Molecular and conventional detection and identification of Cladosporium tenuissimum on two-needle pine rust aeciospores

1999 ◽  
Vol 77 (3) ◽  
pp. 339-347 ◽  
Author(s):  
S Moricca ◽  
A Ragazzi ◽  
K R Mitchelson
Keyword(s):  
Integrated Approach ◽  
Morphological Characters ◽  
Molecular Data ◽  
Selective Medium ◽  
Detection And Identification ◽  
Pcr Method ◽  
Common Substrate ◽  
Polymerase Chain ◽  
Peridermium Pini ◽  
Unambiguous Detection

An integrated approach, based on the analysis of both molecular and morphological characters, has led to the unambiguous detection and identification of the rust hyperparasite Cladosporium tenuissimum from aeciospores of the two-needle pine rust fungi Cronartium flaccidum and Peridermium pini. Cladosporium tenuissimum was first detected from contaminated field-collected rust spores using the polymerase chain reaction (PCR) method. The similar-sized amplified DNA of the parasite was then separated from rust DNA using electrophoretic migration, reamplified separately with the nested PCR, and sequenced. Sequence comparison in the data banks enabled the hyperparasite to be recognised as a species of Cladosporium. Molecular detection was followed by conventional identification, obtained by plating rust spores on potato dextrose agar, a selective medium for rusts, since they are unable to grow on such a common substrate, and isolating the hyperparasite in pure culture. It was subsequently identified as C. tenuissimum. Traditional identification would not have been possible without guidance from the molecular data, which focused attention on the mycoparasite. Macro- and micro-scopic features of colonies are also given to help with future identification on spore sources from other geographical areas and, if this should occur, future identification on other rusts.Key words: mycoparasitism, PCR detection, traditional detection, Cladosporium tenuissimum, Cronartium flaccidum, Peridermium pini.

Multiplex polymerase chain reaction for simultaneous detection and identification of Bursaphelenchus xylophilus, B. mucronatus and B. fraudulentus – three closely related species within the xylophilus group

Nematology ◽  
2017 ◽  
Vol 19 (9) ◽  
pp. 1107-1116 ◽  
Author(s):  
Anna Filipiak ◽  
Przemysław Wieczorek ◽  
Marek Tomalak
Keyword(s):  
Multiplex Pcr ◽  
Simultaneous Detection ◽  
Morphological Characters ◽  
Bursaphelenchus Xylophilus ◽  
Chain Reaction ◽  
Closely Related Species ◽  
Detection And Identification ◽  
Different Populations ◽  
Polymerase Chain ◽  
Simultaneous Identification

Differentiation between Bursaphelenchus xylophilus and other related, non-pathogenic species can be ambiguous when based exclusively on morphological characters. The morphology of B. mucronatus and B. fraudulentus most closely resembles that of B. xylophilus. Moreover, all of these nematodes are found in both Asia and Europe and can colonise various species of pine. Therefore, for phytosanitary purposes it is necessary to identify the three species precisely and rapidly. We report the results of a multiplex PCR that utilises four primers to identify and discriminate the three Bursaphelenchus species simultaneously. The multiplex PCR yielded DNA fragments of 767, 305 and 132 bp, for B. xylophilus, B. mucronatus and B. fraudulentus, respectively. This primer combination has produced reliable results in multiplex PCR assays with a number of different populations of the listed species, and no cross-reactions were observed with other Bursaphelenchus species. The described approach is simple, reliable and cheaper than other molecular methods presently used for simultaneous identification of the above three species within the xylophilus group.

An integrated approach for synonymization of Rotylenchus rhomboides with R. goodeyi (Nematoda: Hoplolaimidae) reveals high intraspecific mitogenomic variation

2021 ◽  
Author(s):  
Phougeishangbam Rolish Singh ◽  
Bart van de Vossenberg ◽  
Katarzynar Rybarczyk-Mydłowska3 ◽  
Magdalena Kowalewska-Groszkowska ◽  
Wim Bert ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Integrated Approach ◽  
Morphological Characters ◽  
Molecular Data ◽  
Cox1 Gene ◽  
Protein Coding ◽  
Genome Shotgun Sequence ◽  
Important Character ◽  
Rna Genes ◽  
Level Identification

Rotylenchus is a widely-distributed economically important plant-parasitic nematode group whose species-level identification relies largely on limited morphological characters including character-based tabular keys and molecular data of ribosomal and mitochondrial genes. In this study, a combined morphological and molecular analysis of three populations of R. goodeyi from Belgium, Poland and the Netherlands revealed important character variations of this species leading to synonymisation of R. rhomboides with R. goodeyi, and a high nucleotide variation within cox1 gene sequences in these populations. Additional Illumina sequencing of DNA from individuals of the Dutch population revealed two variants of mitogenomes each of approximately 23 Kb in size, differing by about 9% and containing eleven protein coding genes, two ribosomal RNA genes and up to 29 transfer RNA genes. In addition to the first representative whole genome shotgun sequence datasets of the genus Rotylenchus, this study also provides the full length mitogenome and the ribosomal DNA sequences of R. goodeyi.

scholarly journals PCR Detection and RFLP Differentiation of Botrytis Species Associated with Neck Rot of Onion

Plant Disease ◽  
2002 ◽  
Vol 86 (6) ◽  
pp. 682-686 ◽  
Author(s):  
Karsten Nielsen ◽  
David S. Yohalem ◽  
Dan Funck Jensen
Keyword(s):  
Pcr Amplification ◽  
Pcr Detection ◽  
Sequence Characterized Amplified Region ◽  
Specific Pcr ◽  
Isolation Techniques ◽  
Detection And Identification ◽  
Fungal Dna ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Direct Amplification

Botrytis aclada and other Botrytis spp. can cause neck rot on onions, a storage disease that normally is very difficult to detect at harvest using traditional isolation techniques. Sequence characterized amplified region primers (BA2f/BA1r) were designed based on a previously cloned and amplified DNA fragment for direct amplification of isolates of Botrytis spp. associated with neck rot of onions. Digestion of the polymerase chain reaction (PCR) amplification product with the restriction enzyme ApoI makes it possible to distinguish the five groups: Botrytis aclada types AI and AII (B. allii); B. byssoidea; B. squamosa; and B. cinerea. The detection limit was 1 to 10 pg of pure fungal DNA. It was possible to detect B. aclada with the PCR method in artificially inoculated onion bulb tissue and in mature onion leaves showing no symptoms of the disease. The availability of a sensitive and specific PCR detection and identification method for Botrytis onion neck rot pathogens should facilitate ecological studies of this group of onion pathogens.

Detection and Identification of Microbial Contaminant in Bakery Products in Yogyakarta City, Indonesia

SCISCITATIO ◽  
2020 ◽  
Vol 1 (1) ◽  
Author(s):  
Evelyn Ferdian ◽  
Catarina Aprilia Ariestanti ◽  
Tri Yahya Budiarso
Keyword(s):  
Staphylococcus Epidermidis ◽  
Bakery Products ◽  
Chain Reaction ◽  
Microbial Contaminant ◽  
Gram Positive Bacteria ◽  
Detection And Identification ◽  
Diet Pattern ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Yogyakarta City

Bread has been chosen as an alternative food because of its availability. In Indonesia, consumption of breads is increased due to the change of diet pattern into packed and ready-made meals. Therefore, it is important to raise the awareness of bakery products quality. The purpose of this study was to detect and identify the microbial contaminant in bakery products in Yogyakarta City, Indonesia. Bacterial colonies from expired bakery products were isolated into pure isolate then confirmed by API Staph and Polymerase Chain Reaction (PCR) method. The results showed there were five kinds of gram-positive bacteria. Isolated bacteria identified by API were Bacillus cereus (52.8%), Bacillus subtilis (97.7%), Staphylococcus aureus (97.7%), Staphylococcus epidermidis (97,9%) and Staphylococcus saprophyticus (72,2% and 61,8%).

scholarly journals Understanding subterranean variability: the first genus of Bathynellidae (Bathynellacea, Crustacea) from Western Australia described through a morphological and multigene approach

2018 ◽  
Vol 32 (2) ◽  
pp. 423 ◽  
Author(s):  
G. Perina ◽  
A. I. Camacho ◽  
J. Huey ◽  
P. Horwitz ◽  
A. Koenders
Keyword(s):  
Western Australia ◽  
New Genus ◽  
Integrated Approach ◽  
Morphological Characters ◽  
Molecular Data ◽  
Additional Species ◽  
The North ◽  
Morphological And Molecular Data ◽  
Taxonomic Framework ◽  
One New Species

The number of subterranean taxa discovered in the north of Western Australia has substantially increased due to the requirements for environmental surveys related to mining development. Challenges in estimating subterranean biodiversity and distributions are related to lack of knowledge of taxa with convergent morphological characters in a largely unobservable ecosystem setting. An integrated approach is warranted to understand such complexity. Bathynellidae occur in most Australian aquifers, but only one species has been described so far, and the group lacks a reliable taxonomic framework. A new genus and one new species from the Pilbara region of Western Australia, Pilbaranella ethelensis, gen. et sp. nov., is described using both morphological and molecular data. Three additional species of Pilbaranella are defined through mitochondrial and nuclear genes, using Automatic Barcode Gap Discovery and Poisson Tree Processes species delimitation methods. A comparison of morphology and 18S rRNA sequences between Pilbaranella, gen. nov. and known lineages provides the evidentiary basis for the decision to establish a new genus. This study provides a morphological and molecular framework to work with Bathynellidae, especially in Australia where a highly diverse fauna remains still undescribed.

Investigation of duck plague virus in hoar areas of Bangladesh

2020 ◽  
Vol 26 (1-2) ◽  
pp. 73-78
Author(s):  
A Hossen ◽  
MH Rahman ◽  
MZ Ali ◽  
MA Yousuf ◽  
MZ Hassan ◽  
...  
Keyword(s):  
Cytopathic Effect ◽  
Clinical Sample ◽  
Chorioallantoic Membrane ◽  
Clinical Samples ◽  
Isolation And Identification ◽  
Duck Plague Virus ◽  
Pcr Method ◽  
Polymerase Chain ◽  
The Individual ◽  
Free Ranging

Duck plague (DP) is the most important infectious disease of geese, ducks and free-ranging water birds. The present study was conducted to determine the prevalence of duck plague virus followed by isolation and identification. For these purposes, a total of 155 cloacal swabs samples were collected randomly from duck of different haor areas of Bangladesh including 45 (41 surveillance and 4 clinical) samples from Netrokona; 42 (40 surveillance and 2 clinical) samples from Kishoregonj; 30 samples from Brahmanbaria and 38 samples from Sunamganj. The samples were processed and pooled (1:5 ratio) for initial screening of target polymerase gene of duck plague virus by polymerase chain reaction (PCR) method. All the samples of a positive pool were then tested individually for identifying the individual positive samples. The result showed that out of 155 samples, 41 (26.45%) were found positive in which 17 were from Netrokona, where 15 (36.58%) were from surveillance samples and 2 (50%) were from clinical sample; 16 were from Kishoregonj, where 14 (35%) were from surveillance samples and 2 (100%) were from clinical sample; 2 (6.6%) were from Brahmanbaria and 5 (13.15%) were from Sunamganj. These positive samples were inoculated into 9-10 days embryonated duck eggs (EDE) through chorioallantoic membrane (CAM) route for the isolation of virus. The EDE died earlier was also chilled, and in a similar way, the CAMs were collected and again performed PCR for id entification of virus. Out of 41 PCR positive samples, 26 samples were isolated and reconfirmed by PCR. Subsequently, DPV was isolated in primary duck embryo fibroblasts cell culture and confirmed by observing cytopathic effect (CPE). Bang. J. Livs. Res. Vol. 26 (1&2), 2019: P. 73-78

Prevalence of SHV-extended spectrum β-lactamase producing carbapenem –resistantKlebsiellapneumoniae among patients with lower respiratory tractinfections in Babylon Province-Iraq.

2018 ◽  
Vol 9 (SPL1) ◽  
Author(s):  
Fatima Moeen Abbas
Keyword(s):  
Resistance Rate ◽  
Combination Method ◽  
Diffusion Method ◽  
Disk Diffusion Method ◽  
Carbapenem Resistant ◽  
Extended Spectrum ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Tract Infections ◽  
Positive Results

This study was carried out to screen the prevalence of Klebsiella pneumoniae isolated from patients with lower respiratory tract infections in Babylon province.From December,2015 to the end of March,2016,a total of 100 sputum samples were collected from patients visited or hospitalized Merjan Teaching Hospital and Al- Hashimya General Hospital. Fifteenth (65%) isolates were identified as Klebsiellapneumoniae. All bacterial isolates were evaluated for extended spectrum β-lactamase (ESBL) production phenotypically using disk combination method. Eleven (73.3%) isolates were detected as ESBL-producers. Kirby-Bauer disk diffusion method was employed to determine resistance profile of ESBLs-positive isolates. Higher rates of resistance were observed for ampicillin and piperacillin antibiotics with (81.8%) and (72.7%) resistance rate, respectively, while the lowest rate was noticed for imipenem antibiotic (14.28%). Carbapenem-resistant isolates were investigated for blaSHV gene by Polymerase Chain Reaction (PCR) method, 2 (100%) isolates gave positive results.

scholarly journals Diversity of Common Bean Landraces Collected in the Western and Eastern Carpatien

2011 ◽  
Vol 39 (No. 3) ◽  
pp. 73-83 ◽  
Author(s):  
O. Horňáková ◽  
M. Závodná ◽  
M. Žáková ◽  
J. Kraic ◽  
F. Debre
Keyword(s):  
Cluster Analysis ◽  
Common Bean ◽  
Morphological Characters ◽  
Molecular Data ◽  
Seed Traits ◽  
Phaseolus Vulgaris L ◽  
Growth Type ◽  
Banding Patterns ◽  
Polymorphism Detection ◽  
Thousand Seed Weight

The study of diversity in common bean was based on morphological and agronomical characteristics, differentiation of collected accessions by morphological and molecular markers, detection of genetic variation, and duplicates detection in bean landraces. The analysed 82 accessions of common bean (Phaseolus vulgaris L.) were collected in the Western andEastern Carpatien as landrace mixtures. Their seeds were segregated and pooled according to their characteristics; they were further multiplicated, and introduced into the collection. An extensive variation in plant and seed traits was discovered in thirty-three morphological and agronomical characteristics. Nevertheless, some of the accessions were identical in these characteristics. Cluster analysis grouped genotypes into two main branches, reflecting the growth type, seed size parameters, and thousand-seed weight. Molecular differentiation studies were performed by multilocus polymorphism detection in microsatellite and minisatellite DNA regions. Cluster analysis based on molecular data also grouped genotypes but no linkage to morphological traits was revealed. Bean accessions with very similar or identical morphological characters were clearly distinguished by DNA banding patterns. The presence of duplicates was excluded.  

scholarly journals Relicts from Glacial Times: The Ground Beetle Pterostichus adstrictus Eschscholtz, 1823 (Coleoptera: Carabidae) in the Austrian Alps

Insects ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 84
Author(s):  
Wolfgang Paill ◽  
Stephan Koblmüller ◽  
Thomas Friess ◽  
Barbara-Amina Gereben-Krenn ◽  
Christian Mairhuber ◽  
...  
Keyword(s):  
Ground Beetle ◽  
Distribution Patterns ◽  
Morphological Characters ◽  
Molecular Data ◽  
Ice Age ◽  
Dispersal Ability ◽  
Austrian Alps ◽  
Alpine Regions ◽  
Extant Species ◽  
Limited Dispersal

The last ice age considerably influenced distribution patterns of extant species of plants and animals, with some of them now inhabiting disjunct areas in the subarctic/arctic and alpine regions. This arctic-alpine distribution is characteristic for many cold-adapted species with a limited dispersal ability and can be found in many invertebrate taxa, including ground beetles. The ground beetle Pterostichus adstrictus Eschscholtz, 1823 of the subgenus Bothriopterus was previously known to have a holarctic-circumpolar distribution, in Europe reaching its southern borders in Wales and southern Scandinavia. Here, we report the first findings of this species from the Austrian Ötztal Alps, representing also the southernmost edge of its currently known distribution, confirmed by the comparison of morphological characters to other Bothriopterus species and DNA barcoding data. Molecular data revealed a separation of the Austrian and Finish specimens with limited to no gene flow at all. Furthermore, we present the first data on habitat preference and seasonality of P. adstrictus in the Austrian Alps.

scholarly journals Investigating the Parasitoid Community Associated with the Invasive Mealybug Phenacoccus solenopsis in Southern China

Insects ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 290
Author(s):  
Hua-Yan Chen ◽  
Hong-Liang Li ◽  
Hong Pang ◽  
Chao-Dong Zhu ◽  
Yan-Zhou Zhang
Keyword(s):  
Biological Control ◽  
Species Delimitation ◽  
Southern China ◽  
Insect Pest ◽  
Integrated Approach ◽  
Molecular Data ◽  
Coi Gene ◽  
Morphological Examination ◽  
Accurate Identification ◽  
Phenacoccus Solenopsis

The cotton mealybug Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae), is an emerging invasive insect pest in China. Hymenopteran parasitoids are the key organisms for suppressing populations of P. solenopsis in the field, and therefore could be used as biological agents. Accurate identification of the associated parasitoids is the critical step to assess their potential role in biological control. In this study, we facilitated the identification of the parasitoid composition of P. solenopsis using an integrated approach of species delimitation, combining morphology with molecular data. Eighteen Hymenoptera parasitoid species belonging to 11 genera of four families are recognized based on morphological examination and molecular species delimitation of the mitochondrial cytochrome c oxidase 1 (COI) gene and the 28S rDNA using the automatic barcode gap discovery (ABGD) and the Bayesian Poisson tree processes model (bPTP). Among these species, eight species are primary parasitoids with Aenasius arizonensis (Girault) (Hymenoptera: Encyrtidae) being the dominant taxon, while the other 10 species are probably hyperparasitoids, with a prevalence of Cheiloneurus nankingensis Li & Xu (Hymenoptera: Encyrtidae). These results indicate that parasitoid wasps associated with P. solenopsis from China are diverse and the integrated taxonomic approach applied in this study could enhance the accurate identification of these parasitoids that should be assessed in future biological control programs.

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