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A novel duplex qPCR assay for stepwise detection of multiple Perkinsea protistan infections of amphibian tissues ArchiMer
Smilansky, Vanessa; Chambouvet, Aurelie; Reeves, Mari; Richards, Thomas A.; Milner, David S..
Alveolate protists within the phylum Perkinsea have been found to infect amphibians across a broad taxonomic and geographic range. Phylogenetic analysis has suggested the existence of two clades of amphibian Perkinsea: a putatively non-pathogenic clade linked to asymptomatic infections of tadpoles in Africa, Europe and South America, and a putatively pathogenic clade linked to disease and mass mortality events of tadpoles in North America. Here, we describe the development of a duplex TaqMan qPCR assay to detect and discriminate between rDNA sequences from both clades of Perkinsea in amphibian tissues. The assay uses a single primer pair to target an 18S small subunit (SSU) ribosomal RNA (rRNA) gene region shared between the two clades, and two...
Tipo: Text Palavras-chave: Frog disease; Alveolate parasites; Quantitative PCR; Perkinsea; NAG01.
Ano: 2021 URL: https://archimer.ifremer.fr/doc/00685/79758/82558.pdf
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Diverse alveolate infections of tadpoles, a new threat to frogs? ArchiMer
Chambouvet, Aurelie; Smilansky, Vanessa; Jirků, Miloslav; Isidoro-ayza, Marcos; Itoïz, Sarah; Derelle, Evelyne; Monier, Adam; Gower, David J.; Wilkinson, Mark; Yabsley, Michael J.; Lukeš, Julius; Richards, Thomas A..
Tipo: Text
Ano: 2020 URL: https://archimer.ifremer.fr/doc/00609/72115/70858.pdf
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Diverse molecular signatures for ribosomally 'active' Perkinsea in marine sediments ArchiMer
Chambouvet, Aurelie; Berney, Cedric; Romac, Sarah; Audic, Stephane; Maguire, Finlay; De Vargas, Colomban; Richards, Thomas A..
Background: Perkinsea are a parasitic lineage within the eukaryotic superphylum Alveolata. Recent studies making use of environmental small sub-unit ribosomal RNA gene (SSU rDNA) sequencing methodologies have detected a significant diversity and abundance of Perkinsea-like phylotypes in freshwater environments. In contrast only a few Perkinsea environmental sequences have been retrieved from marine samples and only two groups of Perkinsea have been cultured and morphologically described and these are parasites of marine molluscs or marine protists. These two marine groups form separate and distantly related phylogenetic clusters, composed of closely related lineages on SSU rDNA trees. Here, we test the hypothesis that Perkinsea are a hitherto under-sampled...
Tipo: Text Palavras-chave: 454 pyrosequencing; Perkinsus; Parvilucifera; Food web; Protist; Parasite.
Ano: 2014 URL: https://archimer.ifremer.fr/doc/00374/48496/48830.pdf
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Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing ArchiMer
Massana, Ramon; Gobet, Angelique; Audic, Stephane; Bass, David; Bittner, Lucie; Boutte, Christophe; Chambouvet, Aurelie; Christen, Richard; Claverie, Jean-michel; Decelle, Johan; Dolan, John R.; Dunthorn, Micah; Edvardsen, Bente; Forn, Irene; Forster, Dominik; Guillou, Laure; Jaillon, Olivier; Kooistra, Wiebe H. C. F.; Logares, Ramiro; Mahe, Frederic; Not, Fabrice; Ogata, Hiroyuki; Pawlowski, Jan; Pernice, Massimo C.; Probert, Ian; Romac, Sarah; Richards, Thomas; Santini, Sebastien; Shalchian-tabrizi, Kamran; Siano, Raffaele; Simon, Nathalie; Stoeck, Thorsten; Vaulot, Daniel; Zingone, Adriana; De Vargas, Colomban.
Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant European coastal sites. Environmental deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from three size fractions (pico-, nano- and micro/mesoplankton), as well as from dissolved DNA and surface sediments were used as templates for tag pyrosequencing of the V4 region of the 18S ribosomal DNA. Beta-diversity analyses split the protist community structure into three main clusters: picoplankton-nanoplankton-dissolved DNA, micro/mesoplankton and sediments. Within each cluster, protist communities from the same site and time clustered together,...
Tipo: Text
Ano: 2015 URL: http://archimer.ifremer.fr/doc/00275/38594/37190.pdf
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Molecular diversity and distribution of marine fungi across 130 European environmental samples ArchiMer
Richards, Thomas A.; Leonard, Guy; Mahe, Frederic; Del Campov, Javier; Romac, Sarah; Jones, Meredith D. M.; Maguire, Finlay; Dunthorn, Micah; De Vargas, Colomban; Massana, Ramon; Chambouvet, Aurelie.
Environmental DNA and culture-based analyses have suggested that fungi are present in low diversity and in low abundance in many marine environments, especially in the upper water column. Here, we use a dual approach involving high-throughput diversity tag sequencing from both DNA and RNA templates and fluorescent cell counts to evaluate the diversity and relative abundance of fungi across marine samples taken from six European near-shore sites. We removed very rare fungal operational taxonomic units (OTUs) selecting only OTUs recovered from multiple samples for a detailed analysis. This approach identified a set of 71 fungal 'OTU clusters' that account for 66% of all the sequences assigned to the Fungi. Phylogenetic analyses demonstrated that this...
Tipo: Text Palavras-chave: 454 pyrosequencing; Chytrids; Dikarya; Sediment communities.
Ano: 2015 URL: https://archimer.ifremer.fr/doc/00374/48490/48880.pdf
Registros recuperados: 5
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