18 research outputs found
Transferability of PCR-based diagnostic protocols: An international collaborative case study assessing protocols targeting the quarantine pine pathogen Fusarium circinatum
[EN] Fusarium circinatum is a harmful pathogenic fungus mostly attacking Pinus species and also Pseudotsuga menziesii, causing cankers in trees of all ages, damping-off in seedlings, and mortality in cuttings and mother plants for clonal production. This fungus is listed as a quarantine pest in several parts of the world and the trade of potentially contaminated pine material such as cuttings, seedlings or seeds is restricted in order to prevent its spread to disease-free areas. Inspection of plant material often relies on DNA testing and several conventional or real-time PCR based tests targeting F. circinatum are available in the literature. In this work, an international collaborative study joined 23 partners to assess the transferability and the performance of nine molecular protocols, using a wide panel of DNA from 71 representative strains of F. circinatum and related Fusarium species. Diagnostic sensitivity, specificity and accuracy of the nine protocols all reached values >80%, and the diagnostic specificity was the only parameter differing significantly between protocols. The rates of false positives and of false negatives were computed and only the false positive rates differed significantly, ranging from 3.0% to 17.3%. The difference between protocols for some of the performance values were mainly due to cross-reactions with DNA from non-target species, which were either not tested or documented in the original articles. Considering that participating laboratories were free to use their own reagents and equipment, this study demonstrated that the diagnostic protocols for F. circinatum were not easily transferable to end-users. More generally, our results suggest that the use of protocols using conventional or real-time PCR outside their initial development and validation conditions should require careful characterization of the performance data prior to use under modified conditions (i.e. reagents and equipment). Suggestions to improve the transfer are proposed.This work was supported by COST action FP1406 Pinestrength . The work of the Estonian team was supported by the Estonian Science Foundation grants PSG136 and IUT21-04. The work of Portuguese team from INIAV was financed by INIAV I.P. Institute. The work at U. Aveiro (Portugal) was financed by European Funds through COMPETE and National Funds through the Portuguese Foundation for Science and Technology (FCT) to CESAM (UID/AMB/50017/2013 POCI-01- 0145-FEDER-007638). The work of Slovenian team was financed through Slovenian Research Agency (P4-0107) and by the Slovenian Ministry of Agriculture, Forestry and Food (Public Forestry Service). The British work was financially supported by the Forestry Commission, UK. The French work was financially supported by the French Agency for Food, environmental and occupational health safety (ANSES). The work in New Zealand was funded by Operational Research Programmes, Ministry for Primary Industries, New Zealand.Ioos, R.; Aloi, F.; Piskur, B.; Guinet, C.; Mullett, M.; Berbegal Martinez, M.; Bragança, H.... (2019). Transferability of PCR-based diagnostic protocols: An international collaborative case study assessing protocols targeting the quarantine pine pathogen Fusarium circinatum. Scientific Reports. 9:1-17. https://doi.org/10.1038/s41598-019-44672-8S1179Schmale, D. G. III & Gordon, T. R. Variation in susceptibility to pitch canker disease, caused by Fusarium circinatum, in native stands of Pinus muricata. Plant Pathol. 52, 720–725 (2003).Gordon, T. R., Kirkpatrick, S. C., Aegerter, B. J., Wood, D. L. & Storer, A. J. 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Needle fungi in young Tasmanian Pinus radiata plantations in relation to elevation and rainfall
Multi-approach analysis of the diversity in Colletotrichum cliviae sensu lato
Colletotrichum cliviae is a fungal speciesreported both as pathogen and endophyte with broadgeographical distribution. Some purported isolates ofthis species have been assigned to different taxa,including Colletotrichum aracearum, Colletotrichumorchidearum and Colletotrichum. sichuanensis, forwhich a preliminary analysis of extensive multilocus(ACT, GAPDH, ITS, TUB2) data in this studyrevealed high sequence similarity with C. cliviae.We further reassessed the species delineation by usingthe coalescent method of the generalized mixed Yulecoalescent(GMYC) and Poisson Tree Processes(PTP). Single and multilocus gene trees stronglysupported a C. cliviae s. lat. clade including the fourspecies. This clade unfolded eight subclades groupedinto three distinct lineages, but no monophyly of anyof the four species. GMYC and PTP analyses confidentlysupported the evolutionary independence ofthese lineages. C. sichuanensis and C. cliviae, exceptone isolate, formed the largest lineage. The secondlineage was made up of isolates named C. aracearumand some of C. orchidearum sharing the haplotype andthe third lineage accommodated two isolates named C.cliviae and C. orchidearum. This finding suggests thesynonymization of C. sichuanensis with C. cliviaewhereas the taxonomic status of C. aracearum and C.orchidearum still needs clarification. This study laysgreat stress upon the use of comprehensive data forsequence-based characterisation of species in the C.cliviae s. lat. It also presents the first report of C.cliviae in tropical Africa and on citrus host
Poroid Hymenochaetaceae from Guineo-Congolian rainforest: Phellinus gabonensis sp. nov. from Gabon - taxonomy and phylogenetic relationships.
Phellinus gabonensis sp. nov. is described and illustrated on the basis of several collections made in three protected areas of primary rain forest in the western edge of the Guineo-Congolian center of endemism, in Gabon. The species is characterized by resupinate, perennial basidiomes, numerous, straight to commonly apically hooked hymenial setae, and ellipsoid to broadly ellipsoid, thin- to thick-walled, hyaline to yellowish basidiospores. Both the morphology and the phylogenetic inferences based on partial nuc-LSU relate this species to Ph. caribaeo-quercicolus
Poroid Hymenochaetaceae from Guineo–Congolian rainforest: Phellinus gabonensis sp. nov. from Gabon – taxonomy and phylogenetic relationships
Étude comparative de la diversité des macrochampignons dans les plantations forestières matures d'eucalyptus et de pins en zone de savanes tropicales à l'Ouest du Cameroun
Ganoderma species, including new taxa associated with root rot of the iconic Jacaranda mimosifolia in Pretoria, South Africa
New distributional data on Geastrum (Geastraceae, Basidiomycota) from Brazil
[EN] (New distributional data on Geastrum (Geastraceae, Basidiomycota) from Brazil). Th e data presented in this article
are the results of fi eld collections and the analysis of fungal specimens deposited in the URM Herbarium. Th e fi eld
trips were carried out in four Atlantic Forest remnants in the state of Pernambuco, between June 2008 and May 2009.
Th e revision of specimens housed in the URM was restricted to the Brazilian exsiccatae. Geastrum specimens were
examined macro- and microscopically following the traditional methodology used in the group. Geastrum javanicum
and G. lloydianum are new records from the Northeastern Region of Brazil. Eight species are new records from the
following states: Pará (G. fi mbriatum), Ceará (G. lloydianum), Paraíba (G. fi mbriatum, G. javanicum, G. schweinitzii
and G. entomophilum), Pernambuco (G. lageniforme and G. triplex) and Rio de Janeiro (G. javanicum). In this article
we present full descriptions for ten species of Geastrum with pictures and an identifi cation key.[POR] (Novos dados de distribuição de Geastrum (Geastraceae, Basidiomycota) no Brasil). Os dados apresentados neste
artigo são resultados de coletas feitas em campo e análise de espécimes fúngicos depositados no Herbário URM. As
coletas foram realizadas em quatro remanescentes de mata atlântica no estado de Pernambuco, entre junho/2008 e
maio/2009. A revisão de espécimes depositados no URM foi restrita a exsicatas brasileiras. Os espécimes de Geastrum
foram examinados macro e microscopicamente segundo a metodologia tradicional do grupo. Geastrum javanicum
e G. lloydianum são novos registros para a região Nordeste do Brasil. Oito espécies são novas ocorrências para os
seguintes estados: Pará (G. fi mbriatum), Ceará (G. lloydianum), Paraíba (G. fi mbriatum, G. javanicum, G. schweinitzii
e G. entomophilum), Pernambuco (G. lageniforme e G. triplex) e Rio de Janeiro (G. javanicum). Apresentamos neste
artigo dez descrições completas de espécies de Geastrum, além de fotos das espécies e uma chave de identifi cação.Peer reviewe