Genetic Diversity and Phylogeny of the Genus Euplotes (Protozoa, Ciliophora) Revealed by the Mitochondrial CO1 and Nuclear Ribosomal Genes

Nuclear ribosomal and mitochondrial genes have been utilized individually or in combination to identify known species and discriminate closely related species. However, compared with metazoans, genetic diversity within the ciliate order Euplotida is poorly known. The aim of this study is to investigate how much nucleotide sequence divergence occurs within Euplotes. A total of 14 new gene sequences, comprising four SSU rDNA and 10 CO1 (including three species for the first time) were obtained. Phylogenetic analyses were carried out based on sequences of two DNA fragments from the same 27 isolates. We found that CO1 revealed a larger interspecific divergence than the SSU rRNA gene, thus demonstrating a higher resolution for separating congeners. Genetic distances differ significantly at the species level. Euplotes balteatus was revealed to have a large intraspecific variation at two loci, while E. vannus showed different levels of haplotype variability, which appeared as a polyphyletic cluster on the CO1 tree. These high genetic divergences suggest the presence of more cryptic species. By contrast, the CO1 gene showed low variability within E. raikovi, appearing as monophyletic clusters, which indicates that this species could be identified based on this gene. Conclusively, CO1 is a suitable marker for the study of genetic diversity within Euplotes, and increased taxon sampling gives an opportunity to screen relationships among members of this genus. Additionally, current data present no clear biogeographical pattern for Euplotes.

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Wide Distribution and Genetic Diversity of “Candidatus Neoehrlichia mikurensis” in Rodents from China

Applied and Environmental Microbiology ◽

10.1128/aem.02917-12 ◽

2012 ◽

Vol 79 (3) ◽

pp. 1024-1027 ◽

Cited By ~ 17

Author(s):

Hao Li ◽

Jiafu Jiang ◽

Fang Tang ◽

Yi Sun ◽

Zengde Li ◽

...

Keyword(s):

Genetic Diversity ◽

16S Rrna ◽

Phylogenetic Analyses ◽

Wide Distribution ◽

Rrna Gene ◽

16S Rrna Gene Sequences ◽

Content Type ◽

Candidatus Neoehrlichia Mikurensis ◽

Geographic Origins ◽

Neoehrlichia Mikurensis

ABSTRACT“CandidatusNeoehrlichia mikurensis” was detected by PCR in 4.0% (34/841) of the rodents tested in this study. The 34 rodents represented nine species from seven regions of China. Phylogenetic analyses based on the partialgroELand nearly entire 16S rRNA gene sequences of the agent revealed genetic diversity, which was correlated with its geographic origins.

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A new species of squat lobster of the genus Hendersonida (Crustacea, Decapoda, Munididae) from Papua New Guinea

ZooKeys ◽

10.3897/zookeys.935.51931 ◽

2020 ◽

Vol 935 ◽

pp. 25-35 ◽

Cited By ~ 1

Author(s):

Paula C. RodrÍguez-Flores ◽

Enrique Macpherson ◽

Annie Machordom

Keyword(s):

New Species ◽

16S Rrna ◽

Papua New Guinea ◽

Phylogenetic Analyses ◽

Sequence Divergence ◽

New Guinea ◽

Genetic Distances ◽

Sister Species ◽

Squat Lobster ◽

A New Species

Hendersonida parvirostrissp. nov. is described from Papua New Guinea. The new species can be distinguished from the only other species of the genus, H. granulata (Henderson, 1885), by the fewer spines on the dorsal carapace surface, the shape of the rostrum and supraocular spines, the antennal peduncles, and the length of the walking legs. Pairwise genetic distances estimated using the 16S rRNA and COI DNA gene fragments indicated high levels of sequence divergence between the new species and H. granulata. Phylogenetic analyses, however, recovered both species as sister species, supporting monophyly of the genus.

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Genetic Diversity of Mitochondrial DNA Cytochrome b in Indonesian Native and Local Cattle Populations

Jurnal Ilmu Ternak dan Veteriner ◽

10.14334/jitv.v25i2.2496 ◽

2020 ◽

Vol 25 (2) ◽

pp. 39

Author(s):

Peni Wahyu Prihandini ◽

A Primasari ◽

M Luthfi ◽

J Efendy ◽

D Pamungkas

Keyword(s):

Genetic Diversity ◽

Bos Taurus ◽

Phylogenetic Analyses ◽

Bos Indicus ◽

Haplotype Diversity ◽

Genetic Distances ◽

Conservation Strategies ◽

Bos Javanicus ◽

Reverse Primer ◽

Relationship Of

Information on the genetic diversity of native and local cattle in Indonesia is vital for the development of breeding and conservation strategies. This study was aimed to assess the genetic diversity and phylogenetic relationship of the Indonesian native (Bali) and local [(Donggala, Madura, Sragen, Galekan, Rambon, dan Peranakan Ongole Grade x Bali (POBA)] cattle populations. Genomic DNA was extracted from blood samples (n= 75). Partial sequences of mtDNA cyt b, 464 bp, were amplified using the polymerase chain reaction technique (forward primer: L14735 and reverse primer: H15149). Thirty-four reference sequences of Bos taurus, Bos indicus, and Bos javanicus were included in the phylogenetic analyses. A total of 55 polymorphic sites and 13 haplotypes were observed in the whole breeds. No variable sites of mtDNA cyt b were observed in Galekan (kept in BCRS) and Rambon cattle. Overall haplotype diversity and nucleotide diversity were 0.515 ± 0.070 and 0.0184 ± 0.0045, respectively. The highest (0.092) and the lowest (0.000) genetic distances were between Bali and Donggala cattle populations and among Galekan (kept in BCRS), Rambon, and POBA cattle populations, respectively. Both mtDNA network and phylogenetic analyses revealed two major maternal lineages (A and B) of the studied population. Most of the sampled individuals (69.33%, present in haplotype H8-H19) were linked to lineage B, which belonged to the same cluster with Bos javanicus. Overall, most of the Indonesian native and local cattle populations had a considerable genetic diversity and shared a common maternal origin with Bos javanicus.

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Revisiting theAcanthamoebaspecies that form star-shaped cysts (genotypes T7, T8, T9, and T17): characterization of seven new Brazilian environmental isolates and phylogenetic inferences

Parasitology ◽

10.1017/s0031182011001648 ◽

2011 ◽

Vol 139 (1) ◽

pp. 45-52 ◽

Cited By ~ 7

Author(s):

ANA C. M. MAGLIANO ◽

MARTA M. G. TEIXEIRA ◽

SILVIA C. ALFIERI

Keyword(s):

Opportunistic Infections ◽

Phylogenetic Analyses ◽

Sequence Divergence ◽

Rrna Gene ◽

Pathogenic Potential ◽

Morphological Group ◽

Isolation And Characterization ◽

Group I ◽

Group 2

SUMMARYFree-living amoebae of the genusAcanthamoebaare the agents of both opportunistic and non-opportunistic infections and are frequently isolated from the environment. Of the 17 genotypes (T1–T17) identified thus far, 4 (T7, T8, T9, and T17) accommodate the rarely investigated species of morphological group I, those that form large, star-shaped cysts. We report the isolation and characterization of 7 new Brazilian environmentalAcanthamoebaisolates, all assigned to group I. Phylogenetic analyses based on partial (∼1200 bp) SSU rRNA gene sequences placed the new isolates in the robustly supported clade composed of the species of morphological group I. One of the Brazilian isolates is closely related toA. comandoni(genotype T9), while the other 6, together with 2 isolates recently assigned to genotype T17, form a homogeneous, well-supported group (2 0% sequence divergence) that likely represents a newAcanthamoebaspecies. Thermotolerance, osmotolerance, and cytophatic effects, features often associated with pathogenic potential, were also examined. The results indicated that all 7 Brazilian isolates grow at temperatures up to 40°C, and resist under hyperosmotic conditions. Additionally, media conditioned by each of the newAcanthamoebaisolates induced the disruption of SIRC and HeLa cell monolayers.

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Phylogenetic identification of Pneumocystis murina sp. nov., a new species in laboratory mice

Microbiology ◽

10.1099/mic.0.26921-0 ◽

2004 ◽

Vol 150 (5) ◽

pp. 1153-1165 ◽

Cited By ~ 54

Author(s):

Scott P. Keely ◽

Jared M. Fischer ◽

Melanie T. Cushion ◽

James R. Stringer

Keyword(s):

Phylogenetic Trees ◽

Statistical Tests ◽

Pneumocystis Carinii ◽

Sequence Divergence ◽

18S Rrna Gene ◽

Genetic Distances ◽

Rrna Gene ◽

Gene Trees ◽

Laboratory Mice ◽

Multiple Species

Pneumocystis is a fungal genus that contains multiple species. One member of the genus that has not been formally analysed for its phylogenetic relationships and possible species status is the Pneumocystis found in laboratory mice, Pneumocystis murina sp. nov. (type strain ATCC PRA-111T=CBS 114898T), formerly known as Pneumocystis carinii f. sp. muris. To advance research in this area, approximately 3000 bp of additional DNA sequence were obtained from the locus encoding rRNAs. This sequence and others were used to determine genetic distances between P. murina and other members of the genus. These distances indicated that P. murina DNA is most similar to that of the species of Pneumocystis found in laboratory rats. Nevertheless, P. murina is at least as diverged from these other Pneumocystis species as species in other fungal genera are from each other. The 18S rRNA gene sequence divergence exhibited by P. murina could not be ascribed to accelerated evolution of this gene as similar levels of divergence were observed at seven other loci. When five genes were used to construct phylogenetic trees for five Pneumocystis taxa, including P. murina, all the trees had the same topology, indicating that genes do not flow among these taxa. The gene trees were all strongly supported by statistical tests. When sequences from the rRNA-encoding locus were used to estimate the time of divergence of P. murina, the results indicated that P. murina is as old as the mouse. Taken together, these data support previous recognition of multiple species in the genus and indicate that P. murina is a phylogenetic species as well.

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Molecular Epidemiology, Genetic Diversity, and Antifungal Susceptibility of Major Pathogenic Dermatophytes Isolated From Human Dermatophytosis

Frontiers in Microbiology ◽

10.3389/fmicb.2021.643509 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zahra Salehi ◽

Masoomeh Shams-Ghahfarokhi ◽

Mehdi Razzaghi-Abyaneh

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analyses ◽

Antifungal Susceptibility ◽

Elongation Factor ◽

Trichophyton Mentagrophytes ◽

Epidemiological Studies ◽

Genetic Distances ◽

Mlst Scheme ◽

Low Genetic Diversity ◽

Starting Point

BackgroundDermatophytes are a homogeneous group of species with low genetic diversity, and there are still many uncertainties about the boundaries among species.ObjectivesAiming at clarifying the relationships among species in the genus and introducing suitable genes for multilocus sequence typing (MLST), a new MLST scheme approach was developed to characterize the major pathogenic dermatophytes.MethodsWe performed maximum parsimony (MP), MrBayes, RAxML, and eBURST analyses, based on the MLST scheme to scrutinize the evolution within 95 clinical isolates and four reference strains belonging to the four major dermatophytes species. Then, the discriminatory power, pairwise genetic distances, ratio dN/dS, and sequence types (STs) of these isolates were determined. Also, to study taxonomy, sequences of the internal transcribed spacer (ITS), Beta-tubulin (BT2), and translation elongation factor 1-α (TEF-1α) genes of other dermatophytes species available in the GenBank were analyzed.ResultsFindings of the present study indicated that three genes: BT2, ITS, and TEF−1α, which showed the greatest diversity among dermatophyte species, were suitable for MLST. The most prevalent STs were seen among the species of Trichophyton interdigitale. Also, two new genotypes, i.e., XXVII and XXVIII, were introduced for T. interdigitale and Trichophyton mentagrophytes. The least informative sites were found in Epidermophyton floccosum, Trichophyton rubrum, and T. mentagrophytes, while the most informative sites were observed in T. interdigitale. Furthermore, the most informative locus was TEF-1α. The phylogenetic tree, constructed by the combination of the three genes, shows a new topological pattern that confirms the derivation of the anthropophilic and zoophilic genera from the geophilic genus. Also, the phylogenetic analyses and pairwise distances of the combination of the three loci showed that Trichophyton tonsurans and Trichophyton equinum were a species complex, where T. equinum is derived from T. tonsurans.ConclusionsResults of this study showed that MLST is very effective in determining the boundaries between species and taxonomy. Considering that there is no database for MLST dermatophytes, further studies are needed to determine the suitable genes for MLST. Also, the determination of STs in epidemiological studies and raising epidemiological information are helpful. This study was a new starting point to determine the ST and a foundation for a dermatophyte MLST database.

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Cryptococcus mujuensis sp. nov. and Cryptococcus cuniculi sp. nov., basidiomycetous yeasts isolated from wild rabbit faeces

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64353-0 ◽

2006 ◽

Vol 56 (9) ◽

pp. 2241-2244 ◽

Cited By ~ 9

Author(s):

Kee-Sun Shin ◽

Hee-Mock Oh ◽

Yong-Ha Park ◽

Kang Hyun Lee ◽

Haryoung Poo ◽

...

Keyword(s):

Type Strain ◽

Yeast Species ◽

Phylogenetic Analyses ◽

Sequence Divergence ◽

Rrna Gene ◽

Wild Rabbit ◽

Faecal Pellets ◽

Phenotypic Differences ◽

Taxonomic Methods ◽

26S Rrna

Two previously undescribed anamorphic yeasts, strains T-11T and T-26T, recovered from wild rabbit faecal pellets collected in Muju, Korea, were identified using phenotypic and molecular taxonomic methods. The isolates were characterized by the proliferation of budding cells, positive diazonium blue B and urease reactions, the presence of Q-10 as the major ubiquinone, the presence of xylose in whole-cell hydrolysates and the inability to ferment sugars. Phylogenetic analyses based on 26S rRNA gene partial sequences revealed that strain T-11T was located in the Bulleromyces clade and was related to Sirobasidium intermedium, Tremella exigua, Cryptococcus cellulolyticus and Bullera pseudoalba. Strain T-26T was located in the Mesenterica clade and was closely related to Cryptococcus sp. F6 and Cryptococcus heveanensis CBS 8976. Sequence divergence values of more than 4 % from other described Cryptococcus species, together with the phenotypic differences, showed that the isolated yeasts represent previously unrecognized members of this genus. Therefore, two novel yeast species are proposed: Cryptococcus mujuensis sp. nov., with strain T-11T (=KCTC 17231T=CBS 10308T) as the type strain, and Cryptococcus cuniculi sp. nov., with strain T-26T (=KCTC 17232T=CBS 10309T) as the type strain.

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A new species of Leptobrachella (Anura, Megophryidae) from Guizhou Province, China

ZooKeys ◽

10.3897/zookeys.923.47172 ◽

2020 ◽

Vol 923 ◽

pp. 115-140 ◽

Cited By ~ 2

Author(s):

Tao Luo ◽

Ning Xiao ◽

Kai Gao ◽

Jiang Zhou

Keyword(s):

New Species ◽

16S Rrna ◽

Dna Sequences ◽

Phylogenetic Analyses ◽

Sequence Divergence ◽

Guizhou Province ◽

Morphological Data ◽

Rrna Gene ◽

Habitat Variation ◽

A New Species

This study describes a new species of the genus Leptobrachella, Leptobrachella suiyangensissp. nov. from the Huoqiuba Nature Reserve, Suiyang County, Guizhou Province, China, based on morphological data and phylogenetic analyses (16S rRNA mtDNA). The new species can be distinguished from other congeners by the molecular divergence and by a combination of morphological characters, including body size, dorsal and ventral patterns, dorsal skin texture, size of the pectoral and femoral glands, degree of webbing and fringing on the toes and fingers, dorsum coloration, and iris coloration in life. Currently, the genus Leptobrachella contains 75 species, 21 of which are found in China, including seven species reported from Guizhou Province. The uncorrected sequence divergence percentage between Leptobrachella suiyangensissp. nov. and all homologous DNA sequences available for the 16S rRNA gene was found to be >4.7%. The new record of the species and its relationships with others in the same genus imply that species distribution, habitat variation, environmental adaptation, and diversity of the genus Leptobrachella in southwest China need to be further investigated.

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Genetic diversity in Dactylonectria pauciseptata associated with black foot disease in New Zealand

New Zealand Plant Protection ◽

10.30843/nzpp.2018.71.157 ◽

2018 ◽

Vol 71 ◽

pp. 1-9

Author(s):

Yu Sheng ◽

Eirian E. Jones ◽

Hayley J. Ridgway

Keyword(s):

Genetic Diversity ◽

New Zealand ◽

Phylogenetic Analyses ◽

Histone Gene ◽

Rrna Gene ◽

Pathogenicity Tests ◽

Foot Disease ◽

Black Foot ◽

Black Foot Disease

The fungal genera Ilyonectria and Dactylonectria are causal agents of black foot disease affecting grapevines. A New Zealand survey of grapevines symptomatic for this disease was conducted in 2005, and 11 D. pauciseptata isolates were recovered. The incidence of this disease has increased over the last decade so a multi-gene approach was used to accurately identify these isolates and to determine whether they could infect grapevine roots in vitro. Eight of the original 11 D. pauciseptata isolates remained viable and were recovered from storage. DNA sequencing, universally primed polymerase chain reaction (UP-PCR) and a detached root assay were used to characterise these eight isolates. Phylogenetic analyses of ITS, Î²-tubulin, EF1-Î± and histone gene regions showed a monophyletic clade using the rRNA gene, EF1-Î± and histone gene, but paraphyletic based on Î²-tubulin. UP-PCR showed genetic diversity, with five major groups (P<0.01), with major groups concordant with the Î²-tubulin phylogeny. Pathogenicity tests with two common rootstocks showed that isolates produced lesions. Two distinct groups of D. pauciseptata were identified. Both groups are capable of infecting grapevine roots.

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Differentiation and classification of phytoplasmas in the pigeon pea witches’-broom group (16SrIX): an update based on multiple gene sequence analysis

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.038273-0 ◽

2012 ◽

Vol 62 (Pt_9) ◽

pp. 2279-2285 ◽

Cited By ~ 26

Author(s):

I.-M. Lee ◽

K. D. Bottner-Parker ◽

Y. Zhao ◽

A. Bertaccini ◽

R. E. Davis

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Phylogenetic Analyses ◽

Forest Tree ◽

Pigeon Pea ◽

Genetic Distances ◽

Rrna Gene ◽

Coding System ◽

Gene Sequences ◽

Genetic Lineages

The pigeon pea witches’-broom phytoplasma group (16SrIX) comprises diverse strains that cause numerous diseases in leguminous trees and herbaceous crops, vegetables, a fruit, a nut tree and a forest tree. At least 14 strains have been reported worldwide. Comparative phylogenetic analyses of the highly conserved 16S rRNA gene and the moderately conserved rplV (rpl22)–rpsC (rps3) and secY genes indicated that the 16SrIX group consists of at least six distinct genetic lineages. Some of these lineages cannot be readily differentiated based on analysis of 16S rRNA gene sequences alone. The relative genetic distances among these closely related lineages were better assessed by including more variable genes [e.g. ribosomal protein (rp) and secY genes]. The present study demonstrated that virtual RFLP analyses using rp and secY gene sequences allowed unambiguous identification of such lineages. A coding system is proposed to designate each distinct rp and secY subgroup in the 16SrIX group.

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