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A transcriptome-targeting EcoChip for assessing functional mycodiversity

Title data

Peršoh, Derek ; Weig, Alfons ; Rambold, Gerhard:
A transcriptome-targeting EcoChip for assessing functional mycodiversity.
In: Microarrays. Vol. 1 (2012) Issue 1 . - pp. 25-41.
ISSN 2076-3905
DOI: https://doi.org/10.3390/microarrays1010025

Abstract in another language

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, whereas functional gene expression was analyzed by conserved domain-specific probes. By unlinking these two target groups, the shortage of broad sequence information of functional enzyme-coding genes in environmental communities became less important. The novel EcoChip microarray could be successfully applied to identify specific degradation activities in environmental samples at considerably high phylogenetic resolution. Reproducible and unbiased microarray signals could be obtained with chemically labeled total RNA preparations, thus avoiding the use of enzymatic labeling steps. ITS precursor rRNA was detected for the first time in a microarray experiment, which confirms the applicability of the EcoChip concept to selectively quantify the transcriptionally active part of fungal communities at high phylogenetic resolution. In addition, the chosen microarray platform facilitates the conducting of experiments with high sample throughput in almost any molecular biology laboratory.

Further data

Item Type: Article in a journal
Refereed: Yes
Additional notes: BAYCEER101780
BAYCEER101548
Keywords: EcoChip; microarray; Transcriptome
Institutions of the University: Faculties
Faculties > Faculty of Biology, Chemistry and Earth Sciences
Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Biology
Research Institutions > Research Centres > Bayreuth Center of Ecology and Environmental Research- BayCEER
Research Institutions
Research Institutions > Research Centres
Result of work at the UBT: Yes
DDC Subjects: 500 Science > 570 Life sciences, biology
Date Deposited: 21 May 2014 09:51
Last Modified: 04 May 2015 06:10
URI: https://eref.uni-bayreuth.de/id/eprint/400