De novo assembly of a transcriptome from juvenile blue crabs (Callinectes sapidus) following exposure to surrogate Macondo crude oil

Joseph E. Neigel,Bree K. Yednock,Timothy J. Sullivan

doi:10.1186/s12864-015-1739-2

Joseph E. Neigel, Bree K. Yednock + Show 1 more

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https://doi.org/10.1186/s12864-015-1739-2

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Abstract

BackgroundThe blue crab, Callinectes sapidus, is economically and ecologically important in western Atlantic and Gulf of Mexico coastal estuaries. In 2010 blue crabs in the northern Gulf of Mexico were exposed to crude oil and chemical dispersants from the Deepwater Horizon oil spill. To characterize the blue crab transcriptome and identify genes that could be regulated in response to oil exposure we sequenced transcriptomes from hepatopancreas and gill tissues of juvenile blue crabs after exposing them to a water-accommodated fraction of surrogate Macondo crude oil in the laboratory and compared them to transcriptomes from an unexposed control group.ResultsIllumina sequencing provided 42.5 million paired-end sequencing reads for the control group and 44.9 million paired-end reads for the treatment group. From these, 73,473 transcripts and 52,663 genes were assembled. Comparison of control and treatment transcriptomes revealed about 100 genes from each tissue type that were differentially expressed. However, a much larger number of transcripts, approximately 2000 from each tissue type, were differentially expressed. Several examples of alternatively spliced transcripts were verified by qPCR, some of which showed significantly different expression patterns. The combined transcriptome from all tissues and individuals was annotated to assign putative gene products to both major gene ontology categories as well as specific roles in responses to cold and heat, metabolism of xenobiotic compounds, defence, hypoxia, osmoregulation and ecdysis. Among the annotations for upregulated and alternatively-spliced genes were candidates for the metabolism of oil-derived compounds.ConclusionsPreviously, few genomic resources were available for blue crabs or related brachyuran crabs. The transcriptome sequences reported here represent a major new resource for research on the biology of blue crabs. These sequences can be used for studies of differential gene expression or as a source of genetic markers. Genes identified and annotated in this study include candidates for responses of the blue crab to xenobiotic compounds, which could serve as biomarkers for oil exposure. Changes in gene expression also suggest other physiological changes that may occur as the result of exposure to oil.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1739-2) contains supplementary material, which is available to authorized users.

Highlights

The blue crab, Callinectes sapidus, is economically and ecologically important in western Atlantic and Gulf of Mexico coastal estuaries
Ammonia levels increased in all chambers (Table 1), but never exceeded the range considered acceptable for aquaculture of blue crabs [22]
Prior to the publication of these transcriptomes, publically available sequence data for blue crabs were limited to 1,677 Deoxyribose Nucleic Acid (DNA) and Ribonucleic Acid (RNA) sequences and 10,930 expressed sequence tags (ESTs)

Summary

Introduction

The blue crab, Callinectes sapidus, is economically and ecologically important in western Atlantic and Gulf of Mexico coastal estuaries. In 2010 blue crabs in the northern Gulf of Mexico were exposed to crude oil and chemical dispersants from the Deepwater Horizon oil spill. During the Deepwater Horizon oil spill (DHOS) in the summer of 2010, crude oil from the Macondo exploration oil well washed ashore along 1,600 km of coastline in the northern Gulf of Mexico [1]. To date, transcriptomes have been generated for only a handful of brachyuran crab species [13,14,15,16]. This deficit is due in part to the challenges associated with assembling a transcriptome without a reference genome from the same or a closely-related species [17]. The only published crustacean genome is from Daphnia pulex [18], a member of the class Branchiopoda, which is estimated to have diverged from the class Malacostraca, to which crabs belong, more than 400 mya [19]

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