Elsevier

Marine Genomics

Volume 42, December 2018, Pages 58-62
Marine Genomics

De novo transcriptome assembly and functional annotation of the southern rock lobster (Jasus edwardsii)

https://doi.org/10.1016/j.margen.2018.05.005Get rights and content

Abstract

Southern rock lobsters (Jasus edwardsii) are a valuable commodity and comprise important fishery resources in Australia and New Zealand. Population genomic methods (e.g. reduced representation sequencing) have been used to investigate patterns of dispersal and recruitment and the role of local adaptation within rock lobster species. However, application of these methods is constrained by the lack of pre-existing reference genome or transcriptome for Jasus and/or closely related species. In this study, we build a reference transcriptome assembly of 187,981 transcripts for Jasus edwardsii based on RNA sequencing data of four tissues (eyestalk, green gland, hepatopancreas and supraesophageal ganglion). This work will provide a significant resource to aid in investigation of the molecular basis of biological and evolutionary processes relevant to the fishing industry of spiny lobster and related taxonomic groups.

Introduction

The spiny rock lobster genus Jasus comprises six species that are distributed throughout the Southern Hemisphere (Phillips, 2013). The genus represents valuable fishery resources worldwide and has been exploited for more than one hundred years (FAO, 2015). The Southern rock lobster, Jasus edwardsii, has the largest geographic distribution whilst the other five species (J. caveorum, J. frontalis, J. lalandii, J. paulensis and J. tristani) maintain relatively limited distributions.

Genomics can provide powerful tools to assess the biological and evolutionary changes in fisheries stocks and therefore assist the fishing industry in performing ecosystem monitoring, resolving mixed-stock fisheries and supporting harvest and post-harvest regulation (Dichmont et al., 2012; Ovenden et al., 2015). In Jasus edwardsii, genomic methods, such as double digest restriction site-associated DNA sequencing (ddRADseq), has been used to assess structure, diversity and post-settlement selection (Villacorta-Rath et al., 2017), but new genomics resources are still required to further explore the link between fundamental biological processes and environmental changes, such as the warming climate impacts on stocks. Ecosystem shifts due to climate change are complex processes that force adaptation responses and shifts in biological systems from organism to species-level (Byrnes et al., 2011; Harley et al., 2012). These can lead to disturbances in the pattern of dispersal, recruitment and settlement of these species and drive evolutionary processes (Caputi et al., 2010; Hobday et al., 2009) that ultimately affect the expression of adaptive traits. Despite the rapid advances in nucleotide sequencing technology and associated reduction in costs, its full-potential application relevant to fisheries management is constrained by the lack of availability of reference genomic or transcriptomic resources for the genus Jasus and closely related species. For instance, a database search of genomic DNA sequences for the entire family Palinuridae via NCBI Entrez retrieves <1000 entries (search on 9/04/2018), mostly encompassing ribosomal RNA, microsatellites and partial sequences of genes. The most comprehensive reference resource is the transcriptome of the American lobster Homarus americanus (McGrath et al., 2016); although this exhibits deep evolutionary divergence from Jasus (Bracken-Grissom et al., 2014) limiting its utility for species within the genus Jasus.

In order to provide comprehensive and accessible genomic resources to studies of stock structure, dispersal, self-recruitment and adaptation in Jasus species, here we used deep RNA sequencing (RNA-seq) data of four somatic tissues obtained from three Jasus edwardsii specimens (one female and two males) to build a reference transcriptome assembly for Jasus edwardsii. Additionally, we performed gene ontology (GO) analysis to examine functional categories enriched across tissues. This work will provide the most comprehensive genomic resource for Jasus species to date that will facilitate the investigation of the molecular basis underlying biological and evolutionary processes. It will also open new avenues to the development of new tools applied to the fishing industry of spiny lobster and related taxonomic groups.

Section snippets

Sampling and RNA extraction

Three sexually mature individuals; one female and two males, of Jasus edwardsii were collected from experimental tanks at the Institute for Marine and Antarctic Studies (IMAS) - University of Tasmania, Australia. Prior to dissections, animals were anesthetized in ice-cold salt water (0 °C) for at least 10 min and then immediately dissected. Full tissues of eyestalk (ommatophore), green gland (also called antennal gland), hepatopancreas (digestive gland) and, supraesophageal ganglion (“brain”)

Conclusion

The transcriptome assembly presented here comprises a comprehensive resource of coding DNA sequences for Jasus edwardsii and closely related species with approximately 35,000 transcripts annotated and GO-enrichment comparison across four tissues. These data will facilitate future investigations of molecular responses to environmental changes and the development of new genomic tools that are likely to deliver meaningful advances to the fishery industry.

Data deposition

The obtained raw RNA-seq data were deposited in the NCBI Sequence Read Archive (SRA) under project number PRJNA386609, accession numbers SRR6364919, SRR6364920, SRR6364917, SRR6364918, SRR6364923, SRR6364924, SRR6364921, SRR6364922, SRR6364915, SRR6364916. The Transcriptome Shotgun Assembly (TSA) project has been deposited at NCBI under the accession GGHM00000000.1 (https://www.ncbi.nlm.nih.gov/nuccore/GGHM00000000.1).

The following are the supplementary data related to this article.

Acknowledgements

Funding for this research was provided by an Australian Research Council Discovery Project grant (Project No. DP150101491) awarded to J.M.S. and N.M. The first author acknowledges the Brazilian Program Science without Borders (CNPq - Conselho Nacional de Desenvolvimento Cientifico e Tecnologico) for the Postdoctoral research grant. We would like to thank Bridget Green and Caleb Gardner (University of Tasmania) for field assistance and specimens provided for sample collection; Brooke Whitelaw

Author contributions statement

C.A.S. and J.M.S. designed the study. C.A.S., N.M., J.M.S. conceived the idea and reviewed the manuscript. C.A.S collected the samples, performed the laboratory work, data analyses and led the writing of the manuscript with contributions from all authors.

Declarations of interest

None.

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