Genomics/technical resourcesComparative analysis of gill transcriptomes of two freshwater crayfish, Cherax cainii and C. destructor
Introduction
Cherax cainii (Marron) and Cherax destructor (Yabby) are freshwater crayfish species, endemic to Australia, with a natural distribution that spans a diverse range of aquatic environments. These crayfish have the capacity to adapt to and tolerate fluctuations in environmental parameters such as dissolved oxygen, pH, temperature and salinity (Bryant and Papas, 2007, McCormack, 2014). Physiological characteristics of these animals, as well as their economic significance, have made them an important model for physiological research in crustaceans. Despite this, genetic information for these crayfish species is still largely limited to mitochondrial and population genetic data (Miller Adam et al., 2004, Gan et al., 2014). Thus, genomic resources from which candidate genes can be identified are crucial for future genetic research aimed at understanding their response to environmental variables including changes in water quality. To address this, our study has generated two large transcriptome datasets, one for each species, which are important resources for the identification of gill expressed candidate genes that may have important roles in response to changes in water quality parameters. (See Fig. 1.)
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Animal collection, RNA extraction and sequencing
C. cainii were collected from a Yabby farm at NSW, Australia and C. destructor from Mudgee, Western Australia. Animals were acclimated to lab conditions for three weeks (21°C, pH 7 and conductivity 1700 μS/cm). Before tissue collection, three C. cainii (body length 11 ± 0.9 cm and wet body weight 57 ± 5 g) and three C. destructor (9 ± 0.7 cm and 45 ± 3 g) were exposed to pH 6, 7 and 8; a natural pH tolerance range of Cherax species (Macaranas et al., 1995, Bryant and Papas, 2007). Gill tissues were extracted
Acknowledgements
This work was funded by the QUT (Queensland University of Technology) (PJP6418) Higher Degree Research Support and a QUT ECARD grant awarded to PP. We are grateful to the valuable guidance and support of all the group members of Physiological Genomics Lab at QUT.
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2020, Developmental and Comparative ImmunologyCitation Excerpt :Donor and acceptor splicing sites were refined using Genie (Reese et al., 1997). Astacidin-like sequences were also searched for in other available transcriptomes from Astacidea, which were either downloaded from the NCBI TSA database (when available), or de novo assembled with the CLC genomics Workbench v.11, including those from: Astacus astacus (Theissinger et al., 2016), various Cambarus species (C. cryptodytes, C. dubius, C. graysoni, C. hamulatus, C. nerterius, C. rusticiformis, C. setosus) (unpublished), Cherax cainii, C. destructor (Ali et al., 2015), C. quadricarinatus (Tan et al., 2016), Enoplometopus cf. daumi MCZ IZ 74073 (unpublished), Homarus americanus (McGrath et al., 2016), Nephrops norvegicus (Rotllant et al., 2017), Pacifastacus leniusculus (unpublished), Pontastacus leptodactylus (Tom et al., 2014), various species of Procambarus (P. fallax, P. horsti, P. lucifugus, P. pallidus) (unpublished), Orconectes (Faxonius) australis and O. (F.) incomptus (unpublished). Positive hits were detected based on a minimum e-value threshold of 1 E−3 and further refined based on detection by a custom HMM profile obtained from the multiple sequences alignment of the conserved signal peptide of all astacidins generated, using HMMER v.3.2.1 (Finn et al., 2011).
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2017, General and Comparative EndocrinologyCitation Excerpt :Fortunately, next-generation sequencing technologies make it possible to identify genes of interest in previously intractable species (van Dijk et al., 2014). Although some genome sequences have been determined for various crustaceans, including water flea Daphnia pulex (PRJNA284847), freshwater amphipod Hyalella azteca (PRJNA342675), Parhyale hawaiensis (PRJNA306836), salmon louse Lepeophtheirus salmonis (PRJNA280127), water louse Asellus aquaticus (PRJNA281276), Jassa slatteryi (PRJNA20517), calanoid copepod Eurytemora affinis (PRJNA203087), marine copepod Tigriopus californicus (PRJNA316512), and cherry shrimp Neocaridina denticulata (PRJNA224755) (Colbourne et al., 2011; Consortium, 2013; Kenny et al., 2014; Kao et al., 2016), the transcriptomes of a few crayfish species, such as Cherax quadricarinatus, Procambarus clarkii, Astacus astacus, Pontastacus leptodactylus, Cherax cainii, C. destructor, and Astacus leptodactylus (PRJNA183420) (Tan et al., 2016; Shen et al., 2014; Ali et al., 2015a; Theissinger et al., 2016; Manfrin et al., 2013; Du, 2016; Du et al., 2016), have been reported. Although some reported crayfish transcriptome data were generated from different tissues (Jiang et al., 2014; Ali et al., 2015b; Manfrin et al., 2015; Du, 2016; Du et al., 2016), data on the transcriptome of the hepatopancreas are limited (Manfrin et al., 2015; Theissinger et al., 2016).