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internal transcribed spacers

Qing Yu, Weimin Ye, Tom Powers
Gracilacus wuae n. sp. from soil associated with cow parsnip in Ontario, Canada is described and illustrated. Morphologically, females have a long stylet ranging from 80 to 93 µm long, the lip region not offset from the body contour, without lateral lips but with large and flat submedian lobes, the mouth opening slit-like elongated laterally and surrounded by lateral flaps, the excretory pore is anterior to the knobs of the stylet; males without stylet and the pharynx degenerated. The fourth-stage juveniles lack a stylet, the pharynx degenerated, and can be differentiated into preadult females and males based on the position of the genital primordia...
September 2016: Journal of Nematology
Harun Cimen, Vladimír Půža, JiŘí NermuŤ, Justin Hatting, Tshima Ramakuwela, Selcuk Hazir
A new species of entomopathogenic nematode (EPN), Steinernema biddulphi n. sp., was isolated from a maize field in Senekal, Free State Province of South Africa. Morphological and molecular studies indicated the distinctness of S. biddulphi n. sp. from other Steinernema species. Steinernema biddulphi n. sp. is characterized IJs with average body length of 663 μm (606-778 μm), lateral fields with six ridges in mid-body region forming the formula 2,6,2. Excretory pore located anterior to mid-pharynx (D% = 46)...
September 2016: Journal of Nematology
Sebastian Rahn, Anna Schuck, Mustafa Kondakci, Rainer Haas, Nicole Neuhausen, Klaus Pfeffer, Birgit Henrich
Fungal infections are recognized in an increasing number of patients with immunological deficits and are associated with high rates of mortality (Brown et al., 2012a). In this pilot-study, a rapid Real time PCR (fuPCR) was designed for the detection and differentiation of fungal pathogens in clinical specimens of haematological patients. The fuPCR, targeting the internal transcribed spacer region 2 (ITS2) of rDNA region, is comprised of seven multiplex reactions, which were shown to be specific and sensitive for a comprehensive spectrum of clinically relevant fungal species...
October 13, 2016: International Journal of Medical Microbiology: IJMM
O M Kandil, K A Abdelrahman, H A Fahmy, M S Mahmoud, A H El Namaky, J E Miller
Haemonchus contortus is a major parasite of small ruminants and its blood-feeding behaviour causes effects ranging from mild anaemia to death. Knowledge of the genetic variation within and among H. contortus populations can provide the foundation for understanding transmission patterns and aid in the control of haemonchosis. Adult male H. contortus were collected from three geographical regions in Egypt. The second internal transcribed spacer (ITS2) of nuclear ribosomal DNA was amplified using the polymerase chain reaction (PCR) and sequenced directly...
October 20, 2016: Journal of Helminthology
Iva Přikrylová, Andrew P Shinn, Giuseppe Paladini
A new genus and species of monogenean belonging to the Gyrodactylidae, Citharodactylus gagei n. gen. et n. sp. (Plathyhelminthes, Monogenea), is described from the gills of the moon fish, Citharinus citharus (Geoffroy Saint-Hilaire), a characiform fish collected from Lake Turkana in northern Kenya. The new viviparous genus can be readily distinguished from the six other gyrodactylid genera recorded from Africa and from the other viviparous genera within the Gyrodactylidae based on the morphology of the male copulatory organ (MCO), which consists of a muscular ovate organ with an opening onto the tegument through which the narrow tapered end of a sclerotised curved cone-shaped structure protrudes...
October 19, 2016: Parasitology Research
Nhu Nguyen, Else C Vellinga, Thomas D Bruns, Peter Kennedy
The genus Suillus represents one of the most recognizable groups of mushrooms in conifer forests throughout the Northern Hemisphere. Although for decades the genus has been relatively well defined morphologically, previous molecular phylogenetic assessments have provided important yet preliminary insights into its evolutionary history. Here we present the first large-scale phylogenetic study of the boundaries of each species in the genus Suillus based on the most current internal transcribed spacer (ITS) barcode sequences available in public databases, as well as sequencing of 224 vouchered specimens and cultures, 15 of which were type specimens from North America...
October 19, 2016: Mycologia
Masoud Abrinbana, Farzaneh Badali, Jafar Abdollahzadeh
Three new species of Pythium: P. ershadii, P. pyrioosporum, and P. urmianum from soils of various regions in Iran are described and illustrated. These species are morphologically distinct from all other known species. Pythium ershadii is morphologically characterized by pyriform ornamented oogonia and rarely production of pyriform oospores. Pythium pyrioosporum differs from other species of the genus by the production of pyriform oospores and smooth walled oogonia, oospores with a tapering elongation toward a hypogynous antheridium and intercalary hypogynous antheridia...
October 19, 2016: Mycologia
Maria Desterro Santos, Maria Esther Fonseca-Boiteux, Leonardo Silva Boiteux, Paulo Eduardo Câmara, Jose Carmine Dianese
Nine Phyllachora species found on hosts belonging to the family Myrtaceae native to the Brazilian Cerrado were described and illustrated. We sequenced nuc rDNA internal transcribed spacer barcode regions for representatives of seven species and conducted phylogenetic analyses, which provided strong support for four new species that we describe as Phyllachora cerradensis, P. ermidensis, P. furnasensis, and P. myrciariae Catacauma nigerrimum was recombined into P. nigerrima, and a key to the common Phyllachora species on myrtaceous hosts from the Brazilian Cerrado was also included...
October 19, 2016: Mycologia
Gerald L Benny, Hsiao-Man Ho, Katy Lazarus, Matthew E Smith
More than 520 soil samples were surveyed for species of the mycoparasitic zygomycete genus Syncephalis using a culture-based approach. These fungi are relatively common in soil using the optimal conditions for growing both the host and parasite. Five species obtained in dual culture are unknown to science and are described here: (i) S. digitata with sporangiophores short, merosporangia separate at the apices, simple, 3-5 spored; (ii) S. floridana, which forms galls in the host and has sporangiophores up to 170 µm long with unbranched merosporangia that contain 2-4 spores; (iii) S...
October 19, 2016: Mycologia
Selwyn Arlington Headley, Lucienne Garcia Pretto-Giordano, Giovana Wingeter Di Santis, Lucas Alécio Gomes, Rafaela Macagnan, Daniela Farias da Nóbrega, Katherine Moura Leite, Brígida Kussumoto de Alcântara, Eiko Nakagawa Itano, Amauri Alcindo Alfieri, Mario Augusto Ono
Paracoccidioidomycosis (PCM) is an endemic disease of humans from Latin America that is caused by Paracoccidioides brasiliensis and P. lutzii, with most cases of PCM in domestic animals being associated with P. brasiliensis. This study presents the clinical, cytological, mycological, serological, and molecular findings associated with P. brasiliensis in a dog from Southern Brazil. Fine needle biopsies were collected from the skin and several lymph nodes of a 5-year-old female Labrador dog that had enlargement of most superficial lymph nodes...
October 18, 2016: Mycopathologia
Shradha Subedi, Fanrong Kong, Peter Jelfs, Timothy J Gray, Meng Xiao, Vitali Sintchenko, Sharon C-A Chen
Accurate identification of slowly growing nontuberculous mycobacteria (SG-NTM) of clinical significance remains problematic. This study evaluated a novel method of SG-NTM identification by amplification of the mycobacterial 16S-23S rRNA internal transcribed spacer (ITS) region followed by resolution of amplified fragments by sequencer-based capillary gel electrophoresis (SCGE). Fourteen American Type Culture Collection (ATCC) strains and 103 clinical/environmental isolates (total n = 24 species) of SG-NTM were included...
2016: PloS One
Atchara Phumee, Apiwat Tawatsin, Usavadee Thavara, Theerakamol Pengsakul, Suwich Thammapalo, Jérôme Depaquit, Frédérick Gay, Padet Siriyasatien
Although female sand flies are best known as the vectors of Leishmania parasites and viruses, several previous reports have demonstrated that these insects can also act as vectors for the trypanosomes of bats, lizards, and snakes. In this report, we created an inventory of Phlebotomine sand flies from southern Thailand. A novel trypanosome was found in a specimen of Phlebotomus stantoni, and two sand fly species newly recorded in the country, Sergentomyia khawi and Sergentomyia hivernus, were described. PCR primer pairs specific for the internal transcribed spacer 1 (ITS1) and the small subunit ribosomal DNA (SSU rDNA) gene of trypanosomatids were used to demonstrate the presence of the parasite in the sand fly...
October 15, 2016: Journal of Medical Entomology
Xiao-Feng Zhu, Dian-Peng Zhang, Sen Yang, Qing-Wen Zhang
Three yeast strains designated as S44, XF1 and XF2, respectively, were isolated from Scolytus scheryrewi Semenov of apricot tree in Shule County, Xinjiang, China, and were demonstrated to be a new member of the genus Candida by sequence comparisons of 26S rRNA gene D1/D2 domain and internal transcribed spacer (ITS) region. BLASTn alignments on NCBI showed that the similarity of 26S rRNA gene sequences of S44 (type strain) to all sequences of other Candida yeasts was very low (≦93 %). The phylogenetic tree based on the 26S rRNA gene D1/D2 domain and ITS region sequences revealed that the strain S44 is closely related to C...
October 14, 2016: Archives of Microbiology
João Paulo Zen Siqueira, Deanna A Sutton, Dania García, Josepa Gené, Pamela Thomson, Nathan Wiederhold, Josep Guarro
Aspergillus section Versicolores includes species of clinical relevance and many others that have been poorly studied but are occasionally found in clinical samples. The aim of this study was to investigate, using a multilocus phylogenetic approach, the spectrum of species of the section Versicolores and to determine their in vitro antifungal susceptibility. The study was based on a set of 77 clinical isolates from different USA medical centres, which had been previously identified as belonging to this section...
November 2016: Fungal Biology
Joey B Tanney, David R McMullin, Blake D Green, J David Miller, Keith A Seifert
The genus Diaporthe comprises close to 800 species, with around 2000 names attributed to it and its asexual morphs previously recognized in Phomopsis. Diaporthe species are common plant associates, including saprotrophs, pathogens, and endophytes affiliated with a diverse range of hosts worldwide. In this study, an unknown Diaporthe sp. was frequently isolated as an endophyte from healthy Picea mariana and Picea rubens needles in the Acadian forest of Eastern Canada. Morphological observations and the application of the genealogical concordance phylogenetic species recognition concept using four unlinked loci (internal transcribed spacer (ITS), DNA-lyase (Apn2), translation elongation factor 1-α (EF1-α), and beta-tubulin (TUB)) support the distinctiveness of this species, described here as Diaporthe maritima...
November 2016: Fungal Biology
Pedro W Crous, Johannes Z Groenewald
Species of Coleophoma have been reported as plant pathogenic, saprobic or endophytic on a wide host range. The genus is characterised by having pycnidial conidiomata, phialidic conidiogenous cells intermingled among paraphyses, and cylindrical conidia. Coleophoma has had a confusing taxonomic history with numerous synonyms, and its phylogeny has remained unresolved. The aim of the present study was to use a polyphasic approach incorporating morphology, ecology, and molecular data of the partial large subunit of nrDNA (LSU), the internal transcribed spacer region with intervening 5...
November 2016: Fungal Biology
Chen Chen, Gerard J M Verkley, Guangyu Sun, Johannes Z Groenewald, Pedro W Crous
Species in Neofabraea, Pezicula, and related genera have been reported as saprobes, plant pathogens or endophytes from a wide range of hosts. The asexual morphs of Neofabraea and Pezicula had been placed in Cryptosporiopsis, now a synonym of Pezicula, while Neofabraea was also linked to Phlyctema. Based on morphology and molecular data of the partial large subunit nrDNA (LSU), the internal transcribed spacer region with intervening 5.8S nrDNA (ITS), partial β-tubulin region (tub2), and the partial RNA polymerase II second largest subunit region (rpb2), the taxonomy and phylogenetic relationships of these fungi were investigated...
November 2016: Fungal Biology
John-Erich Haight, Gary A Laursen, Jessie A Glaeser, D Lee Taylor
Fungal species with a broad distribution may exhibit considerable genetic variation over their geographic ranges. Variation may develop among populations based on geographic isolation, lack of migration, and genetic drift, though this genetic variation may not always be evident when examining phenotypic characters. Fomitopsis pinicola is an abundant saprotrophic fungus found on decaying logs throughout temperate regions of the Northern Hemisphere. Phylogenetic studies have addressed the relationship of F. pinicola to other wood-rotting fungi, but pan-continental variation within F...
September 2016: Mycologia
Saber Reaghi, Ali Haghighi, Majid Fasihi Harandi, Adel Spotin, Kourosh Arzamani, Soheila Rouhani
AIM: Fascioliasis is one of the most zoonotic diseases with global extension. As the epidemiological distribution of Fasciola may lead to various genetic patterns of the parasite, the aim of this study is to identify Fasciola hepatica based on spermatogenesis, and phylogenetic analysis using mitochondrial (nicotiamide adenine dinucleotide dehydrogenase subunit I [ND1] and cytochrome oxidase subunit I) gene marker. MATERIALS AND METHODS: In this study, 90 F. hepatica collected from 30 cattle at slaughterhouse located in three different geographical locations in the North-East of Iran were evaluated based on spermatogenetic ability and internal transcribed spacer 1 gene restriction fragment length polymorphism pattern...
September 2016: Veterinary World
Luciano Toma, Francesco Severini, Roberto Romi, Marco Di Luca
Ochlerotatus caspius is a mosquito of medical and veterinary relevance both for its synanthropy and for its potential role in transmission of viruses and nematodes in the areas that it inhabits. Due to its wide range and the marked variability in the adult colour pattern, some authors have recognized Ochlerotatus caspius as a complex of species. In this study, we purposed to evaluate the possible taxonomic heterogeneity between 2 chromatic forms by using both morphological and molecular approaches. The preliminary results based on the identity of the rRNA internal transcribed spacer 2 (ITS-2) lead us to believe the 2 forms as a single species with a chromatic polymorphism...
August 30, 2016: Veterinaria Italiana
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