-phosphate dehydrogenase, elongation factor 3, alpha-tubulin, and beta-tubulin) at the sporophyte and gametophyte stages. Housekeeping genes were selected by comparing the differences of observed copy numbers in sporophytes and in gametophytes. TubB (beta-tubulin) was found to be the optimal internal control gene, because it showed the smallest difference of gene expression. Compared with TubB, other housekeeping genes had greater variation of expression to different degrees.

ANALYSIS OF SPATIAL AND TEMPORAL DIVERSITY AND DISTRIBUTION OF PORPHYRA (RHODOPHYTA) IN SOUTHEASTERN NEW ZEALAND SUPPORTED BY THE USE OF MOLECULAR TOOLS(1)

Molecular studies have shown that New Zealand's rocky shores are a habitat for >30 species of Porphyra, but little is known of their seasonal and zonal distribution. The spatial and temporal distribution of bladed Porphyra gametophytes at Brighton Beach, southeast New Zealand, were monitored for 32 months. Molecular markers were used for species identification, and a total of nine species was observed as being present during this time. Two species, P. cinnamomea and Porphyra sp. "ROS 54," were the most common, and both were present for most months, while the remaining seven species were present sporadically, for only a few weeks at a time. P. cinnamomea W. A. Nelson and Porphyra sp. "ROS 54" were most common in the midintertidal, and both showed a similar seasonality with the highest presence during spring. They also showed a similar trend of seasonal dieback resulting in at least 1 month (May) in two consecutive years when they were both absent. This is one of the few studies investigating spatial and temporal distribution within a genus and over a 3-year period. Our results show no distinct intertidal zonation patterns within the genus, and we conclude that morphologically similar species in a similar habitat rely on physiological mechanisms for survival.

Estimates of nuclear DNA content in red algal lineages

BACKGROUND AND AIMS

The red algae are an evolutionarily ancient group of predominantly marine organisms with an estimated 6000 species. Consensus higher-level molecular phylogenies support a basal split between the unicellular Cyanidiophytina and morphologically diverse Rhodophytina, the later subphylum containing most red algal species. The Rhodophytina is divided into six classes, of which five represent early diverging lineages of generally uninucleate species, whose evolutionary relationships are poorly resolved. The remaining species compose the large (27 currently recognized orders), morphologically diverse and typically multinucleate Florideophyceae. Nuclear DNA content estimates have been published for <1 % of the described red algae. The present investigation summarizes the state of our knowledge and expands our coverage of DNA content information from 196 isolates of red algae.

METHODOLOGY

The DNA-localizing fluorochrome DAPI (4',6-diamidino-2-phenylindole) and RBC (chicken erythrocytes) standards were used to estimate 2C values with static microspectrophotometry.

PRINCIPAL RESULTS

Nuclear DNA contents are reported for 196 isolates of red algae, almost doubling the number of estimates available for these organisms. Present results also confirm the reported DNA content range of 0.1-2.8 pg, with species of Ceramiales, Nemaliales and Palmariales containing apparently polyploid genomes with 2C = 2.8, 2.3 and 2.8 pg, respectively.

CONCLUSIONS

Early diverging red algal lineages are characterized by relatively small 2C DNA contents while a wide range of 2C values is found within the derived Florideophyceae. An overall correlation between phylogenetic placement and 2C DNA content is not apparent; however, genome size data are available for only a small portion of red algae. Current data do support polyploidy and aneuploidy as pervasive features of red algal genome evolution.

A NEW LOOK AT AN ANCIENT ORDER: GENERIC REVISION OF THE BANGIALES (RHODOPHYTA)(1)

The red algal order Bangiales has been revised as a result of detailed regional studies and the development of expert local knowledge of Bangiales floras, followed by collaborative global analyses based on wide taxon sampling and molecular analyses. Combined analyses of the nuclear SSU rRNA gene and the plastid RUBISCO LSU (rbcL) gene for 157 Bangiales taxa have been conducted. Fifteen genera of Bangiales, seven filamentous and eight foliose, are recognized. This classification includes five newly described and two resurrected genera. This revision constitutes a major change in understanding relationships and evolution in this order. The genus Porphyra is now restricted to five described species and a number of undescribed species. Other foliose taxa previously placed in Porphyra are now recognized to belong to the genera Boreophyllum gen. nov., Clymene gen. nov., Fuscifolium gen. nov., Lysithea gen. nov., Miuraea gen. nov., Pyropia, and Wildemania. Four of the seven filamentous genera recognized in our analyses already have generic names (Bangia, Dione, Minerva, and Pseudobangia), and are all currently monotypic. The unnamed filamentous genera are clearly composed of multiple species, and few of these species have names. Further research is required: the genus to which the marine taxon Bangia fuscopurpurea belongs is not known, and there are also a large number of species previously described as Porphyra for which nuclear SSU ribosomal RNA (nrSSU) or rbcL sequence data should be obtained so that they can be assigned to the appropriate genus.

Taxonomy, molecular phylogeny, and ultrastructural morphology of Olpidiopsis porphyrae sp. nov. (Oomycetes, straminipiles), a unicellular obligate endoparasite of Bangia and Porphyra spp. (Bangiales, Rhodophyta)

Olpidiopsis porphyrae sp. nov., a marine oomycete endoparasite that infects the commercially cultivated red alga Porphyra yezoensis, is described and its phylogenetic position based on molecular data and ultrastructural morphology is discussed. O. porphyrae infects the host Porphyra by means of encysted zoospores. Spherical-shaped holocarpic thalli develop within the cytoplasm of its algal host, which produce monoplanetic, subapically biflagellate zoospores. The characteristic features of this isolate are the ellipsoidal, unicellular thallus and simple holocarpic zoosporangial development, which show morphological similarity with the genus Olpidiopsis. Laboratory infection experiments with a wide range of green, brown, and red algae revealed that O. porphyrae infects several stages of the bangialean red algae (the genera Bangia and Porphyra). Molecular phylogenetic analyses inferred from both SSU rRNA and cox2 genes showed O. porphyrae branched before the main saprolegnian and peronosporalean lineages within the monophyletic oomycete clade, indicating its phylogenetic separation from them. A single or double K-body-like organelle, which contains tubular inclusions, is found located to one side of the zoospore nucleus and shows similarities to homologous organelles previously described in O. saprolegniae. The ultrastructural morphology of O. porphyrae with zoospore initials containing K-bodies and tubular mitochondrial cristae is characteristic of oomycetes. Group I intron-like multiple insertions were found in the SSU rRNA gene of O. porphyrae. This is the first report of SSU group I introns in the class Oomycetes.