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Het OWA, het open archief van het Waterbouwkundig Laboratorium heeft tot doel alle vrij toegankelijke onderzoeksresultaten van dit instituut in digitale vorm aan te bieden. Op die manier wil het de zichtbaarheid, verspreiding en gebruik van deze onderzoeksresultaten, alsook de wetenschappelijke communicatie maximaal bevorderen.

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Mining environmental high-throughput sequence data sets to identify divergent amplicon clusters for phylogenetic reconstruction and morphotype visualization Gimmler, A.; Stoeck, T. (2015). Mining environmental high-throughput sequence data sets to identify divergent amplicon clusters for phylogenetic reconstruction and morphotype visualization. Environmental Microbiology Reports 7(4): 679-686. https://dx.doi.org/10.1111/1758-2229.12307 In: Environmental Microbiology Reports. Wiley-Blackwell. ISSN 1758-2229, meer

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Beschikbaar in	Auteurs
VLIZ: Non-open access 307149 [ aanvragen ]

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Trefwoorden

Marine Sciences Maritime Industries > Blue Biotech Scientific Community Scientific Publication Software/Modelling Tool Marien/Kust

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Project	Top | Auteurs
Association of European marine biological laboratories, meer

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Auteurs		Top
Gimmler, A. Stoeck, T.

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Abstract

Environmental high-throughput sequencing (envHTS) is a very powerful tool, which in protistan ecology is predominantly used for the exploration of diversity and its geographic and local patterns. We here used a pyrosequenced V4-SSU rDNA data set from a solar saltern pond as test case to exploit such massive protistan amplicon data sets beyond this descriptive purpose. Therefore, we combined a Swarm-based blastn network including 11579 ciliate V4 amplicons to identify divergent amplicon clusters with targeted polymerase chain reaction (PCR) primer design for full-length small subunit of the ribosomal DNA retrieval and probe design for fluorescence in situ hybridization (FISH). This powerful strategy allows to benefit from envHTS data sets to (i) reveal the phylogenetic position of the taxon behind divergent amplicons; (ii) improve phylogenetic resolution and evolutionary history of specific taxon groups; (iii) solidly assess an amplicons (species') degree of similarity to its closest described relative; (iv) visualize the morphotype behind a divergent amplicons cluster; (v) rapidly FISH screen many environmental samples for geographic/habitat distribution and abundances of the respective organism and (vi) to monitor the success of enrichment strategies in live samples for cultivation and isolation of the respective organisms.

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