Common frog (Rana temporaria) transcriptomes following Exposure to Ranavirus and Batrachochytrium dendrobatidis
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2500
ORGANISM(S): Rana temporaria
SUBMITTER: Stephen Price
PROVIDER: E-MTAB-3632 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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2012-04-30 | E-GEOD-34235 | biostudies-arrayexpress
Project description:Chytridiomycosis is an emerging infectious disease of amphibians caused by the chytrid Batrachochytrium dendrobatidis (Bd). The disease has been associated with global amphibian declines and is driving the species in the wild to extinction. Using DNA microarray technology we have analysed transcriptional changes in Xenopus tropicalis during the course (7 and 42 days) of infection by Bd under warm (26oC) and cold (18oC) temperatures.
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Project description:In the past century, recently emerged infectious diseases have become major drivers of species decline and extinction. Amphibian declines have occurred due to the fungal disease chytridiomycosis, which has exacerbated the conservation crisis of this taxonomic group. Biologists are beginning to understand what traits are important for susceptibility to this disease, but more work is needed to determine why some species succumb to disease while others do not. We conducted a laboratory experiment to examine how two toad species respond to infection in controlled environment. We selected two related species thought to differ in susceptibility â?? Bufo marinus (an invasive and putatively resistant species) and B. boreas (an endangered and putatively susceptible species). We measured infection intensity, body weight, histological changes at the site of infection, and genome-wide gene expression changes using a custom assay developed from transcriptome sequencing. Our results confirmed that the two species differ in susceptibility. The more susceptible species, B. boreas, experienced higher infection intensities, loss in body weight, more dramatic histological changes, and larger perturbations in gene expression. We found key differences in skin expression responses in multiple pathways including up-regulation of skin integrity-related genes in the resistant B. marinus. Together our results show intrinsic differences in host response between related species, which are likely to be an important factor in explaining variation in response to a deadly emerging pathogen in wild populations. We processed 72 tissue samples in total: six biological replicates, three tissue types (ventral skin, liver, spleen), two treatment groups (pathogen exposed, control), and two host species (Bufo marinus, Bufo boreas). The custom Nimblegen microarray design included 135,200 60-bp probes (excluding control probes) targeting 31,367 transcript contigs from Bufo marinus, Bufo boreas, and model species Xenopus tropicalis, with 4 probes per probe-set. We used the 12-plex microarray platform (12 arrays per glass slide). Differential expression analyses were performed separately for each tissue type and host species.
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Project description:Determining the mechanisms of host-pathogen interaction is critical for understanding and mitigating infectious disease. Mechanisms of fungal pathogenicity are of particular interest given the recent outbreaks of fungal diseases in wildlife populations. Our study focuses on Batrachochytrium dendrobatidis (Bd), the chytrid pathogen responsible for amphibian declines around the world. Previous studies have hypothesized a role for several specific families of secreted proteases as pathogenicity factors in Bd, but the expression of these genes has only been evaluated in laboratory growth conditions. Here we conduct a genome-wide study of Bd gene expression under two different nutrient conditions. We compare Bd gene expression profiles in laboratory growth media and in host tissue (i.e., frog skin). A large proportion of genes in the Bd genome show increased expression when grown in host tissue, indicating the importance of studying pathogens in their infection environment. A number of gene classes show particularly high levels of expression in host tissue, including three families of secreted proteases (metallo-, serine- and aspartyl-proteases), adhesion genes, lipase-3 encoding genes, and a group of phylogenetically unusual crinkler-like effectors. We discuss the roles of these different genes as putative pathogenicity factors and discuss what they can teach us about Bd's metabolic targets, host invasion, and pathogenesis. One 12-plex chip was analyzed from 12 RNA samples extracted from Batrachochytrium dendrobatidis grown in 2 substrates. Six biological replicates were used for each substrate - sterile frog skin and tryptone nutrient broth. The same dye, Cy5, was used for all samples.
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