RNA-Seq analysis of seasonal and individual variation in blood transcriptomes of healthy managed bottlenose dolphins
Identifieur interne : 000019 ( Main/Exploration ); précédent : 000018; suivant : 000020RNA-Seq analysis of seasonal and individual variation in blood transcriptomes of healthy managed bottlenose dolphins
Auteurs : Jeanine S. Morey [États-Unis] ; Marion G. Neely [États-Unis] ; Denise Lunardi [Italie] ; Paul E. Anderson [États-Unis] ; Lori H. Schwacke [États-Unis] ; Michelle Campbell ; Frances M. Van Dolah [États-Unis]Source :
- BMC Genomics [ 1471-2164 ] ; 2016.
Abstract
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.
Illumina based RNA-seq analyses were carried out using both the Ensembl dolphin genome and a
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.
The online version of this article (doi:10.1186/s12864-016-3020-8) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-016-3020-8
PubMed: 27608714
PubMed Central: 5016863
Affiliations:
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Neely</name><affiliation wicri:level="2"><nlm:aff id="Aff1">National Centers for Coastal Ocean Sciences, National Ocean Service, NOAA, 331 Fort Johnson Rd, Charleston, SC 29412 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Caroline du Sud</region></placeName><wicri:cityArea>National Centers for Coastal Ocean Sciences, National Ocean Service, NOAA, 331 Fort Johnson Rd, Charleston</wicri:cityArea></affiliation></author><author><name sortKey="Lunardi, Denise" sort="Lunardi, Denise" uniqKey="Lunardi D" first="Denise" last="Lunardi">Denise Lunardi</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Department of Life Sciences and Biotechnology, University of Ferrara, via L. Borsari 46, 44121 Ferrara, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Life Sciences and Biotechnology, University of Ferrara, via L. 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Morey</name><affiliation wicri:level="2"><nlm:aff id="Aff1">National Centers for Coastal Ocean Sciences, National Ocean Service, NOAA, 331 Fort Johnson Rd, Charleston, SC 29412 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Caroline du Sud</region></placeName><wicri:cityArea>National Centers for Coastal Ocean Sciences, National Ocean Service, NOAA, 331 Fort Johnson Rd, Charleston</wicri:cityArea></affiliation></author><author><name sortKey="Neely, Marion G" sort="Neely, Marion G" uniqKey="Neely M" first="Marion G." last="Neely">Marion G. Neely</name><affiliation wicri:level="2"><nlm:aff id="Aff1">National Centers for Coastal Ocean Sciences, National Ocean Service, NOAA, 331 Fort Johnson Rd, Charleston, SC 29412 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Caroline du Sud</region></placeName><wicri:cityArea>National Centers for Coastal Ocean Sciences, National Ocean Service, NOAA, 331 Fort Johnson Rd, Charleston</wicri:cityArea></affiliation></author><author><name sortKey="Lunardi, Denise" sort="Lunardi, Denise" uniqKey="Lunardi D" first="Denise" last="Lunardi">Denise Lunardi</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Department of Life Sciences and Biotechnology, University of Ferrara, via L. Borsari 46, 44121 Ferrara, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Life Sciences and Biotechnology, University of Ferrara, via L. Borsari 46, 44121 Ferrara</wicri:regionArea><wicri:noRegion>44121 Ferrara</wicri:noRegion></affiliation></author><author><name sortKey="Anderson, Paul E" sort="Anderson, Paul E" uniqKey="Anderson P" first="Paul E." last="Anderson">Paul E. Anderson</name><affiliation wicri:level="2"><nlm:aff id="Aff3">Department of Computer Science, College of Charleston, Charleston, SC 29424 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Caroline du Sud</region></placeName><wicri:cityArea>Department of Computer Science, College of Charleston, Charleston</wicri:cityArea></affiliation></author><author><name sortKey="Schwacke, Lori H" sort="Schwacke, Lori H" uniqKey="Schwacke L" first="Lori H." last="Schwacke">Lori H. Schwacke</name><affiliation wicri:level="2"><nlm:aff id="Aff1">National Centers for Coastal Ocean Sciences, National Ocean Service, NOAA, 331 Fort Johnson Rd, Charleston, SC 29412 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Caroline du Sud</region></placeName><wicri:cityArea>National Centers for Coastal Ocean Sciences, National Ocean Service, NOAA, 331 Fort Johnson Rd, Charleston</wicri:cityArea></affiliation></author><author><name sortKey="Campbell, Michelle" sort="Campbell, Michelle" uniqKey="Campbell M" first="Michelle" last="Campbell">Michelle Campbell</name><affiliation><nlm:aff id="Aff4">Dolphin Quest, Waikoloa, Hawaii USA</nlm:aff><wicri:noCountry code="subfield">Hawaii USA</wicri:noCountry></affiliation></author><author><name sortKey="Van Dolah, Frances M" sort="Van Dolah, Frances M" uniqKey="Van Dolah F" first="Frances M." last="Van Dolah">Frances M. Van Dolah</name><affiliation wicri:level="2"><nlm:aff id="Aff1">National Centers for Coastal Ocean Sciences, National Ocean Service, NOAA, 331 Fort Johnson Rd, Charleston, SC 29412 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Caroline du Sud</region></placeName><wicri:cityArea>National Centers for Coastal Ocean Sciences, National Ocean Service, NOAA, 331 Fort Johnson Rd, Charleston</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff5">Present Address: Graduate Program in Marine Biology, University of Charleston, Charleston, SC 29412 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Caroline du Sud</region></placeName><wicri:cityArea>Present Address: Graduate Program in Marine Biology, University of Charleston, Charleston</wicri:cityArea></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>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.</p></sec><sec><title>Results</title><p>Illumina based RNA-seq analyses were carried out using both the Ensembl dolphin genome and a <italic>de novo</italic> 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.</p></sec><sec><title>Conclusions</title><p>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.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-016-3020-8) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Chaussabel, D" uniqKey="Chaussabel D">D Chaussabel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mohr, S" uniqKey="Mohr S">S Mohr</name></author><author><name sortKey="Liew, Cc" uniqKey="Liew C">CC Liew</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mancia, A" uniqKey="Mancia A">A Mancia</name></author><author><name sortKey="Ryan, Jc" uniqKey="Ryan J">JC 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Robertson</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Italie</li><li>États-Unis</li></country><region><li>Caroline du Sud</li></region></list><tree><noCountry><name sortKey="Campbell, Michelle" sort="Campbell, Michelle" uniqKey="Campbell M" first="Michelle" last="Campbell">Michelle Campbell</name></noCountry><country name="États-Unis"><region name="Caroline du Sud"><name sortKey="Morey, Jeanine S" sort="Morey, Jeanine S" uniqKey="Morey J" first="Jeanine S." last="Morey">Jeanine S. Morey</name></region><name sortKey="Anderson, Paul E" sort="Anderson, Paul E" uniqKey="Anderson P" first="Paul E." last="Anderson">Paul E. Anderson</name><name sortKey="Neely, Marion G" sort="Neely, Marion G" uniqKey="Neely M" first="Marion G." last="Neely">Marion G. Neely</name><name sortKey="Schwacke, Lori H" sort="Schwacke, Lori H" uniqKey="Schwacke L" first="Lori H." last="Schwacke">Lori H. Schwacke</name><name sortKey="Van Dolah, Frances M" sort="Van Dolah, Frances M" uniqKey="Van Dolah F" first="Frances M." last="Van Dolah">Frances M. Van Dolah</name><name sortKey="Van Dolah, Frances M" sort="Van Dolah, Frances M" uniqKey="Van Dolah F" first="Frances M." last="Van Dolah">Frances M. Van Dolah</name></country><country name="Italie"><noRegion><name sortKey="Lunardi, Denise" sort="Lunardi, Denise" uniqKey="Lunardi D" first="Denise" last="Lunardi">Denise Lunardi</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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