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RNA-Seq analysis of seasonal and individual variation in blood transcriptomes of healthy managed bottlenose dolphins

View Article: PubMed Central - PubMed

ABSTRACT

Background: The 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.

Results: Illumina 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.

Conclusions: This 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.

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

No MeSH data available.


Principal components analysis of 31 transcript profiles. The transcript profiles from the females (pink) largely clustered together, while those from the males (blue) were much more variable. Although the profiles from both males were variable, the young male (Hua, 5 years) differed somewhat from those of the older male (Keo, 17 years) along PC2
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Fig3: Principal components analysis of 31 transcript profiles. The transcript profiles from the females (pink) largely clustered together, while those from the males (blue) were much more variable. Although the profiles from both males were variable, the young male (Hua, 5 years) differed somewhat from those of the older male (Keo, 17 years) along PC2

Mentions: Principal components analysis did not reveal strong clustering associated with animal, sex, season, or any other measured parameter. PC1 accounted for 21.8 % of the variance and was somewhat correlated with sex, with females clustering together while the expression profiles from the two males were more variable (Fig. 3). PC2 only accounted for 7.8 % of variance and was not associated with animal, sex, or season. Samples from individual animals did not cluster together on either the PC1 or PC2 axes. The samples from males that clustered with the females on PC1 were not consistent with regard to season of collection. Neither PC1 nor PC2 were correlated with day length, water temperature, month or season of collection, nor with any of the hematological parameters measured.Fig. 3


RNA-Seq analysis of seasonal and individual variation in blood transcriptomes of healthy managed bottlenose dolphins
Principal components analysis of 31 transcript profiles. The transcript profiles from the females (pink) largely clustered together, while those from the males (blue) were much more variable. Although the profiles from both males were variable, the young male (Hua, 5 years) differed somewhat from those of the older male (Keo, 17 years) along PC2
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5016863&req=5

Fig3: Principal components analysis of 31 transcript profiles. The transcript profiles from the females (pink) largely clustered together, while those from the males (blue) were much more variable. Although the profiles from both males were variable, the young male (Hua, 5 years) differed somewhat from those of the older male (Keo, 17 years) along PC2
Mentions: Principal components analysis did not reveal strong clustering associated with animal, sex, season, or any other measured parameter. PC1 accounted for 21.8 % of the variance and was somewhat correlated with sex, with females clustering together while the expression profiles from the two males were more variable (Fig. 3). PC2 only accounted for 7.8 % of variance and was not associated with animal, sex, or season. Samples from individual animals did not cluster together on either the PC1 or PC2 axes. The samples from males that clustered with the females on PC1 were not consistent with regard to season of collection. Neither PC1 nor PC2 were correlated with day length, water temperature, month or season of collection, nor with any of the hematological parameters measured.Fig. 3

View Article: PubMed Central - PubMed

ABSTRACT

Background: The 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.

Results: Illumina 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.

Conclusions: This 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.

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

No MeSH data available.