scholarly journals Analyses of separate and concatenated cox1 and 18S rRNA gene sequences indicate that the bat piroplasm Babesia vesperuginis is phylogenetically close to Cytauxzoon felis and the ‘prototheilerid’ Babesia conradae

2018 ◽  
Vol 66 (1) ◽  
pp. 107-115 ◽  
Author(s):  
Sándor Hornok ◽  
Alexandra Corduneanu ◽  
Jenő Kontschán ◽  
Katinka Bekő ◽  
Krisztina Szőke ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
18S Rrna ◽  
Phylogenetic Analyses ◽  
18S Rrna Gene ◽  
Sensu Stricto ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Important Species ◽  
Cytauxzoon Felis ◽  
Phylogenetic Status

Babesia vesperuginis is the only piroplasm known to infect bats. Unlike most members of the genus Babesia, it is probably transmitted by a soft tick species (i.e. Argas vespertilionis). Recently, two studies have been conducted to clarify the phylogenetic status of this species, and both agreed on placing it into a basal position among Babesia sensu stricto (s.s.). However, several important groups of piroplasms were not included in the already reported phylogenetic trees of B. vesperuginis isolates. Therefore, the aim of the present study was to amplify an approx. 950-bp fragment of the cytochrome c oxidase subunit 1 (cox1) gene of B. vesperuginis from A. vespertilionis specimens, and to compare its sequences with those from other piroplasmid groups in a broader phylogenetic context. Sequence comparisons focusing on either 18S rRNA or cox1 genes, as well as phylogenetic analyses involving separate and concatenated 18S rRNA and cox1 sequences indicate that B. vesperuginis is more closely related to the phylogenetic group of Theileriidae than to Babesia s.s. In particular, B. vesperuginis clustered closest to Cytauxzoon felis and the ‘prototheilerid’ B. conradae. The results of this study highlight that B. vesperuginis is a unique and taxonomically important species, which should be included in future studies aimed at resolving the comprehensive phylogeny of Piroplasmida.

scholarly journals Molecular survey of coccidian infections of the side-blotched lizard Uta stansburiana on San Benito Oeste Island, Mexico

Parasite ◽  
2018 ◽  
Vol 25 ◽  
pp. 43
Author(s):  
Petra Quillfeldt ◽  
Tanja Romeike ◽  
Juan F. Masello ◽  
Gerald Reiner ◽  
Hermann Willems ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
18S Rrna ◽  
Phylogenetic Analyses ◽  
Genetic Network ◽  
18S Rrna Gene ◽  
Blood Parasites ◽  
Rrna Gene ◽  
Uta Stansburiana ◽  
High Prevalence ◽  
High Uncertainty

Blood parasites are found in many vertebrates, but the research on blood parasites of lizards is still at its onset. We analyzed blood samples from side-blotched lizards Uta stansburiana from San Benito Oeste Island, Mexico, to test for the presence of hemoparasites. We found a high prevalence (23 out of 27 samples) of a blood parasite of the genus Lankesterella (Coccidia, Eimeriorina, Lankesterellidae) according to phylogenetic analyses of the parasite 18S rRNA gene. Similar parasites (97–99% similarity) have recently been described for Uta stansburiana from California. The parasite 18S rRNA gene showed high variability, both within San Benito and compared to California. The next closest matches of the parasite DNA with 97–98% similarity included a range of different genera (Lankesterella, Schellackia, Eimeria, Isospora and Caryospora). A high uncertainty in the deeper branches of the phylogenetic trees, and many missing links in genetic network analysis, were in line with previous suggestions that the coccidians are an understudied group with large knowledge gaps in terms of their diversity and taxonomy. Further studies are needed to resolve the evolutionary relationships within the Eimeriorina.

Steinernema borjomiense n. sp. (Rhabditida: Steinernematidae), a new entomopathogenic nematode from Georgia

Nematology ◽  
2018 ◽  
Vol 20 (7) ◽  
pp. 653-669 ◽  
Author(s):  
Oleg Gorgadze ◽  
Elena Fanelli ◽  
Manana Lortkhipanidze ◽  
Alberto Troccoli ◽  
Medea Burjanadze ◽  
...  
Keyword(s):  
New Species ◽  
18S Rrna ◽  
Entomopathogenic Nematode ◽  
Phylogenetic Analyses ◽  
Tail Length ◽  
Morphological Characters ◽  
18S Rrna Gene ◽  
The Body ◽  
Rrna Gene ◽  
A New Species

Summary A new species of entomopathogenic nematode, Steinernema borjomiense n. sp., was isolated from the body of the host insect, Oryctes nasicornis (Coleoptera: Scarabaeidae), in Georgia, in the territory of Borjomi-Kharagauli. Morphological characters indicate that the new species is closely related to species of the feltiae-group. The infective juveniles are characterised by the following morphological characters: body length of 879 (777-989) μm, distance between the head and excretory pore = 72 (62-80) μm, pharynx length = 132 (122-142) μm, tail length = 70 (60-80) μm, ratio a = 26.3 (23.0-29.3), H% = 45 (40-51), D% = 54 (47-59), E% = 102 (95-115), and lateral fields consisting of seven ridges (eight incisures) at mid-body. Steinernema borjomiense n. sp. was molecularly characterised by sequencing three ribosomal regions (the ITS, the D2-D3 expansion domains and the 18S rRNA gene) and the mitochondrial COI gene. Phylogenetic analyses revealed that S. borjomiense n. sp. differs from all other known species of Steinernema and is a member of the monticolum-group.

scholarly journals Redescription and phylogenetic analyses of Thaparocleidus gomtius and T. sudhakari (Monogenea: Dactylogyridae) from Wallago attu (Siluriformes: Siluridae) in India

2017 ◽  
Vol 54 (1) ◽  
pp. 87-96 ◽  
Author(s):  
C. Verma ◽  
A. Chaudhary ◽  
H. S. Singh
Keyword(s):  
Phylogenetic Relationships ◽  
18S Rrna ◽  
Phylogenetic Analyses ◽  
Uttar Pradesh ◽  
18S Rrna Gene ◽  
Morphometric Study ◽  
Rrna Gene ◽  
Molecular Analyses ◽  
Wallago Attu ◽  
Geographical Regions

Summary Two species of Thaparocleidus Jain (1952a) were found harboring W. attu from the Ganga River at two localities, Meerut and Farrukhabad, Uttar Pradesh, India, during the period of 2013-2015. Morphology and morphometric study of specimens identified as Thaparocleidus gomtius (Jain, 1952a) Lim, 1996 and T. sudhakari (Gusev, 1976) Lim, 1996. Molecular analyses using the 18S rRNA gene confirmed the validity of T. gomtius and T. sudhakari and demonstrated that both the species clustered with other Thaparocleidus species from different geographical regions. We aim at reassessing the taxonomy and establishing the phylogenetic relationships among these two redescribed species with other representatives of the genus Thaparocleidus.

Characterization of two novel yeast strains used in mediated biosensors for wastewater

2002 ◽  
Vol 48 (5) ◽  
pp. 418-426 ◽  
Author(s):  
Steve P Trosok ◽  
John H.T Luong ◽  
David F Juck ◽  
Brian T Driscoll
Keyword(s):  
18S Rrna ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Pulp Mill ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Candida Spp ◽  
Yeast Strains ◽  
Physiological Tests

After isolation from a pulp mill wastewater treatment facility, two yeast strains, designated SPT1 and SPT2, were characterized and used in the development of mediated biochemical oxygen demand (BOD) biosensors for wastewater. 18S rRNA gene sequence analysis revealed a one nucleotide difference between the sequence of SPT1 and those of Candida sojae and Candida viswanthii. While SPT2 had the highest overall homology to Pichia norvegensis, at only 73.5%, it is clearly an ascomycete, based on BLAST comparisons and phylogenetic analyses. Neighbor-joining dendrograms indicated that SPT1 clustered with several Candida spp., and that SPT2 clustered with Starmera spp., albeit as a very deep branch. Physiological tests, microscopic observations, and fatty acid analysis confirmed that SPT1 and SPT2 are novel yeast strains. Physiological tests also indicated that both strains had potential for use in mediated biosensors for estimation of BOD in wastewater. The lower detection limits of SPT1- and SPT2-based K3Fe(CN)6-mediated biosensors for a pulp-mill effluent were 2 and 1 mg BOD/L, respectively. Biosensor-response times for effluents from eight different pulp mills were in the range of 5 min. Reliability and sensitivity of the SPT1- and SPT2-based biosensors were good, but varied with the wastewater.Key words: yeast characterization, 18S rRNA gene sequence, pulp-mill wastewater, BOD5, mediated BOD biosensor.

scholarly journals Analysis of Acanthamoeba genotypes from public freshwater sources in Thailand reveals a new genotype, T23 Acanthamoeba bangkokensis sp. nov.

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chaturong Putaporntip ◽  
Napaporn Kuamsab ◽  
Warisa Nuprasert ◽  
Rattanaporn Rojrung ◽  
Urassaya Pattanawong ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
18S Rrna ◽  
Nucleotide Diversity ◽  
Purifying Selection ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Group Iii ◽  
Subtype B ◽  
New Genotype ◽  
Novel Genotype

AbstractA survey of Acanthamoeba in 100 public freshwater sources in 28 provinces across Thailand has identified 9 genotypes comprising T2/6, T3-T5, T9, T11, T12, T18 and a novel ‘T23’ among 131 isolates. Sequencing of the near complete 18S rRNA gene of Acanthamoeba of all isolates has shown that the most predominant genotype T4 found in 87 isolates (66.4%) contained 4 subtypes, i.e. T4A, T4B, T4C and T4F, while all isolates assigned to genotype T2/6 belonged to subtype B. Among intron-bearing genotypes, most isolates harbouring genotype T3 contained S516 introns, characterised by 3 distinct variants whilst all genotypes T4A and T5 were intronless. Identical 18S rRNA sequences of Acanthamoeba were identified across regions of the country and four isolates in this study shared the same sequences with those from remote nations, suggesting that some strains have reproductive success in diverse ecological niche. Nucleotide diversity of genotypes T2/6B, T3, T4, T9 and T11 in this study was significantly less than that among global isolates outside Thailand, implying that limited sequence diversity occurred within local populations. A remarkably higher level of nucleotide diversity in genotype T11 than those of other genotypes (0.041 vs. 0.012–0.024) could be due to cryptic subtypes. Recombination breakpoints have been detected within genotypes and subtypes as well as within isolates despite no evidence for sexual and parasexual cycles in the genus Acanthamoeba. Tajima’s D, Fu & Li’s D* and F* statistics revealed significantly negative deviation from neutrality across genotypes and subtypes, implying purifying selection in this locus. The 18S rRNA gene of the novel genotype ‘T23’ displayed 7.82% to 28.44% sequence differences in comparison with all known genotypes. Both Bayesian and maximum likelihood phylogenetic trees have placed genotype T23 as sister to the clade comprising genotypes T10, T12 and T14, all of these possess cyst structure belonging to morphological group III. Hence, Acanthamoeba bangkokensis sp. nov. is proposed for this novel genotype. It is likely that more genotypes of Acanthamoeba remain to be discovered while the evolution of the 18S rRNA gene of this pathogenic-free living amoeba seems to be ongoing.

scholarly journals Comparison of potential diatom ‘barcode’ genes (the 18S rRNA gene and ITS, COI, rbcL) and their effectiveness in discriminating and determining species taxonomy in the Bacillariophyta

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1369-1380 ◽  
Author(s):  
Liliang Guo ◽  
Zhenghong Sui ◽  
Shu Zhang ◽  
Yuanyuan Ren ◽  
Yuan Liu
Keyword(s):  
Phylogenetic Trees ◽  
18S Rrna ◽  
Mitochondrial Gene ◽  
Large Subunit ◽  
18S Rrna Gene ◽  
Marine Ecology ◽  
The Other ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Potential Marker

Diatoms form an enormous group of photoautotrophic micro-eukaryotes and play a crucial role in marine ecology. In this study, we evaluated typical genes to determine whether they were effective at different levels of diatom clustering analysis to assess the potential of these regions for barcoding taxa. Our test genes included nuclear rRNA genes (the nuclear small-subunit rRNA gene and the 5.8S rRNA gene+ITS-2), a mitochondrial gene (cytochrome c-oxidase subunit 1, COI), a chloroplast gene [ribulose-1,5-biphosphate carboxylase/oxygenase large subunit (rbcL)] and the universal plastid amplicon (UPA). Calculated genetic divergence was highest for the internal transcribed spacer (ITS; 5.8S+ITS-2) (p-distance of 1.569, 85.84 % parsimony-informative sites) and COI (6.084, 82.14 %), followed by the 18S rRNA gene (0.139, 57.69 %), rbcL (0.120, 42.01 %) and UPA (0.050, 14.97 %), which indicated that ITS and COI were highly divergent compared with the other tested genes, and that their nucleotide compositions were variable within the whole group of diatoms. Bayesian inference (BI) analysis showed that the phylogenetic trees generated from each gene clustered diatoms at different phylogenetic levels. The 18S rRNA gene was better than the other genes in clustering higher diatom taxa, and both the 18S rRNA gene and rbcL performed well in clustering some lower taxa. The COI region was able to barcode species of some genera within the Bacillariophyceae. ITS was a potential marker for DNA based-taxonomy and DNA barcoding of Thalassiosirales, while species of Cyclotella, Skeletonema and Stephanodiscus gathered in separate clades, and were paraphyletic with those of Thalassiosira. Finally, UPA was too conserved to serve as a diatom barcode.

scholarly journals Survey and Molecular Study of Babesia gibsoni in Dogs of Baghdad Province, Iraq

2020 ◽  
Vol 44 ((E0)) ◽  
pp. 34-41
Author(s):  
Naseir M. Badawi ◽  
Afaf A. Yousif
Keyword(s):  
Infection Rate ◽  
18S Rrna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Clinical Signs ◽  
Molecular Study ◽  
18S Rrna Gene ◽  
Universal Primers ◽  
Rrna Gene ◽  
Babesia Gibsoni

This study aimed to detect Babesia gibsoni (B. gibsoni) in dogs of different ages, sex and breeds in Baghdad province by microscopic and molecular investigations using polymerase chain reaction (PCR), sequencing, and phylogenetic analyses. The present study was investigated B. gibsoni in 310 blood samples of dogs for the period December 2018 to September 2019 in Baghdad province, Iraq. The molecular study was carried out by using universal primers of Babesia spp. (PIRO-A and PIRO-B) and specific primers of B. gibsoni (BAGIF and BAGIR) products size of 410 bp and 488 bp fragments of 18S rRNA gene respectively. The clinical signs revealed higher percentage and specific clinical signs of B. gibsoni as depression, anorexia, fever, pale mucus membrane, and ticks infestation, however icterus, and dead were low in which only occurred in two dogs out of infected dogs. The PCR assay and microscopic diagnosis revealed the infection rate of B. gibsoni 9 out of 310 (2.9%) in dogs. The sequence data analyses of nine DNA products were 98-100% similar to sequences of 18S rRNA gene of B. gibsoni data available in Gene bank. According to breed, age, and sex, the results revealed a significantly high-risk factor of infection in Husky dogs; B. gibsoni detected in females which was increased non-significantly than males; while the highest occurrence of disease was in young dogs aged three years or less in addition to the above, the infection rate of B. gibsoni was high in the spring season. In conclusion, this study was considered the first molecular record of B. gibsoni in Baghdad, Iraq documented no differences in diagnosis by blood smear and conventional PCR to amplify of 18S rRNA gene and partial sequencing of B. gibsoni with low-cost method and easily done.

Invalidation of Hyperamoeba by Transferring its Species to Other Genera of Myxogastria

2017 ◽  
Author(s):  
Anna Maria Fiore-Donno ◽  
Akiko Kamono ◽  
Ema E. Chao ◽  
Manabu Fukui ◽  
Thomas Cavalier-Smith
Keyword(s):  
Type Species ◽  
18S Rrna ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Life Stages ◽  
Marine Environments ◽  
The Family

The genus Hyperamoeba Alexeieff, 1923 was established to accommodate an aerobic amoeba exhibiting three life stages—amoeba, flagellate, and cyst. As more species/strains were isolated, it became increasingly evident from small subunit (SSU) gene phylogenies and ultrastructure that Hyperamoeba is polyphyletic and its species occupy different positions within the class Myxogastria. To pinpoint Hyperamoeba strains within other myxogastrid genera we aligned numerous myxogastrid sequences: whole small subunit ribosomal (SSU or 18S rRNA) gene for 50 dark-spored (i.e. Stemonitida and Physarida) Myxogastria (including a new ‘‘Hyperamoeba’’/Didymium sequence) and a ca. 400-bp SSU fragment for 147 isolates assigned to 10 genera of the order Physarida. Phylogenetic analyses show unambiguously that the type species Hyperamoeba flagellata is a Physarum (Physarum flagellatum comb. nov.) as it nests among other Physarum species as robust sister to Physarum didermoides. Our trees also allow the following allocations: five Hyperamoeba strains to the genus Stemonitis; Hyperamoeba dachnaya, Pseudodidymium cryptomastigophorum, and three other Hyperamoeba strains to the genus Didymium; and two further Hyperamoeba strains to the family Physaridae. We therefore abandon the polyphyletic and redundant genus Hyperamoeba. We discuss the implications for the ecology and evolution of Myxogastria, whose amoeboflagellates are more widespread than previous inventories supposed, being now found in freshwater and even marine environments.

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