scholarly journals First Report of the Marine Benthic Dinoflagellate Bysmatrum subsalsum from Korean Tidal Pools

2021 ◽  
Vol 9 (6) ◽  
pp. 649
Author(s):  
Joon-Sang Park ◽  
Zhun Li ◽  
Hyun-Jung Kim ◽  
Ki-Hyun Kim ◽  
Kyun-Woo Lee ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Large Subunit ◽  
Small Subunit ◽  
Morphological Features ◽  
Cryptic Diversity ◽  
Apical Pore ◽  
Thecal Plate ◽  
The Right ◽  
Tidal Pools ◽  
Rrna Sequences

Dense patches were observed in the tidal pools of the southern area of Korea. To clarify the causative organisms, the cells were collected and their morphological features were examined using light and scanning electron microscopy (SEM). In addition, after establishing strains for the cells the molecular phylogeny was inferred with concatenated small subunit (SSU) and large subunit (LSU) rRNA sequences. The cells were characterized by a nucleus in the hypotheca, strong reticulations in thecal plates, the separation of plates 2a and 3a, the tear-shaped apical pore complex, an elongated rectangular 1a plate and the absence of the right sulcal list. The thecal plate formula was Po, X, 4′, 3a, 7″, 6c, 4S, 5′′′, 2′′′′. Based on these morphological features, the cells were identified as Bysmatrum subsalsum. In the culture, the spherical cysts of B. subsalsum without thecal plates were observed. Molecular phylogeny revealed two ribotypes of B. subsalsum are identified; The Korean isolates were nested within the ribotype B consisting of the isolates from China, Malaysia and the French Atlantic, whereas the ribotype A includes only the isolates from the Mediterranean Sea. In the phylogeny, B. subsalsum and B. austrafrum were grouped. This can be supported by the morphological similarity between the two species, indicating that the two species may be conspecific, however B. subsalsum may distinguish from B. austrafrum, because of differences in the types of eyespots reported in previous studies. These findings support the idea that there is cryptic diversity within B. subsalsum.

Revisiting the phylogeny of Ocellularieae, the second largest tribe within Graphidaceae (lichenized Ascomycota: Ostropales)

Phytotaxa ◽  
2014 ◽  
Vol 189 (1) ◽  
pp. 52 ◽  
Author(s):  
Ekaphan Kraichak ◽  
Sittiporn Parnmen ◽  
Robert Lücking ◽  
EIMY RIVAS PLATA ◽  
André Aptroot ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Large Subunit ◽  
Small Subunit ◽  
New Combinations ◽  
New Name ◽  
Small Subunit Rdna ◽  
Large Subunit Rdna ◽  
First Time

We present an updated 3-locus molecular phylogeny of tribe Ocellularieae, the second largest tribe within subfamily Graphidoideae in the Graphidaceae. Adding 165 newly generated sequences from the mitochondrial small subunit rDNA (mtSSU), the nuclear large subunit rDNA (nuLSU), and the second largest subunit of the DNA-directed RNA polymerase II (RPB2), we currently distinguish 218 species among the sequenced material, including the outgroup. This corresponds to almost half the species at this point recognized within this tribe. The newly generated sequences include 23 newly described species and one newly described genus published elsewhere in this volume. For the first time, Sarcographina cyclospora Müll. Arg., in spite of its distinctly lirellate ascomata, is shown to belong in tribe Ocellularieae, as strongly supported sister to Ocellularia inturgescens (Müll. Arg.) Mangold. The following six new combinations are proposed: Melanotrema lynceodes (Nyl.) Rivas Plata, Lücking & Lumbsch, Ocellularia curranii (Vain.) Kraichak, Lücking & Lumbsch, O. khasiana (Patw. & Nagarkar) Kraichak, Lücking & Lumbsch, O. cinerea (Müll. Arg.) Kraichak, Lücking & Lumbsch, O. erodens (R. C. Harris) Kraichak, Lücking & Lumbsch, and O. laeviuscula (Nyl) Kraichak, Lücking & Lumbsch. Further, the new name Ocellularia hernandeziana Kraichak, Lücking & Lumbsch is introduced for Myriotrema ecorticatum. The nomenclatural status of the name Ocellularia microstoma is clarified.

scholarly journals Molecular phylogeny reveals the true colours of Myeloconidaceae (Ascomycota: Ostropales)

2014 ◽  
Vol 27 (1) ◽  
pp. 38 ◽  
Author(s):  
Matthew P. Nelsen ◽  
Robert Lücking ◽  
Carrie J. Andrew ◽  
André Aptroot ◽  
Marcela E. S. Cáceres ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Species Concept ◽  
Large Subunit ◽  
Molecular Data ◽  
Small Subunit ◽  
Separate Genus ◽  
The Family ◽  
Single Genus ◽  
Ascospore Septation ◽  
Large Subunit Rdna

The lichen-forming fungal family Myeloconidaceae, with the single genus Myeloconis, has been suggested to share affinities with Porinaceae (Lecanoromycetes: Ostropales). We examined its position relative to this family by using molecular data from the mitochondrial small-subunit and nuclear large-subunit rDNA. Our results revealed that Myeloconis forms a monophyletic group nested within Porinaceae, closely related to Porina farinosa. Neither Porina s.str. nor Clathroporina sensu Harris form monophyletic groups; instead, two strongly supported clades were recovered, which differ in ascospore septation (septate v. muriform), with the clade producing muriform ascospores including Myeloconis. We therefore reduce Myeloconidaceae to synonymy with Porinaceae; however, because generic delimitations within Porinaceae remain unclear, we retain Myeloconis as a separate genus within the family. The species concept currently used in the genus, based largely on secondary metabolites and ascospore measurements, is supported by the phylogeny.

Cryphodera sinensis n. sp. (Nematoda: Heteroderidae), a non-cyst-forming parasitic nematode from the root of ramie Boehmeria nivea in China

2013 ◽  
Vol 88 (4) ◽  
pp. 468-480 ◽  
Author(s):  
K. Zhuo ◽  
H.H. Wang ◽  
W. Ye ◽  
D.L. Peng ◽  
J.L. Liao
Keyword(s):  
Internal Transcribed Spacer ◽  
Parasitic Nematode ◽  
Large Subunit ◽  
Small Subunit ◽  
Cyst Nematodes ◽  
Lateral Field ◽  
Second Stage ◽  
Boehmeria Nivea ◽  
Rdna Sequences ◽  
Rrna Sequences

AbstractCryphodera sinensis n. sp. is described from ramie (Boehmeria nivea) based on the morphology and molecular analyses of rRNA small subunit (SSU), D2D3 expansion domains of large subunit (LSU D2D3) and internal transcribed spacer (ITS). This new species is characterized by oval females with a distinct subcrystalline layer and pronounced and protruding vulval lip, distinctly concave vulva–anus profile and a vulva–anus distance of 29.5–35.8 μm. Males possess two annuli in the lip region, a stylet 27–32.5 μm in length with round knobs sloping slightly posteriorly, lateral fields with three lines, spicules 20–28 μm long and the presence of a short cloacal tube. Second-stage juveniles possess three lip annuli, a stylet 28–31 μm in length with well-developed knobs projected anteriorly and three lines along the lateral field. The pointed tail, 52–65 μm long, possesses a mucro-like tip and a hyaline region, 24.5–35 μm long. Large phasmids with a lens-like structure are located 2–6 annuli posterior to the anus. Phylogenetic analysis shows that the species has unique SSU, LSU D2D3 and ITS rRNA sequences. Phylogenetic relationships of the three rDNA sequences of C. sinensis n. sp. and other cystoid/cyst nematodes are analysed together with a comparison of other species within the genus Cryphodera.

scholarly journals Redefinition of the Dinoflagellate Genus Alexandrium Based on Centrodinium: Reinstatement of Gessnerium and Protogonyaulax, and Episemicolon gen. nov. (Gonyaulacales, Dinophyceae)

2019 ◽  
Vol 2019 ◽  
pp. 1-17 ◽  
Author(s):  
Fernando Gómez ◽  
Luis Felipe Artigas
Keyword(s):  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Ventral Side ◽  
Sensu Stricto ◽  
Alexandrium Tamarense ◽  
Tropical Species ◽  
Rrna Gene ◽  
Apical Pore ◽  
Sister Clade ◽  
The Right

The genus Centrodinium contains oceanic and predominantly tropical species that have received little attention. Three species of Centrodinium were examined using thecal plate dissociation, scanning electron microscopy, and molecular sequences. The apical horn of Centrodinium intermedium and C. eminens is formed by the elongation of the fourth apical plate, and a second apical split into two plates. In C. punctatum two apical plates (2′ and 4′) almost completely encircle the apical pore plate (Po), while the contact with the plate 1′ in the ventral side is much reduced, and the plate 3′ does not reach the Po. Moreover, its left posterior lateral sulcal plate is longer than its right pair, while reversed in the typical Centrodinium spp. The sulcal posterior plate of C. punctatum is located in the left-ventral side below the plates 1′′′ and 2′′′, while the sulcal posterior plate located in the right face below the plates 4′′′ and 5′′′ in the typical Centrodinium spp. Phylogenetic analyses based on the small and large subunit of the rRNA gene showed that Centrodinium spp. and Alexandrium affine/A. gaarderae clustered as a sister clade of the Alexandrium tamarense/catenella/fraterculus groups. The clade of the subgenus Gessnerium, and the clade of the type species of Alexandrium, A. minutum, with four divergent species, clustered in more basal positions. The polyphyly of Alexandrium is solved with the split into four genera: (1) Alexandrium sensu stricto for the species of the clade of A. minutum and four divergent species; (2) the reinstatement of the genus Gessnerium for the species of the clade of A. monilatum; (3) the reinstatement of genus Protogonyaulax for the species of the tamarense/catenella/fraterculus groups, and (4) the new genus Episemicolon gen. nov. for A. affine and A. gaarderae. New combinations in the genera Gessnerium, Protogonyaulax, and Episemicolon are proposed.

Molecular phylogeny of parabasalids inferred from small subunit rRNA sequences, with emphasis on the Hypermastigea

2005 ◽  
Vol 35 (3) ◽  
pp. 646-655 ◽  
Author(s):  
Moriya Ohkuma ◽  
Toshiya Iida ◽  
Kuniyo Ohtoko ◽  
Hiroe Yuzawa ◽  
Satoko Noda ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Small Subunit ◽  
Small Subunit Rrna ◽  
Rrna Sequences

High Apparent Rate of Simultaneous Compensatory Base-Pair Substitutions in Ribosomal RNA

Genetics ◽  
1998 ◽  
Vol 148 (4) ◽  
pp. 1993-2002 ◽  
Author(s):  
Elisabeth R M Tillier ◽  
Richard A Collins
Keyword(s):  
Base Pair ◽  
Large Subunit ◽  
Small Subunit ◽  
High Ratio ◽  
Small Subunit Rrna ◽  
Rna Sequences ◽  
Instantaneous Rate ◽  
The Core ◽  
Rrna Sequences ◽  
Simultaneous Substitution

Abstract We present a model for the evolution of paired bases in RNA sequences. The new model allows for the instantaneous rate of substitution of both members of a base pair in a compensatory substitution (e.g., A-U→G-C) and expands our previous work by allowing for unpaired bases or noncanonical pairs. We implemented the model with distance and maximum likelihood methods to estimate the rates of simultaneous substitution of both bases, αd, vs. rates of substitution of individual bases, αs in rRNA. In the rapidly evolving D2 expansion segments of Drosophila large subunit rRNA, we estimate a low ratio of αd/αs, indicating that most compensatory substitutions involve a G-U intermediate. In contrast, we find a surprisingly high ratio of αd/αs in the core small subunit rRNA, indicating that the evolution of the slowly evolving rRNA sequences is modeled much more accurately if simultaneous substitution of both members of a base pair is allowed to occur approximately as often as substitution of individual bases. Using simulations, we have ruled out several potential sources of error in the estimation of αd/αs. We conclude that in the core rRNA sequences compensatory substitutions can be fixed so rapidly as to appear to be instantaneous.

Molecular phylogeny resolves a taxonomic misunderstanding and places Geisleria close to Absconditella s. str. (Ostropales: Stictidaceae)

2014 ◽  
Vol 46 (1) ◽  
pp. 115-128 ◽  
Author(s):  
André APTROOT ◽  
Sittiporn PARNMEN ◽  
Robert LÜCKING ◽  
Elisabeth BALOCH ◽  
Patricia JUNGBLUTH ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Type Species ◽  
Sequence Data ◽  
Large Subunit ◽  
Parallel Evolution ◽  
Small Subunit ◽  
Phylogenetic Position ◽  
Pioneer Species ◽  
Dry Conditions ◽  
Large Subunit Rdna

AbstractThe phylogenetic position of the genus Geisleria and its type species G. sychnogonioides was reconstructed using sequence data of the mitochondrial small subunit (mtSSU), the nuclear large subunit rDNA (nuLSU) and the first subunit of the RNA polymerase (RPB1). The species, previously classified in Verrucariaceae (Eurotiomycetes) and Strigulaceae (Dothideomycetes), is sister to the type of the genus Absconditella, A. sphagnorum, and nested within the genera Absconditella and Cryptodiscus combined (which also includes the lichenized Bryophagus). At first glance it appears to be a further example of parallel evolution of perithecioid ascomata within Stictidaceae (Lecanoromycetes: Ostropales), besides Ostropa and Robergea, adding to the growing list of perithecioid forms nested within apothecioid lineages in Ostropomycetidae, and specifically Ostropales, with other examples known from Graphidaceae (several genera), Gyalectaceae (Belonia), and Porinaceae. However, revision of type material collected by Nitschke revealed that the species actually develops typical apothecia with a narrowly exposed disc. We conclude that Geisleria sychnogonoides was erroneously considered a pyrenocarpous taxon, because in dry conditions the apothecia are closed and not recognizable as such. The species usually grows on unstable soil and therefore often only develops young, more or less closed ascomata (yet with mature ascospores), and has also been confused with the superficially similar Belonia incarnata, in which the ascomata remain closed even when mature. Geisleriasychnogonioides has so far only been known as a rarely reported pioneer species from loamy soils in Europe and North America. Here it is reported to occur abundantly on lateritic soils in subtropical Brazil, suggesting that it is cosmopolitan and possibly common, but much overlooked.

scholarly journals Amphidinium stirisquamtum sp. nov. (Dinophyceae), a new marine sand-dwelling dinoflagellate with a novel type of body scale

ALGAE ◽  
2021 ◽  
Vol 36 (4) ◽  
pp. 241-261
Author(s):  
Zhaohe Luo ◽  
Na Wang ◽  
Hala F. Mohamed ◽  
Ye Liang ◽  
Lulu Pei ◽  
...  
Keyword(s):  
Large Subunit ◽  
Detailed Examination ◽  
Small Subunit ◽  
Sensu Stricto ◽  
Small Subunit Rrna ◽  
Body Scale ◽  
Benthic Dinoflagellates ◽  
Marine Sand ◽  
Molecular Tree ◽  
The Right

Amphidinium species are amongst the most abundant benthic dinoflagellates in marine intertidal sandy ecosystems. Some of them produce a variety of bioactive compounds that have both harmful effects and pharmaceutical potential. In this study, Amphidinium cells were isolated from intertidal sand collected from the East China Sea. The two strains established were subjected to detailed examination by light, and scanning and transmission electron microscopy. The vegetative cells had a minute, irregular, and triangular-shaped epicone deflected to the left, thus fitting the description of Amphidinium sensu stricto. These strains are distinguished from other Amphidinium species by combination characteristics: (1) longitudinal flagellum inserted in the lower third of the cell; (2) icicle-shaped scales, 276 ± 17 nm in length, on the cell body surface; (3) asymmetrical hypocone with the left side longer than the right; and (4) presence of immotile cells. Therefore, they are described here as Amphidinium stirisquamtum sp. nov. The molecular tree inferred from small subunit rRNA, large subunit rRNA, and internal transcribed spacer-5.8S sequences revealed that A. stirisquamtum is grouped together with the type species of Amphidinium, A. operculatum, in a fully supported clade, but is distantly related to other Amphidinium species bearing body scale. Live A. stirisquamtum cells greatly affected the survival of rotifers and brine shrimp, their primary grazers, making them more susceptible to predation by the higher tropic level consumers in the food web. This will increase the risk of introducing toxicity, and consequently, the bioaccumulation of toxins through marine food webs.

scholarly journals Phylogenetic analysis of Pneumocystis from pig lungs obtained from slaughterhouses in southern and midwestern regions of Brazil

2011 ◽  
Vol 63 (5) ◽  
pp. 1154-1159 ◽  
Author(s):  
E.M.C Sanches ◽  
L Ferreiro ◽  
M.R Borba ◽  
A Spanamberg ◽  
A.P Ravazzolo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Respiratory Failure ◽  
Large Subunit ◽  
Molecular Genetic ◽  
Small Subunit ◽  
Genetic Studies ◽  
Severe Impairment ◽  
Rrna Sequences ◽  
Aquatic Mammals

The Pneumocystis genus is comprised of pathogens dwelling in the lungs of terrestrial, aerial, and aquatic mammals. Occasionally they induce severe pneumonitis, particularly in hosts with severe impairment of the immune system and progressively may fill pulmonary alveolar cavities causing respiratory failure. Molecular genetic studies revealed that Pneumocystis gene sequences present a marked divergence with the host species concerned. In the present study, the genetic diversity of Pneumocystis obtained from lungs of swines was examined by analyzing mitochondrial large subunit (mtLSU) and small subunit (mtSSU) rRNA sequences. The samples were obtained from two slaughterhouses located in two Brazilian states. Phylogenetic analysis demonstrated that genetic groupings within Pneumocystis organisms were in accordance with those of the corresponding hosts and that two clusters were formed. In conclusion, these data show that there are genetically distinct porcine Pneumocystis genotypes with at least two separate clusters in Brazil.

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