Cladistic analysis of blue-green procaryote interrelationships and chloroplast origin based on 16S rRNA oligonucleotide catalogues

Oligonucleotide catalogues from 16S rRNA have been a major source of information for phylogenetic reconstruction among procaryotes. Several large procaryote groups have been analyzed and phylogenies presented. Catalogues are also available for many chloroplasts. The hypotheses of phylogeny are derived mainly from similarity (phenetic) comparisons of the catalogues and the extent of the homoplasy (parallelisms and reversals) involved has not been estimated properly. Although catalogues are currently being superseded by complete sequence data, an evaluation of the strength of catalogue data, and hence of the strength of the extensive phylogenetic hypotheses derived from them, is in order. Cladistic analysis of 16S rRNA oligonucleotide catalogues from three blue-green procaryotes, Prochloron, and chloroplasts of a red alga, Euglena, a green alga and two flowering plants shows that there is extensive homoplasy in the catalogues and several phylogenetic trees are possible. The corresponding consensus trees indicate that little or nothing can be said about interrelationships and chloroplast origin on the basis of these particular catalogues, except that Prochloron may be more closely related to the blue-greens than to chloroplasts.     

The relatedness of Prochloron sp. Isolated from different didemnid ascidian hosts

The relationship of Prochloron sp. isolated from four different didemnid ascidian hosts, namely Lissoclinum patella, Lissoclinum voeltzkowi, Diplosoma virensand Trididemnum cyclops was elucidated by comparative analysis of their 16S ribosomal ribonucleic acid (RNA). The oligonucleotide catalogues of the 16S rRNA obtained are almost identical, indicating a very close relationship among the prochlorophytes investigated. Phylogenetically Prochloron is a member of Cyanobacteriales.     

DNA-DNA REASSOCIATION STUDIES WITH DNA FROM PROCHLORON (PROCHLOROPHYTA) SAMPLES OF INDO-WEST PACIFIC ORIGIN1

Seven Indo-West Pacific Prochloron Lewin samples and one Caribbean cyanobacterial sample were compared by DNA-DNA reassociation experiments. The quality and quantity of extracted DNA were affected by several cell preservation methods and DNA extraction and purification procedures. We conclude that Prochloron samples from six different hosts and three different geographical locations spanning ca. 9000 km belong to a single species but are not closely related to the strain of cyanohacteria used. The intraspecific genotypic variation within Prochloron is discussed with respect to host specificity and geographical distribution.     

The phylogeny of Prochloron

Abstract

Prochloron, a unicellular alga that combines some features of cyanophytes with others of chlorophytes, is a phylogenetic enigma. Mounting evidence from electron microscopy, comparative biochemistry and molecular biology now suggests that prochlorophytes probably arose from blue-green algal ancestors, perhaps less than 10³ years ago.     

Genotypic relationships between Prochloron samples from different localities and hosts as determined by DNA-DNA reassociations

Genotypic relationships between seven Prochloron samples isolated from different didemnid ascidian hosts collected at the Palau archipelago and Munda (Solomon Islands) and one cyanobacterial (Synechocystis) strain were determined by DNA-DNA reassociations. Thermal stability values of DNA-DNA hybrids indicate that all Prochloron samples involved are mutually very closely related and only slightly related with the Synechocystis strain. It is concluded that the Prochloron samples tested are representatives of one and the same species.     

Prochlorophyta – a matter of class distinctions

Prochloron (a marine symbiont) and Prochlorothrix (from freshwater plankton) contain chlorophylls a and b; Prochlorococcus (common in marine picoplankton) contains divinyl-chlorophylls a and b. Like cyanophytes they are all clearly photosynthetic prokaryotes, but since they contain no blue or red bilin pigment they were assigned to a new algal sub-class, the Prochlorophyta. However, since their possible phylogenetic relationships to ancestral green-plant chloroplasts have not received support from molecular biology, it now seems expedient to consider them as aberrant cyanophytes. This revised version was published online in June 2006 with corrections to the Cover Date.     

Prevalence,complete genome,and metabolic potentials of a phylogenetically novel cyanobacterial symbiont in the coral-killing sponge,Terpios hoshinota

Terpios hoshinota is an aggressive, space-competing sponge that kills various stony corals. Outbreaks of this species have led to intense damage to coral reefs in many locations. Here, the first large-scale 16S rRNA gene survey across three oceans revealed that bacteria related to the taxa Prochloron, Endozoicomonas, SAR116, Ruegeria, and unclassified Proteobacteria were prevalent in T. hoshinota. A Prochloron-related bacterium was the most dominant and prevalent cyanobacterium in T. hoshinota. The complete genome of this uncultivated cyanobacterium and pigment analysis demonstrated that it has phycobiliproteins and lacks chlorophyll b, which is inconsistent with the definition of Prochloron. Furthermore, the cyanobacterium was phylogenetically distinct from Prochloron, strongly suggesting that it should be a sister taxon to Prochloron. Therefore, we proposed this symbiotic cyanobacterium as a novel species under the new genus Candidatus Paraprochloron terpiosi. Comparative genomic analyses revealed that ‘Paraprochloron’ and Prochloron exhibit distinct genomic features and DNA replication machinery. We also characterized the metabolic potentials of ‘Paraprochloron terpiosi’ in carbon and nitrogen cycling and propose a model for interactions between it and T. hoshinota. This study builds a foundation for the study of the T. hoshinota microbiome and paves the way for better understanding of ecosystems involving this coral-killing sponge.     

Partial sequence of ribulose-1,5-bisphosphate carboxylase/oxygenase and the phylogeny of Prochloron and Prochlorococcus (Prochlorales)

The prochlorophytes, oxygenic photosynthetic prokaryotes having no phycobiliprotein but possessing chlorophylls a and b, have been proposed to have a common ancestry with green chloroplasts, yet this is still controversal. We report here that partial sequence comparisons of the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase, including sequence data from two prochlorophytes, Prochlorococcus and Prochloron, indicate that Prochlorococcus is more closely related to a photosynthetic bacterium, Chromatium vinosum (-purple bacteria), than to cyanobacteria, while Prochloron is closely related to the prochlorophyte Prochlorothrix and to cyanobacteria. The molecular phylogenetic tree indicates that a common ancestor of Prochlorococcus and -purple bacteria branched off from the land plant lineage earlier than Prochloron, Prochlorothrix, and cyanobacteria.Correspondence to: A. Shimada     

Photoadaptation and Protection against Active Forms of Oxygen in the Symbiotic Procaryote Prochloron sp. and Its Ascidian Host

Superoxide dismutase, ascorbate peroxidase, and catalase activities were studied in the symbiotic photosynthetic procaryote Prochloron sp. and its ascidian host Lissoclinum patella. The protein-specific activities of these antioxidant enzymes in the Prochloron sp. and L. patella collected at different depths from the Great Barrier Reef, Australia, were directly proportional to irradiance, whereas the pigment concentrations in the Prochloron sp. were inversely proportional to irradiance. The presence of a cyanide-sensitive superoxide dismutase, presumably a Cu-Zn metalloprotein, in the Prochloron sp. extends the possible phylogenetic distribution of this protein. The concentration of UV-absorbing mycosporine-like amino acids is inversely proportional to irradiance in both the host and symbiont, suggesting that these compounds may not provide sufficient protection against UV radiation in high-irradiance environments. The significant differences in the specific activities of these antioxidant enzymes, cellular photosynthetic pigment concentrations, and UV-absorbing compounds from high- and low-irradiance habitats constitute an adaptive response to different photic environments. These photoadaptive responses are essential to prevent inhibition of photosynthesis by high fluxes of visible and UV radiation.     

Deoxyribonucleic acid base composition and genome size of Prochloron

The DNA base composition of the photosynthetic prokaryote Prochloron was determined (on samples collected from the natural environment) to be 40.8 mol% GC. The sharp differential melting curve indicated the absence of significant quantities of contaminating DNA from other organisms. The genome size, estimated from the renaturation kinetics of thermally denatured DNA, was 3.59×10⁹ daltons mol. wt, similar to that of many other prokaryotes. The fact that Prochloron has not yet been cultured in the laboratory cannot, therefore, be attributed to a reduced genetic information content.     

CYTOCHEMICAL STUDIES ON PROCHLOROPHYTES: LOCALIZATION OF DNA AND RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE-OXYGENASE1

We studied the distribution of the DNA-containing region and the ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCo) content of polyhedral bodies in three different prochlorophyte cell types in a search for broad evolutionary affinities of these chlorophyll b-containing prokaryotes. DNA was localized by DAPI staining and electron microscopy utilizing monoclonal anti-DNA antibody 2C-10 plus a secondary antibody labeled with colloidal gold. Antibodies against the large RuBisCo subunit from a higher plant raised in rabbits were used to localize RuBisCo in polyhedral bodies. We studied Prochloron Lewin cells from two different didemnid ascidian hosts (Lissoclinum patella and Didemnum molle) collected in Palau, West Caroline Islands, and cells of Prochlorothrix hollandica Burger-Wiersma, Stal, and Mur grown in laboratory culture. Cells of the blue-green alga Anabaena 7120 were studied for comparison. The DNA distribution was markedly different in the two Prochloron cell types. The thylakoids in cells from L. patella were concentrically arranged around a large central vacuole; the DNA-containing stromal areas appeared in thin sections as a concentric arcs between the thylakoid stacks. The central vacuole was lacking in cells from D. molle, and the thylakoid stacks and strands of DNA-containing stroma showed a more haphazard arrangement. In the filamentous Prochlorothrix the DNA-containing stroma was largely limited to a central nucleoid structure running the length of the cell. Although the DNA arrangements in Prochloron might be considered “chloroplast-like” since DNA-containing stroma is distributed, as in chloroplasts, in scattered sites among photosynthetic membranes, this is not so in Prochlorothrix, where there is an axial nucleoid, as in many filamentous cyanobacteria. Our anti-RuBisCo antibodies were selectively bound to the polyhedral bodies of all three cell types, indicating that Prochloron and Prochlorothrix, like many other autotrophic prokaryotes, possess typical carboxysomes.     

Contents of ultraviolet-absorbing substances in two color morphs of the photosymbiotic ascidian Didemnum molle

The contents of mycosporine-like amino acids (MAAs) were compared in the two color morphs (dark-gray and brown colonies) of the tropical ascidian Didemnum molle (Herdman, 1886), which harbors the photosymbiotic prokaryote Prochloron. The colonies of each color morph were exclusively distributed in shallow reef lagoons at the different sites. Spectroscopic and chromatographic analyses showed that the Prochloron cell density and MAA concentration in the dark-gray colonies were an estimated 1.4 and 2.4 times higher, respectively, than in the brown colonies. The significant difference in MAA contents between the color morphs was primarily due to the difference in shinorine contents (p < 0.01, Mann–Whitney U-test). The high concentration of MAAs in the dark-gray colonies may provide better conditions for Prochloron cells, compared to the brown colonies with lower MAA concentrations.     

Prochloron (Prochlorophyta): Biochemical Contributions to the Chlorophyll and RNA Composition

The prochlorophyte Prochloron, a symbiont of the colonial ascidianDidemnum molle, was collected in the Indian Ocean around Giravaru(Maldives) in depths between 1 and 40 m. The chlorophyll a tob ratio of the algal symbionts was higher in colonies livingbetween 1–6 m, compared to that determined for Prochloronfrom a depth of 30 m. This property for chromatic adaptationin correlation with changes in the total content of chlorophyllis dependent upon environmental factors. The association betweenDidemnum and Prochloron is only a facultative symbiosis. Thesize of the colonies, growing near the water surface is large(up to 3 cm), and it gradually decreases to 0.2 cm in a depthof 30 m dim locations. At a depth of 40 m the tunicates do notcontain the algal symbionts. Applying quantitative preparative isolation and sensitive immunologicalas well as biochemical detection techniques we have no evidencefor the existence of poly(A) stretches in RNA species from Prochloron.Moreover, we failed to detect both sn/scRNAs and their proteins,typically associated with them in RNP complexes from eukaryotes.From the data we suggest that mRNA synthesis proceeds in Prochloronin a way similar to prokaryotes. ¹ This contribution is dedicated to Prof. Dr. Dr. B. Schmidton the occasion of his 50th birthday.     

Molecular phylogeny of Pamphagidae (Acridoidea,Orthoptera) from China based on mitochondrial cytochrome oxidase II sequences

Abstract Phylogenetic relationships of Pamphagidae were examined using cytochrome oxidase subunit II (COII) mtDNA sequences (684 bp). Twenty‐seven species of Acridoidea from 20 genera were sequenced to obtain mtDNA data, along with four species from the GenBank nucleotide database. The purpose of this study was analyzing the phylogenetic relationships among subfamilies within Pamphagidae and interpreting the phylogenetic position of this family within the Acridoidea superfamily. Phylogenetic trees were reconstructed using neighbor‐joining (NJ), maximum parsimony (MP) and Bayesian inference (BI) methods. The 684 bp analyzed fragment included 126 parsimony informative sites. Sequences diverged 1.0%–11.1% between genera within subfamilies, and 8.8%–12.3% between subfamilies. Amino acid sequence diverged 0–6.1% between genera within subfamilies, and 0.4%–7.5% between subfamilies. Our phylogenetic trees revealed the monophyly of Pamphagidae and three distinct major groups within this family. Moreover, several well supported and stable clades were found in Pamphagidae. The global clustering results were similar to that obtained through classical morphological classification: Prionotropisinae, Thrinchinae and Pamphaginae were monophyletic groups. However, the current genus Filchnerella (Prionotropisinae) was not a monophyletic group and the genus Asiotmethis (Prionotropisinae) was a sister group of the genus Thrinchus (Thrinchinae). Further molecular and morphological studies are required to clarify the phylogenetic relationships of the genera Filchnerella and Asiotmethis.     

Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles

Background  

Section Calochroi is one of the most species-rich lineages in the genus Cortinarius (Agaricales, Basidiomycota) and is widely distributed across boreo-nemoral areas, with some extensions into meridional zones. Previous phylogenetic studies of Calochroi (incl. section Fulvi) have been geographically restricted; therefore, phylogenetic and biogeographic relationships within this lineage at a global scale have been largely unknown. In this study, we obtained DNA sequences from a nearly complete taxon sampling of known species from Europe, Central America and North America. We inferred intra- and interspecific phylogenetic relationships as well as major morphological evolutionary trends within section Calochroi based on 576 ITS sequences, 230 ITS + 5.8S + D1/D2 sequences, and a combined dataset of ITS + 5.8S + D1/D2 and RPB1 sequences of a representative subsampling of 58 species.     

Photosynthesis of Prochloron as Affected by Environmental Factors

The effects of light intensity, pH, temperature, and UV irradiation on the photosynthetic rate of Prochloron isolated from the ascidian host Lissoclinum patella, collected from Palau, were examined. Photosynthesis increased with light intensity with saturation at 500 μmol/m² per second. It was maximum at pH 8 to 9 but almost completely suppressed below pH 7. The optimum temperature was 35° to 40°C, but the photosynthesis was absent at ≤20°C and at 45°C. It was recovered when the symbiont was transferred from 1 hour of incubation at ≤20°C to 35°C but not when transferred from incubation at 45°C. Ultraviolet irradiation severely inhibited the photosynthesis of Prochloron in isolation but not in vivo. This protection was brought about by the tunic covering the ascidian colony, which contains UV-absorbing mycosporine-like amino acids. These results indicate that the characteristic condition of the tropical marine environment largely determines the ecological distribution of Prochloron, and the ascidian tunic protects the organism from UV radiation. Received February 17, 2000; accepted August 8, 2000.     

Muramic acid in the cell walls of Prochloron

Muramic acid has been detected in Prochloron with the aid of two different techniques. It was assayed by cleaving D-lactate from muramic acid and then reducing NAD with D-lactate dehydrogenase and measuring the NADH with bacterial luciferase. Gas-liquid chromatography of trimethylsilyl derivatives of cell extracts confirmed that muramic acid was present in about the quantity given by the D-lactate assay. The amount of muramic acid present was 1.7±0.2 g/mg dry weight or 1.3fg/m² of cell surface. This suggests that the thickness of the peptidoglycan layer in Prochloron is similar to that in blue-green algae.Abbreviations D-LDH d-lactate dehydrogenase - MA muramic acid - TMS trimethylsilyl - TLE thin layer electrophoresis - GLC gas-liquid chromatography     

Mitochondrial <Emphasis Type="Italic">matR</Emphasis> sequences help to resolve deep phylogenetic relationships in rosids

Background  

Rosids are a major clade in the angiosperms containing 13 orders and about one-third of angiosperm species. Recent molecular analyses recognized two major groups (i.e., fabids with seven orders and malvids with three orders). However, phylogenetic relationships within the two groups and among fabids, malvids, and potentially basal rosids including Geraniales, Myrtales, and Crossosomatales remain to be resolved with more data and a broader taxon sampling. In this study, we obtained DNA sequences of the mitochondrial matR gene from 174 species representing 72 families of putative rosids and examined phylogenetic relationships and phylogenetic utility of matR in rosids. We also inferred phylogenetic relationships within the "rosid clade" based on a combined data set of 91 taxa and four genes including matR, two plastid genes (rbcL, atpB), and one nuclear gene (18S rDNA).     

Phylogeny and systematics of Old World serotine bats (genus Eptesicus,Vespertilionidae, Chiroptera): an integrative approach

Integrative taxonomy aims to document biodiversity by incorporating all useful characters to increase confidence in hypotheses about phylogenetic relationships. In this study, we combine data obtained independently from morphology, two maternally inherited mtDNA genes and two biparentally inherited nuDNA genes to make phylogenetic and taxonomic hypotheses about the Palaearctic members of the bat genus Eptesicus (Vespertilionidae). This genus is distributed worldwide (except for Antarctica) and is highly diversified, presenting one of the most entangled taxonomic puzzles among all mammals. Our results support restoring the genus Rhyneptesicus and separating E. isabellinus and E. pachyomus from E. serotinus and E. ognevi and E. anatolicus from E. bottae. Differences in the phylogenetic hypotheses from mtDNA and nuDNA data suggest the occurrence within E. serotinus of evolutionary processes such as mtDNA capture and secondary contacts between partially differentiated ecomorphs. These two evolutionary processes deserve more in‐depth studies within the group.     

A novel clade of sporocarp-forming species of glomeromycotan fungi in the <Emphasis Type="Italic">Diversisporales</Emphasis> lineage

In the early times of taxonomy of arbuscular mycorrhizal fungi (Glomeromycota), exclusively sporocarpic species were described. Since then the focus has mainly shifted to species forming spores singly. For many of the sporocarpic species, no molecular data have been made available, and their phylogenetic position has remained unclear. We obtained small subunit ribosomal rDNA and internal transcribed spacer data from specimens of glomeromycotan sporocarps from tropical areas that were assigned to three morphospecies. The complete sequence of the 18S small rDNA subunit sequence, internal transcribed spacers (ITS) 1 and 2 and 5.8S rDNA subunit, was determined from a sporocarp of Glomus fulvum. Partial sequences of the small subunit and the other regions were obtained from Glomus pulvinatum and the newly described species Glomus megalocarpum. Molecular phylogenetic analyses placed all species analyzed as a monophyletic sister group to the Diversispora spurca/Glomus versiforme clade group (“Glomus group C”) within the Diversisporales. The phylogenetic divergence from other known species suggests that this clade may constitute a new genus. These findings will have important consequences for taxon definition in the Diversisporales. They will facilitate identification of these fungi using rDNA sequences within colonized roots or the environment. Taxonomic novelties: Glomus megalocarpum D. Redecker