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.

Discovery of a free-living nematode phylogenetically related to vertebrate parasites of the genus Strongyloides (Nematoda : Strongyloidoidea): morphological, anatomical and molecular characterisation

2016 ◽  
Vol 30 (4) ◽  
pp. 387
Author(s):  
Ren-E Huang ◽  
Runsheng Li ◽  
Zhongying Zhao
Keyword(s):  
Culture Media ◽  
Large Subunit ◽  
Molecular Genetic ◽  
Small Subunit ◽  
Land Snails ◽  
Rrna Genes ◽  
Lsu Rdna ◽  
Free Living ◽  
Rdna Sequences ◽  
Free Living Nematode

Nematodes are important, largely because they frequently act as parasites and threaten the health of plants, animals and even humans. Here, we describe an interesting free-living nematode from land snails on Luofu Mountain, Guangdong, China. Alloionema luofuensis, sp. nov. is phylogenetically related to slug-parasite A. appendiculatum and the well-known vertebrate parasites Strongyloides spp. based on small subunit (SSU) and the D2-D3 domain of large subunit (LSU) rDNA sequences. The new species possesses an extremely transparent body and is easily maintained using C. elegans culture media, suggesting a possible application prospect of this free-living nematode as a comparative model system for its related parasites. Morphology and anatomy of the gonochoristic A. luofuensis, sp. nov. adult were described and illustrated. The species is characterised by a filiform tail bisexually, ‘rhabditiform’ oesophagus and ‘rhabditid-like’ female anatomy, but its male caudal region is completely different from that of typical rhabditid nematodes, being absent from an enveloping bursa. It is the first marker taxon characterised morphologically as well as molecularly from the family Alloionematidae, a group of nematodes with hyperdiverse molecular genetic variations underlying highly conserved anatomy. Further molecular and genetic studies on A. luofuensis, sp. nov. populations hold promise to provide insight into evolution of the clade consisting of vertebrate parasites of the heterogonic nematode genus Strongyloides. This is because of its unusual high levels of heterozygosity maintained by the conserved rRNA genes of partial SSU and the D2-D3 domain of LSU for the type isolate of this species.

scholarly journals Naganishia floricola sp. nov., a novel basidiomycetous yeast species isolated from flowers of Sorbaria sorbifolia

2020 ◽  
Vol 70 (8) ◽  
pp. 4496-4501 ◽  
Author(s):  
Yu Zhou ◽  
Bi-Si Jia ◽  
Yu-Guang Zhou ◽  
Ai-Hua Li ◽  
Lu Xue
Keyword(s):  
Phylogenetic Analysis ◽  
Rna Polymerase Ii ◽  
Novel Species ◽  
Large Subunit ◽  
Elongation Factor ◽  
Sequence Divergence ◽  
Its Region ◽  
Small Subunit ◽  
Basidiomycetous Yeast ◽  
D2 Domain

Two yeast strains representing a novel species in the basidiomycetous yeast genus Naganishia were isolated from flowers of Sorbaria sorbifolia collected in Beijing Olympic Forest Park, PR China. Results of multi-gene phylogenetic analysis indicated that the two strains were closely related to the type strains of Naganishia bhutanensis (CBS 6294T) and Naganishia antarctica (CBS 7687T). However, the new isolates differed from N. bhutanensis CBS 6294T by 1.79 % sequence divergence in the D1/D2 domain (11 nt substitutions and three indels), and 2.42 % (15 nt differences and one indel) to N. antarctica CBS 7687T. In the ITS region, the new isolates showed 1.15 % divergence (7 nt substitutions and one indel) to N. bhutanensis CBS 6294T and 0.92 % divergence (5 nt substitutions and no indels) to N. antarctica CBS 7687T. A phylogenetic analysis employing the sequences of six genes (D1/D2 domain of large subunit rDNA, ITS, small subunit rDNA, two subunits of the RNA polymerase II and elongation factor-1α) indicated that the novel species belonged to the genus Naganishia and formed a well-supported clade with N. bhutanensis, N. antarctica and N. indica. Moreover, the two strains differed from their closest relatives by the ability to grow on distinct carbon and nitrogen sources and ability to grow at 30 °C. On the basis of these findings, we propose a novel species in the genus Naganishia (Filobasidiales), Naganishia floricola sp. nov. (holotype CGMCC 2.5856).

Spissiomyces endophytica (Dothideomycetes, Ascomycota), a new endophytic fungus from Thailand

Phytotaxa ◽  
2018 ◽  
Vol 333 (2) ◽  
pp. 219 ◽  
Author(s):  
NAKARIN SUWANNARACH ◽  
JATURONG KUMLA ◽  
SAISAMORN LUMYONG
Keyword(s):  
Phylogenetic Analysis ◽  
Large Subunit ◽  
Small Subunit ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Full Description ◽  
Morphological Investigation ◽  
Lampang Province ◽  
A New Species ◽  
Β Tubulin

A new species of endophytic fungi, described herein as Spissiomyces endophytica, was isolated from tubers of Balanophora fungosa in Lampang Province, Thailand. A morphological investigation revealed that this species was distinguished from the previously described Spissiomyces species by its lager conidial size. Phylogenetic analysis was performed using combined sequence datasets of the small subunit (SSU), large subunit (LSU) and internal transcribed spacers (ITS) of the nuclear ribosomal DNA (rDNA), a part of the RNA polymerase (RPB2) and β-tubulin (TUB) genes, in order to support the morphological results. A full description, illustrations, phylogenetic tree and key to the species are provided.

scholarly journals Genetic diversity of Microsporidia in the circulatory system of endemic amphipods from different locations and depths of ancient Lake Baikal

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5329 ◽  
Author(s):  
Mariya Dimova ◽  
Ekaterina Madyarova ◽  
Anton Gurkov ◽  
Polina Drozdova ◽  
Yulia Lubyaga ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Lake Baikal ◽  
Deep Water ◽  
Endemic Species ◽  
Sequence Data ◽  
Molecular Genetic ◽  
Circulatory System ◽  
Geographic Location ◽  
Small Subunit ◽  
Amphipod Species

Endemic amphipods (Amphipoda, Crustacea) of the most ancient and large freshwater Lake Baikal (Siberia, Russia) are a highly diverse group comprising >15% of all known species of continental amphipods. The extensive endemic biodiversity of Baikal amphipods provides the unique opportunity to study interactions and possible coevolution of this group and their parasites, such as Microsporidia. In this study, we investigated microsporidian diversity in the circulatory system of 22 endemic species of amphipods inhabiting littoral, sublittoral and deep-water zones in all three basins of Lake Baikal. Using molecular genetic techniques, we found microsporidian DNA in two littoral (Eulimnogammarus verrucosus,Eulimnogammarus cyaneus), two littoral/sublittoral (Pallasea cancellus,Eulimnogammarus marituji) and two sublittoral/deep-water (Acanthogammarus lappaceus longispinus,Acanthogammarus victorii maculosus) endemic species. Twenty sequences of the small subunit ribosomal (SSU) rDNA were obtained from the haemolymph of the six endemic amphipod species sampled from 0–60 m depths at the Southern Lake Baikal’s basin (only the Western shore) and at the Central Baikal. They form clusters with similarity toEnterocytospora,Cucumispora,Dictyocoela, and several unassigned Microsporidia sequences, respectively. Our sequence data show similarity to previously identified microsporidian DNA from inhabitants of both Lake Baikal and other water reservoirs. The results of our study suggest that the genetic diversity of Microsporidia in haemolymph of endemic amphipods from Lake Baikal does not correlate with host species, geographic location or depth factors but is homogeneously diverse.

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.

scholarly journals Sequences of psychrophilic fungi amplified from glacier-preserved ascolichens

2000 ◽  
Vol 78 (11) ◽  
pp. 1450-1459 ◽  
Author(s):  
Paula T DePriest ◽  
Natalia V Ivanova ◽  
Dianne Fahselt ◽  
Vagn Alstrup ◽  
Andrea Gargas
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Large Subunit ◽  
Ice Core ◽  
Small Subunit ◽  
Rdna Sequences ◽  
Three Samples ◽  
Tyrolean Iceman ◽  
Small Subunit Ribosomal Dna

Ribosomal DNA sequences were amplified from subfossils of the ascolichen Umbilicaria cylindrica (L.) Delise ex Duby collected at the ablating edges of Greenland glaciers. Surprisingly, phylogenetic analysis indicated that the amplified rDNA sequences were not closely related to those of the lichen-forming fungus but rather represented two groups of psychrophilic basidiomycetes (orders Cystofilobasidiales and Sporidiales) and one group of ascomycetes (order Leotiales). Two of these groups, the Sporidiales and the Leotiales, include other fungi previously detected in DNA extracted from the grass clothing of the Tyrolean Iceman desiccated and frozen for over 3000 years and also in 2000- and 4000-year-old ice core samples from northern Greenland. Large subunit ribosomal DNA sequences representing the group Cystofilobasidiales were nearly identical to those of the basidioyeast saprobe Mrakia frigida. The adjacent internal transcribed spacer sequence was more than 98% similar to those from three samples of U. cylindrica from different sites that had been subjected to ice burial for various lengths of time, suggesting they also were Mrakia sequences. Although ancient contamination of multiple U. cylindrica specimens with fungi such as Mrakia cannot be ruled out, it is more probable that saprobic colonization of the subfossil tissues by psychrophilic fungi proceeded during recent ice melt.Key words: ancient DNA, small subunit ribosomal DNA, 18S ribosomal DNA, phylogenetic analysis, psychrophilic fungi, lichen-forming fungi.

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 Genetic Diversity of Archaea in Deep-Sea Hydrothermal Vent Environments

Genetics ◽  
1999 ◽  
Vol 152 (4) ◽  
pp. 1285-1297 ◽  
Author(s):  
Ken Takai ◽  
Koki Horikoshi
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Small Subunit ◽  
Molecular Phylogenetic Analysis ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Rdna Sequencing ◽  
Molecular Phylogenetic

Abstract Molecular phylogenetic analysis of naturally occurring archaeal communities in deep-sea hydrothermal vent environments was carried out by PCR-mediated small subunit rRNA gene (SSU rDNA) sequencing. As determined through partial sequencing of rDNA clones amplified with archaea-specific primers, the archaeal populations in deep-sea hydrothermal vent environments showed a great genetic diversity, and most members of these populations appeared to be uncultivated and unidentified organisms. In the phylogenetic analysis, a number of rDNA sequences obtained from deep-sea hydrothermal vents were placed in deep lineages of the crenarchaeotic phylum prior to the divergence of cultivated thermophilic members of the crenarchaeota or between thermophilic members of the euryarchaeota and members of the methanogen-halophile clade. Whole cell in situ hybridization analysis suggested that some microorganisms of novel phylotypes predicted by molecular phylogenetic analysis were likely present in deep-sea hydrothermal vent environments. These findings expand our view of the genetic diversity of archaea in deep-sea hydrothermal vent environments and of the phylogenetic organization of archaea.

scholarly journals Genetic Diversity within Cryptosporidium parvum and Related Cryptosporidium Species

1999 ◽  
Vol 65 (8) ◽  
pp. 3386-3391 ◽  
Author(s):  
Lihua Xiao ◽  
Una M. Morgan ◽  
Josef Limor ◽  
Ananias Escalante ◽  
Michael Arrowood ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cryptosporidium Parvum ◽  
Fragment Length Polymorphism ◽  
Distinct Species ◽  
Small Subunit ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Specific Host ◽  
Pcr Product ◽  
Rrna Sequences

ABSTRACT To assess the genetic diversity in Cryptosporidium parvum, we have sequenced the small subunit (SSU) rRNA gene of seven Cryptosporidium spp., various isolates of C. parvum from eight hosts, and a Cryptosporidiumisolate from a desert monitor. Phylogenetic analysis of the SSU rRNA sequences confirmed the multispecies nature of the genusCryptosporidium, with at least four distinct species (C. parvum, C. baileyi, C. muris, and C. serpentis). Other species previously defined by biologic characteristics, including C. wrairi, C. meleagridis, and C. felis, and the desert monitor isolate, clustered together or within C. parvum. Extensive genetic diversities were present among C. parvum isolates from humans, calves, pigs, dogs, mice, ferrets, marsupials, and a monkey. In general, specific genotypes were associated with specific host species. A PCR-restriction fragment length polymorphism technique previously developed by us could differentiate mostCryptosporidium spp. and C. parvum genotypes, but sequence analysis of the PCR product was needed to differentiateC. wrairi and C. meleagridis from some of theC. parvum genotypes. These results indicate a need for revision in the taxonomy and assessment of the zoonotic potential of some animal C. parvum isolates.

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