- Volume 53, Issue 6, 2003
Volume 53, Issue 6, 2003
- Evolution, Phylogeny And Biodiversity
-
-
-
Phylogenetic affinities of the Trentepohliales inferred from small-subunit rDNA
More LessPhylogenetic analyses of the nuclear-encoded small-subunit rDNA sequences from taxa representing all of the major lineages of green algae, including new sequences for the Trentepohliales, consistently indicated that the subaerial Trentepohliales are closely related to ulvophycean marine green algae, particularly to the siphonous and hemisiphonous orders. The presence of phragmoplast-type cytokinesis in the order Trentepohliales remains enigmatic, and it is interesting that this type of cell division is associated with terrestrial (subaerial) habits.
-
-
- Methods
-
-
-
Rapid identification of filamentous actinomycetes to the genus level using genus-specific 16S rRNA gene restriction fragment patterns
More LessA rapid method for identifying filamentous actinomycete genera was developed based on 16S rRNA gene restriction fragment patterns. The patterns were generated by using specific restriction endonucleases to perform in silico digestions on the 16S rRNA gene sequences of all validly published filamentous actinomycete species. The method was applied to identifying actinomycete isolates from soil. Amplified 16S rDNA of soil actinomycetes was restricted with selected endonucleases and electrophoresed on agarose gels. The restriction fragment patterns of the unknown isolates were easily compared to the established patterns. Significantly, the genus Streptomyces could be differentiated from all other actinomycete genera by using only four restriction endonucleases, Sau3AI, AsnI, KpnI and SphI. This could be achieved in a time period of as little as a week, following PCR-template DNA isolation by a simple method. The identification method allowed unknown, non-Streptomyces soil isolates to be identified to a genus or small subgroup of genera. The genera in these subgroups could, in some cases, be distinguished by virtue of colony-morphology differences.
-
-
- International Committee On Systematics Of Prokaryotes
-
- Request For An Opinion
-
-
The genus name Ensifer Casida 1982 takes priority over Sinorhizobium Chen et al. 1988, and Sinorhizobium morelense Wang et al. 2002 is a later synonym of Ensifer adhaerens Casida 1982. Is the combination ‘Sinorhizobium adhaerens’ (Casida 1982) Willems et al. 2003 legitimate? Request for an Opinion
More LessThe synonymy of the genera Ensifer and Sinorhizobium was recently reported, but it was proposed that the later-named genus, Sinorhizobium, take priority in nomenclature. There is no justification in the International Code of Nomenclature of Bacteria (Prokaryotes) for this step; Ensifer is the correct name of the genus, with Ensifer adhaerens as the type species. Species previously allocated to Sinorhizobium are here proposed as the new combinations Ensifer arboris, Ensifer fredii, Ensifer kostiensis, Ensifer kummerowiae, Ensifer medicae, Ensifer meliloti, Ensifer saheli, Ensifer terangae and Ensifer xinjiangensis. Sinorhizobium morelense was proposed in 2002 [ Wang, E. T., Tan, Z. Y., Willems, A., Fernández-López, M., Reinhold-Hurek, B. & Martínez-Romero, E., Int J Syst Evol Microbiol 52, 1687–1693, 2002 ], but a consideration of all published data indicate that it is a nitrogen-fixing genomovar and later heterotypic synonym of Ensifer adhaerens. A Request for an Opinion is made as to whether or not the combination ‘Sinorhizobium adhaerens’ ( Casida 1982 ) Willems et al. 2003 is legitimate.
-
-
-
Proposal to conserve the adjectival form of the specific epithet in the reclassification of Bacteroides forsythus Tanner et al. 1986 to the genus Tannerella Sakamoto et al. 2002 as Tannerella forsythia corrig., gen. nov., comb. nov. Request for an Opinion
More LessWith reference to the first Principle of the International Code of Nomenclature of Bacteria, which emphasizes stability of names, it is proposed that the original adjectival form of the specific epithet be conserved in the reclassification of Bacteroides forsythus to the new genus Tannerella. Thus, Tannerella forsythensis Sakamoto et al. 2002 should be Tannerella forsythia Sakamoto et al. 2002 corrig., gen. nov., comb. nov., and we put forward a Request for an Opinion to the Judicial Commission regarding this correction.
-
- Isep
-
-
-
The collapse of the two-kingdom system, the rise of protistology and the founding of the International Society for Evolutionary Protistology (ISEP)
More LessThis paper provides a brief summary of the rise and acceptance of protistology as a modern, realistic approach to the evolutionary relationships and classification of unicellular eukaryotic organisms as well as the origins of the multicellular groups. The apparent reasons for the renaissance of this 19th-century concept in the 1970s are reviewed, with electron microscopy considered to be the key factor, strongly reinforced by molecular phylogenetic studies in the 1980s and 1990s. The foundation of the International Society for Evolutionary Protistology in 1975 accompanied this major alteration in the view of biological diversity. The current status of protistology relative to protozoology and phycology is discussed.
-
-
-
-
Phragmoplastin, green algae and the evolution of cytokinesis
More LessPhragmoplast-mediated cell division characterizes the land plants in the streptophyte lineage and some species of the green algal orders Coleochaetales, Charales and Zygnematales that are basal to that lineage. This type of cell division is generally not found in the other green plant lineage, the chlorophyte algae. A well-developed phragmoplast-type cell division has been documented, however, in two subaerial green algae (Cephaleuros parasiticus and Trentepohlia odorata) belonging to the order Trentepohliales – an order that molecular sequence data place unequivocally within the chlorophytes rather than streptophytes. Is the phragmoplast-mediated cell division of the Trentepohliales a case of homology or non-homology? To gain more insight into this question, we are exploring the potential phylogenetic information inferred from gene sequences of phragmoplastin, a dynamin-like protein that has been associated with cell-plate formation during phragmoplast-mediated cytokinesis in land plants. Primers for green algae were designed based on an available phragmoplastin sequence from soybean and yielded PCR amplifications from the trentepohlialean green algae Trentepohlia and Cephaleuros and the leafy liverwort Bazzania. These are the first published data for phragmoplastins in algae and liverworts. Analysis of phragmoplastin gene sequences in chlorophyte and streptophyte green algae may help to chart the evolution of the development of the phragmoplast.
-
-
-
Comparison of plastid 16S rRNA (rrn16) genes from Helicosporidium spp.: evidence supporting the reclassification of Helicosporidia as green algae (Chlorophyta)
More LessThe Helicosporidia are invertebrate pathogens that have recently been identified as non-photosynthetic green algae (Chlorophyta). In order to confirm the algal nature of the genus Helicosporidium, the presence of a retained chloroplast genome in Helicosporidia cells was investigated. Fragments homologous to plastid 16S rRNA (rrn16) genes were amplified successfully from cellular DNA extracted from two different Helicosporidium isolates. The fragment sequences are 1269 and 1266 bp long, are very AT-rich (60·7 %) and are similar to homologous genes sequenced from non-photosynthetic green algae. Maximum-parsimony, maximum-likelihood and neighbour-joining methods were used to infer phylogenetic trees from an rrn16 sequence alignment. All trees depicted the Helicosporidia as sister taxa to the non-photosynthetic, pathogenic alga Prototheca zopfii. Moreover, the trees identified Helicosporidium spp. as members of a clade that included the heterotrophic species Prototheca spp. and the mesotrophic species Chlorella protothecoides. The clade is always strongly supported by bootstrap values, suggesting that all these organisms share a most recent common ancestor. Phylogenetic analyses inferred from plastid 16S rRNA genes confirmed that the Helicosporidia are non-photosynthetic green algae, close relatives of the genus Prototheca (Chlorophyta, Trebouxiophyceae). Such phylogenetic affinities suggest that Helicosporidium spp. are likely to possess Prototheca-like organelles and organelle genomes.
-
-
-
Highly organized structure in the non-coding region of the psbA minicircle from clade C Symbiodinium
More LessThe chloroplast genes of dinoflagellates are distributed among small, circular dsDNA molecules termed minicircles. In this paper, we describe the structure of the non-coding region of the psbA minicircle from Symbiodinium. DNA sequence was obtained from five Symbiodinium strains obtained from four different coral host species (Goniopora tenuidens, Heliofungia actiniformis, Leptastrea purpurea and Pocillopora damicornis), which had previously been determined to be closely related using LSU rDNA region D1/D2 sequence analysis. Eight distinct sequence blocks, consisting of four conserved cores interspersed with two metastable regions and flanked by two variable regions, occurred at similar positions in all strains. Inverted repeats (IRs) occurred in tandem or ‘twin’ formation within two of the four cores. The metastable regions also consisted of twin IRs and had modular behaviour, being either fully present or completely absent in the different strains. These twin IRs are similar in sequence to double-hairpin elements (DHEs) found in the mitochondrial genomes of some fungi, and may be mobile elements or may serve a functional role in recombination or replication. Within the central unit (consisting of the cores plus the metastable regions), all IRs contained perfect sequence inverses, implying they are highly evolved. IRs were also present outside the central unit but these were imperfect and possessed by individual strains only. A central adenine-rich sequence most closely resembled one in the centre of the non-coding part of Amphidinium operculatum minicircles, and is a potential origin of replication. Sequence polymorphism was extremely high in the variable regions, suggesting that these regions may be useful for distinguishing strains that cannot be differentiated using molecular markers currently available for Symbiodinium.
-
-
-
Foraminifera and Cercozoa share a common origin according to RNA polymerase II phylogenies
More LessPhylogenetic analysis of small and large subunits of rDNA genes suggested that Foraminifera originated early in the evolution of eukaryotes, preceding the origin of other rhizopodial protists. This view was recently challenged by the analysis of actin and ubiquitin protein sequences, which revealed a close relationship between Foraminifera and Cercozoa, an assemblage of various filose amoebae and amoeboflagellates that branch in the so-called crown of the SSU rDNA tree of eukaryotes. To further test this hypothesis, we sequenced a fragment of the largest subunit of the RNA polymerase II (RPB1) from five foraminiferans, two cercozoans and the testate filosean Gromia oviformis. Analysis of our data confirms a close relationship between Foraminifera and Cercozoa and points to Gromia as the closest relative of Foraminifera.
-
-
-
The excavate protozoan phyla Metamonada Grassé emend. (Anaeromonadea, Parabasalia, Carpediemonas, Eopharyngia) and Loukozoa emend. (Jakobea, Malawimonas): their evolutionary affinities and new higher taxa
More LessIt is argued here that the anaerobic protozoan zooflagellate Parabasalia, Carpediemonas and Eopharyngia (diplomonads, enteromonads, retortamonads) constitute a holophyletic group, for which the existing name Trichozoa is adopted as a new subphylum. Ancestrally, Trichozoa probably had hydrogenosomes, stacked Golgi dictyosomes, three anterior centrioles and one posterior centriole: the typical tetrakont pattern. It is also argued that the closest relatives of Trichozoa are Anaeromonada (Trimastix, oxymonads), and the two groups are classified as subphyla of a revised phylum Metamonada. Returning Parabasalia and Anaeromonadea to Metamonada, as in Grassé's original classification, simplifies classification of the kingdom Protozoa by reducing the number of phyla within infrakingdom Excavata from five to four. Percolozoa (Heterolobosea plus Percolatea classis nov.) and Metamonada are probably both ancestrally quadriciliate with a kinetid of four centrioles attached to the nucleus; the few biciliates among them are probably secondarily derived. Metamonada ancestrally probably had two divergent centriole pairs, whereas, in Percolozoa, all four centrioles are parallel. It is suggested that Discicristata (Percolozoa, Euglenozoa) are holophyletic, ancestrally with two parallel centrioles. In the phylum Loukozoa, Malawimonadea classis nov. is established for Malawimonas (with a new family and order also) and Diphyllatea classis nov., for Diphylleida (Diphylleia, Collodictyon), is transferred back to Apusozoa. A new class, order and family are established for the anaerobic, biciliate, tricentriolar Carpediemonas, transferring it from Loukozoa to Trichozoa because of its triply flanged cilia; like Retortamonas, it may be secondarily biciliate – its unique combination of putative hydrogenosomes and flanged cilia agree with molecular evidence that Carpediemonas is sister to Eopharyngia, diverging before their ancestor lost hydrogenosomes and acquired a cytopharynx. Removal of anaeromonads and Carpediemonas makes Loukozoa more homogeneous, being basically biciliate, aerobic and free-living, in contrast to Metamonada. A new taxon-rich rRNA tree supports holophyly of Discicristata and Trichozoa strongly, holophyly of Metamonada and Excavata and paraphyly of Loukozoa weakly. Mitochondria were probably transformed into hydrogenosomes independently in the ancestors of lyromonad Percolozoa and Metamonada and further reduced in the ancestral eopharyngian. Evidence is briefly discussed that Metamonada and all other excavates share a photosynthetic ancestry with Euglenozoa and are secondarily non-photosynthetic, as predicted by the cabozoan hypothesis for a single secondary symbiogenetic acquisition of green algal plastids by the last common ancestor of Euglenozoa and Cercozoa. Excavata plus core Rhizaria (Cercozoa, Retaria) probably form an ancestrally photophagotrophic clade. The origin from a benthic loukozoan ancestor of the characteristic cellular features of Percolozoa and Euglenozoa through divergent adaptations for feeding on or close to surfaces is also discussed.
-
-
-
Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota)
More LessAn overview of the controversial proposal for the major eukaryote taxon ‘Excavata’ is presented. Excavata is predicted to include at least ten distinct groups: jakobids, Malawimonas, Trimastix, Carpediemonas, retortamonads, diplomonads, Heterolobosea, oxymonads, parabasalids and Euglenozoa. These ‘excavates' have broadly similar flagellar apparatus organizations, for which a ‘universal’ terminology is provided. Most, but not all, of these organisms share a distinctive suspension-feeding groove, as well as some or all of a set of seven other proposed cytoskeletal apomorphies. Cladistic analyses of morphological data do not resolve high-level relationships within Excavata. Excavate-rich molecular phylogenies recover some robust clades, but do not support or strongly refute the monophyly of Excavata. A partial classification for excavates is presented, with phylogenetic diagnoses for Excavata and for two novel taxon names, Fornicata (Carpediemonas, retortamonads, diplomonads) and Preaxostyla (Trimastix, oxymonads).
-
Volumes and issues
-
Volume 74 (2024)
-
Volume 73 (2023)
-
Volume 72 (2022 - 2023)
-
Volume 71 (2020 - 2021)
-
Volume 70 (2020)
-
Volume 69 (2019)
-
Volume 68 (2018)
-
Volume 67 (2017)
-
Volume 66 (2016)
-
Volume 65 (2015)
-
Volume 64 (2014)
-
Volume 63 (2013)
-
Volume 62 (2012)
-
Volume 61 (2011)
-
Volume 60 (2010)
-
Volume 59 (2009)
-
Volume 58 (2008)
-
Volume 57 (2007)
-
Volume 56 (2006)
-
Volume 55 (2005)
-
Volume 54 (2004)
-
Volume 53 (2003)
-
Volume 52 (2002)
-
Volume 51 (2001)
-
Volume 50 (2000)
-
Volume 49 (1999)
-
Volume 48 (1998)
-
Volume 47 (1997)
-
Volume 46 (1996)
-
Volume 45 (1995)
-
Volume 44 (1994)
-
Volume 43 (1993)
-
Volume 42 (1992)
-
Volume 41 (1991)
-
Volume 40 (1990)
-
Volume 39 (1989)
-
Volume 38 (1988)
-
Volume 37 (1987)
-
Volume 36 (1986)
-
Volume 35 (1985)
-
Volume 34 (1984)
-
Volume 33 (1983)
-
Volume 32 (1982)
-
Volume 31 (1981)
-
Volume 30 (1980)
-
Volume 29 (1979)
-
Volume 28 (1978)
-
Volume 27 (1977)
-
Volume 26 (1976)
-
Volume 25 (1975)
-
Volume 24 (1974)
-
Volume 23 (1973)
-
Volume 22 (1972)
-
Volume 21 (1971)
-
Volume 20 (1970)
-
Volume 19 (1969)
-
Volume 18 (1968)
-
Volume 17 (1967)
-
Volume 16 (1966)
-
Volume 15 (1965)
-
Volume 14 (1964)
-
Volume 13 (1963)
-
Volume 12 (1962)
-
Volume 11 (1961)
-
Volume 10 (1960)
-
Volume 9 (1959)
-
Volume 8 (1958)
-
Volume 7 (1957)
-
Volume 6 (1956)
-
Volume 5 (1955)
-
Volume 4 (1954)
-
Volume 3 (1953)
-
Volume 2 (1952)
-
Volume 1 (1951)