Transcriptomic effects of dispersed oil in a non-model decapod crustacean
- Published
- Accepted
- Subject Areas
- Genetics, Genomics, Marine Biology
- Keywords
- gene ontology enrichment, crabs, RNA-seq, gene expression, oil spills, N50, ExN50, BUSCO, orthology
- Copyright
- © 2017 Vazquez-Miranda et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2017. Transcriptomic effects of dispersed oil in a non-model decapod crustacean. PeerJ Preprints 5:e2977v1 https://doi.org/10.7287/peerj.preprints.2977v1
Abstract
Background. Oil spills are major environmental disasters. Dispersants help control spills, as they emulsify oil into droplets to speed bioremediation. Although dispersant toxicity is controversial, the genetic consequences and damages of dispersed oil exposure are poorly understood. We used RNA-seq to measure gene expression of flatback mudcrabs (Eurypanopeus depressus, Decapoda, Brachyura, Panopeidae) exposed to dispersed oil. Methods. Our experimental design included two control types, oil-only, and oil-dispersant treatments with three replicates each. We prepared 100 base pair-ended libraries from total RNA and sequenced them in one Illumina HiSeq2000 lane. We assembled a reference transcriptome with all replicates per treatment, assessed quality with novel metrics, identified transcripts, and quantified gene expression with open source software. Results. Our mudcrab transcriptome included 500,008 transcripts from 347,082,962 pair-end raw reads. In oil-only treatments, we found few significant differences. However, in oil-dispersant treatments, over 4000 genes involved with cellular differentiation, primordial cellular component upkeep, apoptosis, and immune response were downregulated. A few muscle structure and development genes were upregulated. Discussion. Our results provide evidence that exposure to chemically dispersed oil causes a generalized cellular shutdown and muscular repair attempts. Our results suggest current oil-spill treatment procedures could be detrimental to crustaceans and indicate additional research is needed to evaluate the impact of oil spills in gene expression. Finally, traditional quality metrics such as N50s have limitations to explain the nature of RNA-seq compared to new methods in non-model decapod crustaceans.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Table S1. Sample information.
Specimen voucher number (HBG) deposited at Florida International University, locality, experimental treatment, Genbank BioSample accession, and number of pair-end reads obtain per stranded RNAseq HiSeq2000 Illumina library. Experimental conditions were: aerated, negative control (AC), non-aerated, negative control (NC), non-aerated treatment with oil (WAF; OO), and non-aerated treatment with oil mixed with dispersant (CEWAF; OD). The letter ‘R’ represents the individual replicate number. Reference treatments were used exclusively for the de novo transcriptome assembly.
Table S2. Pairwise counts of differentially expressed features between aerated and non-aerated experimental treatments.
Numbers represent transcripts with significant differential expression in a log2 fold change scale after passing an FDR of 1% in edgeR and DEseq2. Each treatment included three replicates. Experimental conditions were: aerated, negative control (AC) and non-aerated, negative control (NC). These comparisons exclude non-aerated treatments with oil and dispersant (OO and OD) to determine transcripts expressed in hypoxic conditions.
Table S3. Pairwise counts of differentially expressed features between non-aerated experimental treatments with and without oil and dispersant.
Numbers represent transcripts with significant differential expression in a log2 fold change scale after passing an FDR of 1% in edgeR and DESeq2. Each treatment included three replicates. Experimental conditions were: non-aerated, negative control (NC), non-aerated oil-only treatment (WAF; OO), and non-aerated oil-dispersant treatment (CEWAF; OD). These comparisons exclude the aerated, negative control (AC) to avoid masking the effects of experimental manipulation and low oxygen in expressed transcripts.
Table S4. Gene ontology and gene regulation direction.
These gene ontology terms were detected by both statistical methods for Trinity genes and isoforms and are listed in alphabetical order following the oil-dispersant treatment (OD) directionality. Left column correspond to the list number, central column to the gene ontology term for downregulated features, and right column corresponds to upregulated features. The non-aerated, negative control (NC) replicates had the inverse regulation directionality.
Table S5. Tumor necrosis factor (TNF) and Cytochrome P450 (CYP) downregulated transcripts.
(3 and 19 total respectively) in the oil-dispersant treatment (OD) detected by DESeq2 (and thus upregulated in the negative control). These features were not detected by edgeR. Transcripts blasted to the same GO molecular functions, for TNF: receptor binding, and for CYP: Heme binding, iron ion binding, monooxygenase activity, and oxydoreductase activity. Organism Uniprot identity: Kuruma prawn – PENJP (Penaeus japonicus), fruit fly - DROME (Drosophila melanogaster), house mouse - MOUSE (Mus musculus), and tropical cockroach - BLADI (Blaberus discoidalis). For full annotations see DS1, and DS4-5.