De novo assembly and analysis of changes in the protein-coding transcriptome of the freshwater shrimp Paratya australiensis (Decapoda: Atyidae) in response to acid sulfate drainage water

Abstract

BackgroundThe atyid shrimp Paratya australiensis occurs in surface freshwater habitats throughout eastern Australia and has been used to study the ecotoxicology of contaminants such as pesticides and metals. The acidification of surface water that can occur after acid sulfate material in soils and sediments is oxidised and subsequently re-wetted is a serious environmental issue in coastal regions and inland riverine floodplains worldwide. Solubilisation of soil-associated minerals can result in high waterborne concentrations of mineral salts and dissolved metals, which together with low pH represent a potential threat to aquatic ecosystems in affected regions. The aims of the present study were to gain insight into stress responses induced by exposure to acid drainage water (ADW) in P. australiensis by determining changes in the abundance of protein-coding transcripts and to generate a comprehensive transcriptomic resource to facilitate further research into gene regulation or protein structure and function in this species. Adult P. australiensis were exposed for 24 h to undiluted ADW, 50 % ADW diluted in river water, or to river water as control, and high-throughput mRNA sequencing (RNA-Seq) conducted on whole-body tissues. A reference transcriptome was generated using de novo assembly and putative protein-coding regions were identified and annotated. Changes in transcript abundance in response to ADW exposure were determined by aligning reads to the reference transcriptome and quantifying coverage.ResultsA high proportion of arthropod benchmarking universal single-copy orthologues were present in the reference transcriptome. Functions associated with cuticle biosynthesis and oxidative stress were significantly enriched in the lists of transcripts exhibiting differential abundance in either direction after exposure to 50 % or 100 % ADW. Transcripts involved in osmoregulation exhibited decreased abundance following exposure to ADW. The transcriptome contained full-length coding sequences for numerous proteins known to be involved in environmental response pathways, including two putative metallothioneins, four glutathione peroxidases and 19 nuclear receptors.ConclusionsThe results of the present study provide insight into stress response pathways induced in crustaceans by short-term exposure to multiple stressors present in ADW such as low pH, high salinity and dissolved metals, and represent a resource for future toxicogenomics and protein functional studies in P. australiensis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3208-y) contains supplementary material, which is available to authorized users.

Comparative Transcriptome Analysis of the Gills from the Chinese Mitten Crab (Eriocheir japonica sinensis) Exposed to the Heavy Metal Cadmium

“…According previous research, GPx is anti-oxidative enzyme that reduces organic and inorganic hydroperoxides to the corresponding alcohols at the expense of reduced glutathione (Borchert et al, 2018). GPx can keep the cellular redox balance and protect against oxidative damage by reducing hydroperoxides at the expense of glutathione (Bain et al, 2016). These results revealed that the upregulation of GST and GPx was involved in stress response and adaptation, and similar upregulation was observed in Sinopotamon henanense (Sun et al 2016).…”

“…In recent years, with the development of nextgeneration sequencing, de novo transcriptomic approaches have been increasingly used to investigate physiological process and molecular characteristics of model and non-model organisms (Lou et al, 2017). Additionally, de novo transcriptome provides great breadth and depth of information that can be used to catalog all the genes expressed in the tissue, and facilitates detailed functional research of various proteins (Bain et al, 2016). To get better understanding about the molecular basis responses to Cd stress in E. j. sinensis, we used the comparative transcriptome of the gills to analyze the differentially expressed genes (DEGs) between exposed and unexposed to Cd by using Illumina sequencing platform and quantitative real-time PCR (RT-qPCR).…”

De novo assembly and transcriptome characterization of the freshwater prawn Palaemonetes argentinus: Implications for a detoxification response

“…Although it may appear controversial, there are similitudes between the decapod and the termite neuropeptidomes that would need to be further studied into an evolutionary perspective (Veenstra, 2016). Noteworthy is that for the de novo transcriptome of the freshwater shrimp Paratya australiensis (Decapoda: Atyidae), the termite Z. nevadensis appears as one of the best hits in their species transcriptome comparison (Bain et al, 2016).…”

Transcriptomics in aquaculture: current status and applications

“…Whole transcriptome profiling of the freshwater shrimp, Paratya australiensis has analysed the stress response pathway in response to the short term exposure of acid sulphate drainage water (Bain et al . ). Hepatopancreas transcriptome of mantis shrimp ( Oratosquilla oratoria ) was studied to assess the toxic effect of chromium hexavalent that revealed up regulation of genes associated with protein digestion and absorption to resist the toxic effect (Zhang et al .…”