Transcriptome profiling and digital gene expression analysis of the skin of Dybowski’s frog (Rana dybowskii) exposed to Aeromonas hydrophila

Abstract

Recently, populations of Rana dybowskii, an important amphibian species in Northeast China, have decreased, mainly owing to the disease caused by Aeromonas hydrophila. However, effective control methods have not yet been developed. In order to explore the immune responses of R. dybowskii upon exposure to A. hydrophila infection, Illumina high-throughput transcriptome sequencing and digital gene expression (DGE) technology were employed to investigate transcriptomic changes in the skin of R. dybowskii exposed to A. hydrophila. In this work, a total of 26,244,446 transcriptome sequencing reads were obtained and assembled into 109,089 unique unigenes using de novo assembly, and a total of 37,105 unigenes (34.0%) were functionally annotated against the non-redundant (Nr), Swiss-Prot, Cluster of Orthologous Groups of Proteins (COG), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) databases. Gene expression changes in the skin tissue of R. dybowskii exposed to A. hydrophila were investigated by a tag-based DGE system, and a total of 1435 significantly differentially expressed genes were identified, including 460 that were up-regulated and 975 that were down-regulated, indicating a large change in the host transcriptome profile exposed to A. hydrophila. Among these, 478 genes were associated with immune-relevant pathways, metabolic pathways, cellular components, growth, migration, and muscle and hormone signaling pathways. We confirmed the differential expression of 106 immune-relevant genes associated with innate and adaptive immune responses. Our data provide a fairly comprehensive molecular biology background for the deeper understanding of the amphibian immune system following A. hydrophila infection.

Comparative analysis of cutaneous bacterial communities of farmed Rana dybowskii after gentamycin bath

“…Two potentially pathogenic genera, namely Aeromonas and Chryseobacterium, were significantly inhibited by the gentamicin bath. Aeromonas is an important genus causing damage to amphibians in northeastern China (Xu et al, 2017). In this experiment, the gentamicin bath had a significant inhibitory effect on Aeromonas.…”

“…Rana dybowskii is susceptible to red-leg syndrome, gastroenteritis and rotten-skin disease (Pasteris, Bühler & Nadermacías, 2006;Shu et al, 1997). The pathogenic bacteria causing these diseases are mostly opportunistic, with an onset season from June to September, which is closely related to the health of the host and the cleanliness of the environment (Xu et al, 2017). Generally, only insects, such as yellow mealworm (Tenebrio molitor), can be used as feed in artificial breeding because R. dybowskii only prey on active food.…”

Molecular and Functional Characterization of a Novel Plasmid-Borne blaNDM-Like Gene, blaAFM-1, in a Clinical Strain of Aeromonas hydrophila

“…Aeromonas hydrophila is a gram-negative bacterium that is ubiquitous in aquatic environments and can cause infections in fish, 1 amphibians, 2 reptiles, 3 and humans. 4 It has been identified as an antibiotic-resistant and virulent etiologic agent in an increasing list of human diseases, including gastroenteritis, 5 diarrhea, 6 necrotizing fasciitis, 7 septicemia, 8 meningitis, 9 and hemolytic uremic syndrome.…”

De novo assembly and analysis of the transcriptome of the Siberian wood frog Rana amurensis

“…In recent years, transcriptome analysis is increasingly used for amphibians, e. g., to study the effects of pathogens (Price et al, 2015;Xu et al, 2017), insecticides (Ma et al, 2018), or the changes occurring during metamorphosis (Birol et al, 2015;Zhao et al, 2016). Many of those studies combine data from different tissues to obtain a more or less comprehensive set of transcripts expressed in the most important organs (Yang et al, 2012;Qiao et al, 2013;Robertson, Cornman, 2014;Christenson et al, 2014).…”