scholarly journals Genetic Diversity and Pathogenic Variability Among Isolates of Colletotrichum Species from Strawberry

2003 ◽  
Vol 93 (2) ◽  
pp. 219-228 ◽  
Author(s):  
Béatrice Denoyes-Rothan ◽  
Guy Guérin ◽  
Christophe Délye ◽  
Barbara Smith ◽  
Dror Minz ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Sequence Data ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Data ◽  
Its2 Sequence ◽  
Host Specialization ◽  
Pathogenicity Tests ◽  
Colletotrichum Spp ◽  
Rapd Polymorphism ◽  
Pathogenic Variability

Ninety-five isolates of Colletotrichum including 81 isolates of C. acutatum (62 from strawberry) and 14 isolates of C. gloeosporioides (13 from strawberry) were characterized by various molecular methods and pathogenicity tests. Results based on random amplified polymorphic DNA (RAPD) polymorphism and internal transcribed spacer (ITS) 2 sequence data provided clear genetic evidence of two subgroups in C. acutatum. The first subgroup, characterized as CA-clonal, included only isolates from strawberry and exhibited identical RAPD patterns and nearly identical ITS2 sequence analysis. A larger genetic group, CA-variable, included isolates from various hosts and exhibited variable RAPD patterns and divergent ITS2 sequence analysis. Within the C. acutatum population isolated from strawberry, the CA-clonal group is prevalent in Europe (54 isolates of 62). A subset of European C. acutatum isolates isolated from strawberry and representing the CA-clonal and CA-variable groups was assigned to two pathogenicity groups. No correlation could be drawn between genetic and pathogenicity groups. On the basis of molecular data, it is proposed that the CA-clonal subgroup contains closely related, highly virulent C. acutatum isolates that may have developed host specialization to strawberry. C. gloeosporioides isolates from Europe, which were rarely observed were either slightly or nonpathogenic on strawberry. The absence of correlation between genetic polymorphism and geographical origin in Colletotrichum spp. suggests a worldwide dissemination of isolates, probably through international plant exchanges.

scholarly journals Occurrence and genetic variability of Candida parapsilosis sensu lato in Hungary

2007 ◽  
Vol 56 (2) ◽  
pp. 190-195 ◽  
Author(s):  
Sándor Kocsubé ◽  
Mónika Tóth ◽  
Csaba Vágvölgyi ◽  
Ilona Dóczi ◽  
Miklós Pesti ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Candida Parapsilosis ◽  
Sequence Data ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Its Region ◽  
Molecular Data ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Group I

The occurrence and genetic variability of Candida parapsilosis isolates in two Hungarian hospitals, located in Debrecen and Pécs, were examined. Among the 209 Candida isolates examined, 20 were found to belong to C. parapsilosis sensu lato, based on morphological, physiological and molecular data. The frequency of occurrence of C. parapsilosis isolates (9.6 %) was lower than that observed in Europe but higher than that observed previously in Hungary. The genetic variability of C. parapsilosis sensu lato isolates was also examined using random amplified polymorphic DNA (RAPD) analysis and sequence analysis of the intergenic transcribed spacer (ITS) region of the rRNA gene cluster. The genetic variability of the isolates was relatively high, as revealed by RAPD analysis. Two isolates were found to belong to the recently described Candida metapsilosis species (C. parapsilosis group III), based on ITS sequence data, RAPD analysis and phenotypic data. These two isolates could also be distinguished from C. parapsilosis sensu stricto isolates using a primer pair developed for the detection of C. parapsilosis group I isolates. To the best of the authors' knowledge, this is the first report on the identification of C. metapsilosis from bloodstream infection.

Molecular characterization of pouched amphistome parasites (Trematoda: Gastrothylacidae) using ribosomal ITS2 sequence and secondary structures

2011 ◽  
Vol 86 (1) ◽  
pp. 117-124 ◽  
Author(s):  
S. Ghatani ◽  
J.A. Shylla ◽  
V. Tandon ◽  
A. Chatterjee ◽  
B. Roy
Keyword(s):  
Sequence Analysis ◽  
Secondary Structure ◽  
Molecular Characterization ◽  
Structure Data ◽  
Sequence Data ◽  
Its2 Sequence ◽  
Primary Sequence ◽  
Sequence Structure ◽  
Interspecific Variations ◽  
Primary Sequence Data

AbstractMembers of the family Gastrothylacidae (Trematoda: Digenea: Paramphistomata) are parasitic in ruminants throughout Africa and Asia. In north-east India, five species of pouched amphistomes, namely Fischoederius cobboldi, F. elongatus, Gastrothylax crumenifer, Carmyerius spatiosus and Velasquezotrema tripurensis, belonging to this family have been reported so far. In the present study, the molecular phylogeny of these five gastrothylacid species is derived using the second internal transcribed spacer (ITS2) sequence and secondary structure analyses. ITS2 sequence analysis was carried out to see the occurrence of interspecific variations among the species. Phylogenetic analyses were performed for primary sequence data alone as well as the combined sequence-structure information using neighbour-joining and Bayesian approaches. The sequence analysis revealed that there exist considerable interspecific variations among the various gastrothylacid fluke species. In contrast, the inferred secondary structures for the five species using minimum free energy modelling showed structural identities, in conformity with the core four-helix domain structure that has been recently identified as common to almost all eukaryotic taxa. The phylogenetic tree reconstructed using combined sequence–structure data showed a better resolution, as compared to the one using sequence data alone, with the gastrothylacid species forming a monophyletic group that is well separated from members of the other family, Paramphistomidae, of the amphistomid flukes group. The study provides the molecular characterization based on primary sequence data of the rDNA ITS2 region of the gastrothylacid amphistome flukes. Results also demonstrate the phylogenetic utility of the ITS2 sequence–secondary structure data for inferences at higher taxonomic levels.

scholarly journals Taxonomic Re-Examination of Nine Rosellinia Types (Ascomycota, Xylariales) Stored in the Saccardo Mycological Collection

2021 ◽  
Vol 9 (3) ◽  
pp. 666
Author(s):  
Niccolò Forin ◽  
Alfredo Vizzini ◽  
Federico Fainelli ◽  
Enrico Ercole ◽  
Barbara Baldan
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Illumina Miseq ◽  
Botanical Garden ◽  
Molecular Study ◽  
Its2 Sequence ◽  
Type Specimens ◽  
Its1 Sequence ◽  
Dna Sequence Data ◽  
Nomen Novum

In a recent monograph on the genus Rosellinia, type specimens worldwide were revised and re-classified using a morphological approach. Among them, some came from Pier Andrea Saccardo’s fungarium stored in the Herbarium of the Padova Botanical Garden. In this work, we taxonomically re-examine via a morphological and molecular approach nine different Roselliniasensu Saccardo types. ITS1 and/or ITS2 sequences were successfully obtained applying Illumina MiSeq technology and phylogenetic analyses were carried out in order to elucidate their current taxonomic position. Only the ITS1 sequence was recovered for Rosellinia areolata, while for R. geophila, only the ITS2 sequence was recovered. We proposed here new combinations for Rosellinia chordicola, R. geophila and R. horridula, while for R. ambigua, R. areolata, R. australis, R. romana and R. somala, we did not suggest taxonomic changes compared to the current ones. The name Rosellinia subsimilis Sacc. is invalid, as it is a later homonym of R. subsimilis P. Karst. & Starbäck. Therefore, we introduced Coniochaeta dakotensis as a nomen novum for R. subsimilis Sacc. This is the first time that these types have been subjected to a molecular study. Our results demonstrate that old types are an important source of DNA sequence data for taxonomic re-examinations.

The status of Myriangiaceae (Dothideomycetes)

Phytotaxa ◽  
2014 ◽  
Vol 176 (1) ◽  
pp. 219 ◽  
Author(s):  
ASHA J. DISSANAYAKE ◽  
RUVISHIKA S. JAYAWARDENA ◽  
SARANYAPHAT BOONMEE ◽  
KASUN M. THAMBUGALA ◽  
QING TIAN ◽  
...  
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
The Family ◽  
The Status ◽  
Sexual State ◽  
Morphological And Molecular Data ◽  
Asexual State ◽  
Molecular Characters

The family Myriangiaceae is relatively poorly known amongst the Dothideomycetes and includes genera which are saprobic, epiphytic and parasitic on the bark, leaves and branches of various plants. The family has not undergone any recent revision, however, molecular data has shown it to be a well-resolved family closely linked to Elsinoaceae in Myriangiales. Both morphological and molecular characters indicate that Elsinoaceae differs from Myriangiaceae. In Elsinoaceae, small numbers of asci form in locules in light coloured pseudostromata, which form typical scab-like blemishes on leaf or fruit surfaces. The coelomycetous, “Sphaceloma”-like asexual state of Elsinoaceae, form more frequently than the sexual state; conidiogenesis is phialidic and conidia are 1-celled and hyaline. In Myriangiaceae, locules with single asci are scattered in a superficial, coriaceous to sub-carbonaceous, black ascostromata and do not form scab-like blemishes. No asexual state is known. In this study, we revisit the family Myriangiaceae, and accept ten genera, providing descriptions and discussion on the generic types of Anhellia, Ascostratum, Butleria, Dictyocyclus, Diplotheca, Eurytheca, Hemimyriangium, Micularia, Myriangium and Zukaliopsis. The genera of Myriangiaceae are compared and contrasted. Myriangium duriaei is the type species of the family, while Diplotheca is similar and may possibly be congeneric. The placement of Anhellia in Myriangiaceae is supported by morphological and molecular data. Because of similarities with Myriangium, Ascostratum (A. insigne), Butleria (B. inaghatahani), Dictyocyclus (D. hydrangea), Eurytheca (E. trinitensis), Hemimyriangium (H. betulae), Micularia (M. merremiae) and Zukaliopsis (Z. amazonica) are placed in Myriangiaceae. Molecular sequence data from fresh collections is required to confirm the relationships and placement of the genera in this family.

scholarly journals Origin of the European avian-like swine influenza viruses

2014 ◽  
Vol 95 (11) ◽  
pp. 2372-2376 ◽  
Author(s):  
Andi Krumbholz ◽  
Jeannette Lange ◽  
Andreas Sauerbrei ◽  
Marco Groth ◽  
Matthias Platzer ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Swine Influenza ◽  
H1n1 Influenza ◽  
Molecular Data ◽  
Influenza Viruses ◽  
Time Resolved ◽  
Genotype Constellation ◽  
Tree Inference

The avian-like swine influenza viruses emerged in 1979 in Belgium and Germany. Thereafter, they spread through many European swine-producing countries, replaced the circulating classical swine H1N1 influenza viruses, and became endemic. Serological and subsequent molecular data indicated an avian source, but details remained obscure due to a lack of relevant avian influenza virus sequence data. Here, the origin of the European avian-like swine influenza viruses was analysed using a collection of 16 European swine H1N1 influenza viruses sampled in 1979–1981 in Germany, the Netherlands, Belgium, Italy and France, as well as several contemporaneous avian influenza viruses of various serotypes. The phylogenetic trees suggested a triple reassortant with a unique genotype constellation. Time-resolved maximum clade credibility trees indicated times to the most recent common ancestors of 34–46 years (before 2008) depending on the RNA segment and the method of tree inference.

scholarly journals Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions

2018 ◽  
Vol 20 (4) ◽  
pp. 1542-1559 ◽  
Author(s):  
Damla Senol Cali ◽  
Jeremie S Kim ◽  
Saugata Ghose ◽  
Can Alkan ◽  
Onur Mutlu
Keyword(s):  
Sequence Analysis ◽  
Genome Assembly ◽  
Sequence Data ◽  
Error Rates ◽  
Nanopore Sequencing ◽  
Memory Usage ◽  
Sequencing Technology ◽  
Assembly Pipeline ◽  
And Performance ◽  
Polishing Tool

Abstract Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating accurate genome assemblies. The tools used for nanopore sequence analysis are of critical importance, as they should overcome the high error rates of the technology. Our goal in this work is to comprehensively analyze current publicly available tools for nanopore sequence analysis to understand their advantages, disadvantages and performance bottlenecks. It is important to understand where the current tools do not perform well to develop better tools. To this end, we (1) analyze the multiple steps and the associated tools in the genome assembly pipeline using nanopore sequence data, and (2) provide guidelines for determining the appropriate tools for each step. Based on our analyses, we make four key observations: (1) the choice of the tool for basecalling plays a critical role in overcoming the high error rates of nanopore sequencing technology. (2) Read-to-read overlap finding tools, GraphMap and Minimap, perform similarly in terms of accuracy. However, Minimap has a lower memory usage, and it is faster than GraphMap. (3) There is a trade-off between accuracy and performance when deciding on the appropriate tool for the assembly step. The fast but less accurate assembler Miniasm can be used for quick initial assembly, and further polishing can be applied on top of it to increase the accuracy, which leads to faster overall assembly. (4) The state-of-the-art polishing tool, Racon, generates high-quality consensus sequences while providing a significant speedup over another polishing tool, Nanopolish. We analyze various combinations of different tools and expose the trade-offs between accuracy, performance, memory usage and scalability. We conclude that our observations can guide researchers and practitioners in making conscious and effective choices for each step of the genome assembly pipeline using nanopore sequence data. Also, with the help of bottlenecks we have found, developers can improve the current tools or build new ones that are both accurate and fast, to overcome the high error rates of the nanopore sequencing technology.

Host range and physiologic specialization in Rhynchosporium secalis

1974 ◽  
Vol 25 (1) ◽  
pp. 21 ◽  
Author(s):  
SM Ali ◽  
WJR Boyd
Keyword(s):  
Genetic Diversity ◽  
Host Range ◽  
Environmental Conditions ◽  
Host Specialization ◽  
Rhynchosporium Secalis ◽  
Host Reaction ◽  
Genetic Studies ◽  
Barley Cultivars ◽  
Adequate Sampling ◽  
Pathogenic Variability

The pathogenic variability of isolates of R. secalis collected in Western Australia has been examined on different host genera of the Gramineae and on selected barley cultivars. Depending on the host-isolate combination and the conditions of the test, evidence has been obtained of inter- and intra-isolate variability in both host reaction and isolate pathogenicity. This complicates definitive interpretation of the results, militates against identification of conventional 'races' of the pathogen and shows that R. secalis does not exhibit strict host specialization. Hosts which consistently express resistance or susceptibility under different environmental conditions, and isolates which express their pathogenic characteristics consistently, have been identified. The need for more precise genetic studies and adequate sampling of genetic diversity is emphasized.

Higher-level relationships among the eucalypts are resolved by ITS-sequence data

2002 ◽  
Vol 15 (1) ◽  
pp. 49 ◽  
Author(s):  
Dorothy A. Steane ◽  
Dean Nicolle ◽  
Gay E. McKinnon ◽  
René E. Vaillancourt ◽  
Brad M. Potts
Keyword(s):  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Its Sequence ◽  
Phylogenetic Groups ◽  
Single Section ◽  
Western Australian ◽  
Genus Eucalyptus

This expanded survey of ITS sequences represents the largest analysis of molecular data ever attempted on Eucalyptus. Sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA were included in an analysis of 90 species of Eucalyptus s.s. and 28 species representing eight other genera (Allosyncarpia, Angophora, Arillastrum, Corymbia, Eucalyptopsis, Stockwellia, Lophostemon and Metrosideros). The results of the study indicate that Angophora and Corymbia form a well-supported clade that is highly differentiated from Eucalyptus s.s. Corymbia species are divided between two clades, one of which may be the sister to Angophora. Allosyncarpia, Arillastrum, Eucalyptopsis and ‘Stockwellia’ are also highly differentiated from Eucalyptus s.s. If the genus Eucalyptus is to be expanded to include Angophora and Corymbia(sensu Brooker 2000), ITS data suggest that Allosyncarpia, Eucalyptopsis, ‘Stockwellia’ and potentially Arillastrum should also be included in Eucalyptus s.l. The ITS data suggest that subg. Symphyomyrtus is paraphyletic and that subg. Minutifructus should be included within it. Within subg.Symphyomyrtus, only sect. Maidenaria appears to be monophyletic. Sections Adnataria and Dumaria are probably monophyletic; sections Exsertaria and Latoangulatae are very close and probably should be combined in a single section. Section Bisectae is polyphyletic and is divided into two distinct lineages. The phylogenetic groups depicted by ITS data are consistent with the frequency of natural inter-specific hybridisations as well as data from controlled crosses within subgenus Symphyomyrtus. The ITS data illustrate that subg. Idiogenes and western Australian monocalypts are early evolutionary lines relative to E. diversifolia, E. rubiginosa (monotypic subg. Primitiva) and the eastern monocalypts and that subg. Primitiva should be sunk into subg. Eucalyptus. Subgenus Eudesmia may be monophyletic, grouping with subgenera Idiogenes and Eucalyptus. Further work is required to confirm the phylogenetic positions of the monotypic subgenera Alveolata, Cruciformes, Acerosae and Cuboidea.

scholarly journals Identification of Fusarium Species Isolated From Stored Apple Fruit in Croatia / Identifikacija Vrsta Roda Fusarium Izoliranih S Plodova Jabuke Nakon Skladištenja

2012 ◽  
Vol 63 (4) ◽  
pp. 463-470 ◽  
Author(s):  
Zdravka Sever ◽  
Dario Ivić ◽  
Tomislav Kos ◽  
Tihomir Miličević
Keyword(s):  
Fusarium Species ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Apple Fruit ◽  
Fusarium Avenaceum ◽  
Human Consumption ◽  
Low Oxygen ◽  
Fusarium Rot ◽  
Pathogenicity Tests ◽  
Apple Fruits

AbstractSeveral species of the genus Fusarium can cause apple fruit to rot while stored. Since Fusarium taxonomy is very complex and has constantly been revised and updated over the last years, the aim of this study was to identify Fusarium species from rotten apples, based on combined morphological characteristics and molecular data.We identified 32 Fusarium isolates from rotten apple fruit of cultivars Golden Delicious, Jonagold, Idared, and Pink Lady, stored in Ultra Low Oxygen (ULO) conditions. Fusarium rot was detected in 9.4 % to 33.2 % of naturally infected apples, depending on the cultivar. The symptoms were similar in all four cultivars: a soft circular brown necrosis of different extent, with or without visible sporulation. Fusarium species were identified by the morphology of cultures grown on potato-dextrose agar (PDA) and carnation leaf agar (CLA). Twenty one isolates were identified as Fusarium avenaceum and confirmed as such with polymerase chain reaction (PCR) using specific primer pair FA-ITSF and FA-ITSR. F. pseudograminearum,F. semitectum, F. crookwellense, and F. compactum were identified by morphological characteristics. F.avenaceum can produce several mycotoxins and its dominance in Fusarium rot points to the risk of mycotoxin contamination of apple fruit juices and other products for human consumption. Pathogenicity tests showed typical symptoms of Fusarium rot in most of the inoculated wounded apple fruits. In this respect Fusarium avenaceum, as the dominant cause of Fusarium rot in stored apple fruits is a typical wound parasite.

scholarly journals A fungus-eat-fungus world: Digitopodium, with particular reference to mycoparasites of the coffee leaf rust, Hemileia vastatrix

IMA Fungus ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Adans A. Colmán ◽  
Harry C. Evans ◽  
Sara S. Salcedo-Sarmiento ◽  
Uwe Braun ◽  
Kifle Belachew-Bekele ◽  
...  
Keyword(s):  
Leaf Rust ◽  
Democratic Republic Of Congo ◽  
Sequence Data ◽  
Molecular Study ◽  
Classical Biological Control ◽  
Coffea Canephora ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Hemileia Vastatrix ◽  
Coffee Leaf Rust

AbstractDigitopodium hemileiae was described originally in 1930 as Cladosporium hemileiae; growing as a mycoparasite of the coffee leaf rust (CLR), Hemileia vastatrix, in a sample of diseased leaves of Coffea canephora collected in the Democratic Republic of Congo. No cultures from this material exist. More recently, the type material was re-examined and, based on morphological features, considered to be incorrectly placed in Cladosporium. The new genus Digitopodium was erected to accommodate this species. Interest in fungal antagonists of H. vastarix, as potential biocontrol agents of CLR, led to comprehensive surveys for mycoparasites, both in the African centre of origin of the rust, as well as in its South American exotic range. Among the rust specimens from Ethiopia, one was found to be colonized by a fungus congeneric with, and similar to, D. hemileiae. Pure cultures obtained from the Ethiopian material enabled a molecular study and for its phylogenetic position to be elucidated, based on DNA sequence data from the ITS and LSU regions. Molecular data showed that two members of the recently erected genus Hyalocladosporiella (Herpotrichiellaceae: Chaetothyriales) are congeneric with Digitopodium from Ethiopia and morphologically similar to both D. hemileiae and the two Ethiopian isolates. These isolates were found to be morphologically and genetically identical to H. tectonae, described previously from Brazil. Thus, species of Hyalocladosporiella are re-allocated to Digitopodium here; including D. tectonae, and a novel species, D. canescens, recently found in Brazil growing as a mycoparasite of Puccinia thaliae. The potential use of D. hemileiae and D. tectonae for classical biological control of CLR is discussed.

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