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a transcriptome—targeting ecochip for assessing functional mycodiversity一个transcriptome-targeting ecochip评估功能mycodiversity.pdf

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a transcriptome—targeting ecochip for assessing functional mycodiversity一个transcriptome-targeting ecochip评估功能mycodiversity

Microarrays 2012, 1, 25-41; doi:10.3390/microarrays1010025 OPEN ACCESS microarrays ISSN 2076-3905 /journal/microarrays Article A Transcriptome—Targeting EcoChip for Assessing Functional Mycodiversity Derek Peršoh 1, Alfons R. Weig 2,* and Gerhard Rambold 1,2 1 Mycology, University of Bayreuth, 95440 Bayreuth, Germany; E-Mails: derek.persoh@uni-bayreuth.de (D.P.); gerhard.rambold@uni-bayreuth.de (G.R.) 2 DNA-Analytics and Ecoinformatics, University of Bayreuth, 95440 Bayreuth, Germany * Author to whom correspondence should be addressed; E-Mail: a.weig@uni-bayreuth.de; Tel.: +49-921-552457; Fax: +49-921 Received: 1 September 2011; in revised form: 14 October 2011 / Accepted: 17 October 2011 / Published: 31 October 2011 Abstract: A functional biodiversity microarray (EcoChip) prototype has been developed to facilitate the analysis of fungal communities in environmental samples with broad functional and phylogenetic coverage and to enable the incorporation of nucleic acid sequence data as they become available from large-scale (next generation) sequencing projects. A dual probe set (DPS) was designed to detect a) functional enzyme transcripts at conserved protein sites and b) phylogenetic barcoding transcripts at ITS regions present in precursor rRNA. Deviating from the concept of GeoChip-type microarrays, the presented EcoChip microarray phylogenetic information was obtained using a dedicated set of barcoding microarray probes,