Phylogenetic analysis of Sarcocystis spp. of mammals and reptiles supports the coevolution of Sarcocystis spp. with their final hosts1Note: The nucleotide sequences of Sarcocystis dispersa and Sarcocystis sp. have been deposited in the GenBank™ under the accession numbers AF120115 and AF120114, respectively.1

1999 ◽  
Vol 29 (5) ◽  
pp. 795-798 ◽  
Author(s):  
D. Doležel ◽  
B. Koudela ◽  
M. Jirků ◽  
V. Hypša ◽  
M. Obornı́k ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Nucleotide Sequences ◽  
Sarcocystis Spp

scholarly journals Molecular Systematics, Taxonomy and Distribution of the Pyrrhura Picta–Leucotis Complex

2017 ◽  
Vol 10 (1) ◽  
pp. 53-91 ◽  
Author(s):  
Thomas Arndt ◽  
Michael Wink
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Phylogeny ◽  
Molecular Systematics ◽  
Species Complex ◽  
Morphological Analysis ◽  
Nucleotide Sequences ◽  
Mitochondrial Cytochrome ◽  
Species Status ◽  
New Subspecies ◽  
Paraphyletic Group

Introduction: The relationships within the Pyrrhura species complex are partly unresolved. In this study, a comprehensive phylogenetic analysis of the Pyrrhura picta-leucotis complex was carried out, covering all species except P. subandina. Material and Methods: We made a morphological analysis of 745 preserved specimens of all the taxa in different museums. Nucleotide sequences of the mitochondrial cytochrome gene were generated and used to reconstruct a molecular phylogeny of Pyrrhura. Results and Discussion: Our results show that the complex is divided into 6 main groups comprising 15 species. P. dilutissima, regarded up to now as a subspecies of P. peruviana, acquires species status and three new subspecies are described. We also provide evidence that P. roseifrons is a paraphyletic group, indicating the existence of probably 3 lineages of which 2 deserve species status.

Phylogenetic Analysis and Rapid Detection of GenusPhellinususing the Nucleotide Sequences of 18S Ribosomal RNA

Mycobiology ◽  
2003 ◽  
Vol 31 (3) ◽  
pp. 133 ◽  
Author(s):  
Byung-Hyouk Nam ◽  
Jae-Yun Lee ◽  
Gi-Young Kim ◽  
Heon-Ho Jung ◽  
Hyung-Sik Park ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Rna ◽  
Rapid Detection ◽  
Nucleotide Sequences ◽  
18S Ribosomal Rna

Morphological and molecular identification of some species of nematode of the family Protostrongylidae Leiper, 1926

2016 ◽  
Vol 3 (4) ◽  
pp. 454-461
Author(s):  
Салахутдинов ◽  
I. Salakhutdinov ◽  
Рузиев ◽  
B. Ruziev ◽  
Каримова ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Trees ◽  
Molecular Genetic ◽  
Digital Camera ◽  
Molecular Genetic Analysis ◽  
Nucleotide Sequences ◽  
Genetic Identification ◽  
Mountain Area ◽  
Phylogenetic Relations ◽  
The Family

Objective of research: conducting morphological and molecular-genetic identification and studying phylogenetic relations between protostrongylids. Materials and methods: helminthological material was collected from wild (Capra sibirica, C. falconeri, Ovis vignei and O. ammon) and domestic hollow horned ruminants (C. hircus and O. aries), and land mollusks of the family Xeropicta in the piedmont and mountain area of Uzbekisan. The morphology of protostrongylids was studied using the methods of Boev (1975) and Anderson (1978). To identify the nematode type we used temporary preparations treated with glycerol. The first-stage larvae were investigated by examination of fecal samples from animals taking into account the length, tail form and body size. To study the morphology of the third-stage protostrongylid larvae the feet of infected mollusks Xeropicta candaсharica were separated and placed into the artificial gastric juice where the cap was destroyed and the infected larvae were eliminated. After determination of species belonging of mature and larval nematodes the material was stored in separate test-tubes with distilled water under the low temperature (- 20 ºС) or in 70 % Ethanol for the molecular analysis. We used microscopes ML 2000 with a digital camera and Olympus CX3. DNA extraction, amplification and sequencing were performed with an automated sequencer. Phylogenetic analysis was conducted using the software Clustal X 2.0. Phylogenetic trees were created by the Neighbor–Joining method. Nucleotide sequences ITS-2 regions of species Protostrongylus rufescens (EU018485), P. shiozawai (AB478249), Ortostrongylus macrotis (EU018483), Cystocaulus ocreatus (EU018481) and Umingmakstrongylus pallikuukensis (AY648409) received from the NCBI GenBank were used in phylogenetic analysis. Results and discussion: Four species of adult protostrongylid nematodes: Protostrongylus rufescens, P. hobmaieri, Spiculocaulus leuckarti and Cystocaulus ocreatus were determined. DNA from four species of mature protostrongylids and larvae was amplified by using ITS-2 regions. Amplificate dimension of nematodes P. rufescens and P. hobmaieri was 380 base pairs (b.p.), S. leuckarti – 388, C. ocreatus – 399 b.p. According to the results of phylogenetic analysis and comparison of nucleotide sequences, five protostrongylid species were found in animals of the Caprinae subfamily: P. rufescens, P. hobmaieri, Protostrongylus sp., S. leuckarti and C. ocreatus. The morphological and molecular-genetic analysis of detected nematodes enables the precise identification.

Amanita glarea, a new species in section Vaginatae from Pakistan

Phytotaxa ◽  
2017 ◽  
Vol 306 (2) ◽  
pp. 135 ◽  
Author(s):  
SANA JABEEN ◽  
MUNAZZA KIRAN ◽  
SADIQ ULLAH ◽  
ANDREW W. WILSON ◽  
GREGORY M. MUELLER ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Morphological Characters ◽  
Nucleotide Sequences ◽  
Phylogenetic Data ◽  
Molecular Phylogenetic ◽  
A New Species ◽  
Molecular Phylogenetic Data

A new species, Amanita glarea, is described and illustrated from Pakistan. Molecular phylogenetic data derived from internal transcribed spacer (ITS) and nuclear ribosomal large subunit (LSU) regions along with morphological characters make it distinct from other currently known Amanita species. Amanita glarea is characterized by a grayish brown, slightly umbonate, pileus having universal veil remnants and striate margins, a long ringless stipe with a saccate volva bearing yellowish brown patches on the verrucose surface, inamyloid globose to subglobose basidiospores, and a filamentous pileipellis with some inflated round to elongated cells. Phylogenetic analysis of nuclear ribosomal ITS and LSU nucleotide sequences resolve A. glarea with other taxa in Amanita section Vaginatae.

scholarly journals Phylogenetic analysis of the genus Aeromonas based on two housekeeping genes

2004 ◽  
Vol 54 (5) ◽  
pp. 1511-1519 ◽  
Author(s):  
L. Soler ◽  
M. A. Yáñez ◽  
M. R. Chacon ◽  
M. G. Aguilera-Arreola ◽  
V. Catalán ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Housekeeping Genes ◽  
Nucleotide Sequences ◽  
Aeromonas Salmonicida ◽  
Species Level ◽  
Substitution Rates ◽  
Aeromonas Veronii ◽  
Taxonomic Organization ◽  
Phylogenetic Divergence

The phylogenetic relationships of all known species of the genus Aeromonas, and especially Aeromonas bestiarum and Aeromonas salmonicida, were investigated on 70 strains using the rpoD sequence, which encodes the σ 70 factor. This analysis was complemented with the sequence of gyrB, which has already proven useful for determining the phylogenetic relationships in the genus. Nucleotide sequences of rpoD and gyrB showed that both genes had similar substitution rates (<2 %) and a similar number of variable positions (34 % for rpoD versus 32 % for gyrB). Strain groupings by analysis of rpoD, gyrB and a combination of both genes were consistent with the taxonomic organization of all Aeromonas species described to date. However, the simultaneous analysis of both clocks improved the reliability and the power to differentiate, in particular, closely related taxa. At the inter-species level, gyrB showed a better resolution for differentiating Aeromonas sp. HG11/Aeromonas encheleia and Aeromonas veronii/Aeromonas culicicola/Aeromonas allosaccharophila, while rpoD more clearly differentiated A. salmonicida from A. bestiarum. The analysis of rpoD provided initial evidence for clear phylogenetic divergence between the latter two species.

scholarly journals Morphological and molecular characterization of Sarcocystis wenzeli in chickens (Gallus gallus) in China

2020 ◽  
Author(s):  
Jing Pan ◽  
Chunli Ma ◽  
Zhumei Huang ◽  
Yulong Ye ◽  
Hongxia Zeng ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
18S Rdna ◽  
Sequence Similarity ◽  
Rpob Gene ◽  
28S Rdna ◽  
Ground Substance ◽  
Molecular Characteristics ◽  
Cox1 Gene ◽  
Intermediate Hosts ◽  
Sarcocystis Spp

Abstract Background: There has been considerable confusion concerning the number and classification of Sarcocystis spp. in chickens. Scarce nucleotide data of Sarcocystis spp. from chickens are provided in GenBank. The study aimed to investigate the morphological and molecular characteristics of Sarcocystis spp. found in chickens in China.Methods: Tissues from 33 chickens were collected in 2019. Sarcocysts were observed using light (LM) and transmission electron microscopy (TEM). Individual sarcocysts from different chickens were selected for DNA extraction, and five loci, 18S rDNA, 28S rDNA, ITS1 region, the mitochondrial cox1 gene and the apicoplastic rpoB gene, were amplified from each sarcocyst, sequenced and analyzed.Results: Only S. wenzeli was found in 14 of 33 (42.4%) chickens. Under LM, the sarcocysts were microscopic and exhibited palisade-like villar protrusions measuring 1.5–2.8 μm. Ultrastructurally, the sarcocyst wall contained numerous stubby hill-like villar protrusions. The protrusions included scattered microtubules, which extended from the tips of the protrusions into the ground substance. The five loci were successfully sequenced and the sequences deposited in GenBank. At 18S rDNA, ITS1 and cox1, the most similar sequences in GenBank were those of Sarcocystis sp. obtained from the brains of chickens, i.e. 99.9–100%, 98.1–98.5% and 99.3% identity, respectively. The five loci (18S rDNA, 28S rDNA, ITS1, cox1 and rpoB) showed different levels of interspecific sequence similarity with other closely related species of Sarcocystis (e.g. 99.8%, 99.0–99.2%, 89.3-89.7%, 98.5%, and 97.5%, respectively, with S. anasi). Phylogenetic analysis based on four of the loci (18S rDNA, cox1, rpoB and ITS1) revealed that S. wenzeli formed an independent clade with Sarcocystis spp. that utilize geese or ducks as intermediate hosts and canines as the known or presumed definitive host.Conclusions: To our knowledge, the sequences of 28S rDNA and rpoB reported here constitute the first records of genetic markers of Sarcocystis spp. in chickens. Based on molecular analysis, S. wenzeli might be responsible for the neurological disease in chickens, and ITS1 and rpoB are more suitable for discriminating it from closely related Sarcocystis spp. Phylogenetic analysis revealed that S. wenzeli presents a close relationship with Sarcocystis spp. in geese or ducks.

Periconia citlaltepetlensis sp. nov. (Periconiaceae, Pleosporales): a psychrotolerant fungus from high elevation volcanic glacier (Mexico)

Phytotaxa ◽  
2020 ◽  
Vol 459 (3) ◽  
pp. 235-247
Author(s):  
ROSA P. CALVILLO-MEDINA ◽  
AURORA COBOS-VILLAGRÁN ◽  
TANIA RAYMUNDO
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
First Record ◽  
High Elevation ◽  
Nucleotide Sequences ◽  
Species Level ◽  
Rdna Analysis

Periconia citlaltepetlensis sp. nov. is the first record of a fungus identified to species level from high elevation volcanic glacier in Mexico. It is a novel dothideomycete species supported by morphological, cultural characters and phylogenetic analysis (nucleotide sequences data rDNA analysis). The new species is characterized by conidiophores often with 2–4 enteroblastic, percurrent proliferations, large, globose, golden brown or reddish brown conidia that are borne singly or in basipetal chains, verrucose to irregular lobate crests, born singly or in basipetal chains of two conidia; acropetally proliferating; conidiogenesis holoblastic. The morphology of P. citlaltepetlensis is compared to other Periconia species and a detailed description and morphological illustrations are provided.

scholarly journals Molecular Detection of Pseudorabies Virus (PrV), Porcine Parvovirus (PPV) and Porcine Circovirus 2 (PCV2) in Swine in Republic of Montenegro

2016 ◽  
Vol 66 (3) ◽  
pp. 347-358 ◽  
Author(s):  
Radoš Miković ◽  
Aleksandra Knežević ◽  
Nenad Milić ◽  
Dejan Krnjaić ◽  
Marina Radojičić ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Pseudorabies Virus ◽  
Nucleotide Sequences ◽  
Porcine Circovirus ◽  
Porcine Parvovirus ◽  
Genotype I ◽  
Three Samples ◽  
Porcine Circovirus 2 ◽  
Spleen And Lymph Nodes ◽  
High Level

Abstract The presence of pseudorabies virus (PrV), porcine parvovirus (PPV) and porcine circovirus 2 (PCV2) was examined in sixty samples (spleen and lymph nodes) and thirty samples of sacral ganglia collected from non-vaccinated swine by virus isolation and polymerase chain reaction (PCR). Using PCR method PrV was detected in three samples, PPV in seven samples and six samples were found positive for PCV2. The phylogenetic analysis of the nucleotide sequences of three PrV isolates identified in this study showed high similarity and significant clustering within the PrV genotype I strains such as Kaplan and Bartha isolated from pigs in Hungary, strain Becker isolated in USA and strain Kolchis isolated in Greece. The nucleotide sequences of two PPV isolates showed high level of similarity with the strain Challenge isolated from pigs in UK, strain Kresse isolated in USA and strains 77 and LZ isolated in China. The phylogenetic analysis of the nucleotide sequences of two PCV2 isolates showed high level of similarity and significant clustering within genotype PCV2b strains such as NIVS-3, NIVS-5 and NIVS-6 isolated in Serbia, strain 3959 isolated in Austria, strain PM165 isolated from pigs in Brasil, and strain XT2008 isolated in China. The results of our study present the molecular characterization of PrV, PPV and PCV2 identified in swine in Republic of Montenegro. Besides that, these results confirmed that PCR is a very useful method for rapid detection of these viruses in subclinically infected swine.

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