Detecting unknown sequences with DNA microarrays: explorative probe design strategies

Abstract

SummaryDesigning environmental DNA microarrays that can be used to survey the extreme diversity of microorganisms existing in nature, represents a stimulating challenge in the field of molecular ecology. Indeed, recent efforts in metagenomics have produced a substantial amount of sequence information from various ecosystems, and will continue to accumulate large amounts of sequence data given the qualitative and quantitative improvements in the next-generation sequencing methods. It is now possible to take advantage of these data to develop comprehensive microarrays by using explorative probe design strategies. Such strategies anticipate genetic variations and thus are able to detect known and unknown sequences in environmental samples. In this review, we provide a detailed overview of the probe design strategies currently available to construct both phylogenetic and functional DNA microarrays, with emphasis on those permitting the selection of such explorative probes. Furthermore, exploration of complex environments requires particular attention on probe sensitivity and specificity criteria. Finally, these innovative probe design approaches require exploiting newly available high-density microarray formats.

Rhizosphere microbiome assemblage is affected by plant development

“…In soils, functional microarrays or GeoChip that target specific microbial functions have been successfully used to determine the metabolic potential of the microbial communities (He et al, 2007(He et al, , 2011Bai et al, 2013;Zhang et al, 2013). A drawback of the GeoChip is the fact that novel functions and transcripts cannot be identified, and one is biased to the probes present in the chip (Dugat-Bony et al, 2012). Recently, metatranscriptomics in soil has been attempted on the rRNA to identify the active members of the microbial community in the rhizosphere of various crop species (Turner et al, 2013); Urich et al (2008) described the isolation and sequencing of mRNA from a sandy lawn as a means of describing the microbial transcriptome in the soil.…”

A microarray for assessing transcription from pelagic marine microbial taxa

“…Future technological improvements, such as automated probe design including probes for other marker genes and exploratory probes (Chung et al, 2005;Dugat-Bony et al, 2011), would improve the performance of the microarray. In addition to the utility of the MicroTOOLs array for incubation experiments, this microarray could be applied as a tool for pelagic marine microbiological studies for standardized information across study types and ocean basins.…”

A Review of Detection Methods for the Plant Viruses

“…Most drawback is cost since it requires the highly sophisticated processing machine for spotting probes and reading reactions and also needs dust-free room (Wang et al, 2002). The other problem is construction of oligonucleotide to be hybridized to target DNAs in terms of specificity and sensitivity (Dugat-Bony et al, 2012). Because of those, it has not been widely used and is still under research phase.…”

“…Because of those, it has not been widely used and is still under research phase. However, some trials to use this method can be found because it is able to detect both known and unknown sequences in environmental samples, resulted in identifying unknown viruses by Oligo-chip (Boonham et al, 2007;Dugat-Bony et al, 2012;Nam et al, 2014;Schena et al, 1995). This method was used detection for potato viruses such as Potato virus A (PVA), Potato virus M (PVM), Potato virus S (PVS), PVX, PVY and PLRV and cucurbit-infecting plant viruses (Bystricka et al, 2005;Lee et al, 2003).…”