RNA-Seq analysis of seasonal and individual variation in blood transcriptomes of healthy managed bottlenose dolphinsReport as inadecuate

RNA-Seq analysis of seasonal and individual variation in blood transcriptomes of healthy managed bottlenose dolphins - Download this document for free, or read online. Document in PDF available to download.

BMC Genomics

, 17:720

Non-human and non-rodent vertebrate genomics


BackgroundThe blood transcriptome can reflect both systemic exposures and pathological changes in other organs of the body because immune cells recirculate through the blood, lymphoid tissues, and affected sites. In human and veterinary medicine, blood transcriptome analysis has been used successfully to identify markers of disease or pathological conditions, but can be confounded by large seasonal changes in expression. In comparison, the use of transcriptomic based analyses in wildlife has been limited. Here we report a longitudinal study of four managed bottlenose dolphins located in Waikoloa, Hawaii, serially sampled approximately monthly over the course of 1 year to establish baseline information on the content and variation of the dolphin blood transcriptome.

ResultsIllumina based RNA-seq analyses were carried out using both the Ensembl dolphin genome and a de novo blood transcriptome as guides. Overall, the blood transcriptome encompassed a wide array of cellular functions and processes and was relatively stable within and between animals over the course of 1 year. Principal components analysis revealed moderate clustering by sex associated with the variation among global gene expression profiles PC1, 22 % of variance. Limited seasonal change was observed, with < 2.5 % of genes differentially expressed between winter and summer months FDR < 0.05. Among the differentially expressed genes, cosinor analysis identified seasonal rhythmicity for the observed changes in blood gene expression, consistent with studies in humans. While the proportion of seasonally variant genes in these dolphins is much smaller than that reported in humans, the majority of those identified in dolphins were also shown to vary with season in humans. Gene co-expression network analysis identified several gene modules with significant correlation to age, sex, or hematological parameters.

ConclusionsThis longitudinal analysis of healthy managed dolphins establishes a preliminary baseline for blood transcriptome analysis in this species. Correlations with hematological parameters, distinct from muted seasonal effects, suggest that the otherwise relatively stable blood transcriptome may be a useful indicator of health and exposure. A robust database of gene expression in free-ranging and managed dolphins across seasons with known adverse health conditions or contaminant exposures will be needed to establish predictive gene expression profiles suitable for biomonitoring.

KeywordsTursiops truncatus Bottlenose dolphin Blood transcriptome RNA-seq Globin-reduction AbbreviationsAMMPAAlliance of marine mammal parks and aquariums

BARBright, alert responsive

BLASTBasic local alignment search tool

CEGCore eukaryotic gene

CEGMACore eukaryotic genes mapping approach

FPKMFragments per kilobase of transcript per million mapped reads

GEOGene expression omnibus

GOGene ontology

PCPrincipal component

PCAPrincipal component analysis

PCBPolychlorinated biphenyl

PCRPolymerase chain reaction

RINRNA integrity number

RSEMRNA-seq by expectation maximization

WGCNAWeighted gene co-expression network analysis

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-016-3020-8 contains supplementary material, which is available to authorized users.

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