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.

Peter A Bain,Adrienne L Gregg,Anupama Kumar

doi:10.1186/s12864-016-3208-y

Peter A Bain, Adrienne L Gregg + Show 1 more

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https://doi.org/10.1186/s12864-016-3208-y

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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.

Highlights

The 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 high proportion of arthropod proteins with unknown function represents a significant challenge for researchers in the field of environmental toxicogenomics, which relies on similarity-based functional inference to decipher gene regulatory networks related to toxicant effects
Efforts in this area will undoubtedly be aided by the i5K project, which aims to sequence the genomes of 5000 arthropods including a list of 20 decapods [89], and transcriptomics surveys such as the present study will assist researchers studying species for which genome sequencing projects are unlikely to be available in the near future

Summary

Introduction

The 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. Following rainfall or the resumption of irrigation, highly acidic runoff can dissolve soil-associated minerals, resulting in high concentrations of salts and metals entering surface water bodies via drainage channels [13,14,15,16,17]. Thousands of hectares of reclaimed floodplains in the Lower Murray region of southern Australia were subjected to an extended period of drying as a result of hydrological changes and reduced irrigation associated with a prolonged drought This was followed by a series of heavy rainfall events that flushed large volumes of highly acidic water containing metals and salts into drainage channels that discharge into the Murray River [18]. Because of the presence of multiple potential stressors (low pH, high ionic strength and high dissolved metal concentrations), determining the response pathways induced by exposure to ADW may provide insight into mechanisms of adaptation in crustaceans in response to diverse environmental challenges

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