Comparative transcriptomics: are transcriptional stress responses comparable among closely related species?
Background
Soil-dwelling springtails (Collembola), such as Folsomia candida, are ecologically relevant indicator species for soil quality, and are therefore often used for environmental risk assessment. Recently, we have developed a microarray containing over 5000 unique genes (invertebrate soil quality chip, iSQ chip) in order to study transcriptome-wide responses of F. candida to abiotic stress. This has generated a wealth of information on gene function and biochemical pathways associated with stress, which calls for further genetical and biochemical characterizations. Folsomia candida is, however, an obligate parthenogenic species and cannot be used in genetic segregation analysis or genotype-phenotype studies. The closely related species F. fimetaria reproduces sexually and would be an ideal alternative to study genetics of stress responses.
The aim of this study is to investigate whether the iSQ chip can be used to study transcriptome-wide reponses in F. fimetaria. Due to common ancestry we hypothesise that both species will show comparable transcriptional responses to identical effect concentrations of toxicants in soil.
Approach
First, equal amounts of genomic DNA from both F. candida and an F. fimetaria will be labeled and hybridized to the iSQ chip to verify if all probes give an equal hybridization signal. Subsequently, F. candida and F. fimetaria will be subjected to ecotoxocological testing to estimate toxicant (cadmium and/or phenanthrene) concentrations that exert 50% decrease in reproduction (EC50). Microarray experiments with animals exposed to EC50 concentrations will be conducted to study and compare transcriptional responses of the two species.Bioinformatics and gene annotation information available in public databases, will be used to interpret shared and species-specific transcriptional responses.
Supervision and information
Dr. Ir. Dick Roelofs (Room H147, W&N building, Vrije Universiteit)
Email: dick.roelofs@falw.vu.nl
Ph: +31-20-5987078
