Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals.

dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
dc.contributor.authorBayer, Till
dc.contributor.authorAranda, Manuel
dc.contributor.authorSunagawa, Shinichi
dc.contributor.authorYum, Lauren
dc.contributor.authorDesalvo, Michael K
dc.contributor.authorLindquist, Erika
dc.contributor.authorCoffroth, Mary Alice
dc.contributor.authorVoolstra, Christian R.
dc.contributor.authorMedina, Mónica
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentMarine Science Program
dc.contributor.departmentRed Sea Research Center (RSRC)
dc.contributor.departmentReef Genomics Lab
dc.contributor.institutionEuropean Molecular Biology Laboratory, Heidelberg, Germany
dc.contributor.institutionDepartment of Anesthesia, UCSF School of Medicine, University of California San Francisco, San Francisco, CA, United States
dc.contributor.institutionDepartment of Energy Joint Genome Institute, Walnut Creek, CA, United States
dc.contributor.institutionGraduate Program in Evolution, Ecology and Behavior, Department of Geology, State University of New York at Buffalo, Buffalo, NY, United States
dc.contributor.institutionSchool of Natural Sciences, University of California Merced, Merced, CA, United States
dc.date.accessioned2014-07-21T12:53:49Z
dc.date.available2014-07-21T12:53:49Z
dc.date.issued2012-04-18
dc.description.abstractDinoflagellates are unicellular algae that are ubiquitously abundant in aquatic environments. Species of the genus Symbiodinium form symbiotic relationships with reef-building corals and other marine invertebrates. Despite their ecologic importance, little is known about the genetics of dinoflagellates in general and Symbiodinium in particular. Here, we used 454 sequencing to generate transcriptome data from two Symbiodinium species from different clades (clade A and clade B). With more than 56,000 assembled sequences per species, these data represent the largest transcriptomic resource for dinoflagellates to date. Our results corroborate previous observations that dinoflagellates possess the complete nucleosome machinery. We found a complete set of core histones as well as several H3 variants and H2A.Z in one species. Furthermore, transcriptome analysis points toward a low number of transcription factors in Symbiodinium spp. that also differ in the distribution of DNA-binding domains relative to other eukaryotes. In particular the cold shock domain was predominant among transcription factors. Additionally, we found a high number of antioxidative genes in comparison to non-symbiotic but evolutionary related organisms. These findings might be of relevance in the context of the role that Symbiodinium spp. play as coral symbionts.Our data represent the most comprehensive dinoflagellate EST data set to date. This study provides a comprehensive resource to further analyze the genetic makeup, metabolic capacities, and gene repertoire of Symbiodinium and dinoflagellates. Overall, our findings indicate that Symbiodinium possesses some unique characteristics, in particular the transcriptional regulation in Symbiodinium may differ from the currently known mechanisms of eukaryotic gene regulation.
dc.description.sponsorshipThis study was supported through NSF (National Science Foundation) awards IOS 0644438 and IOS 0926906 (MM), OCE 0424994 (MAC), a KAUST AEA (King Abdullah University of Science and Technology) 3 Joint Collaborative Research award (CRV), and through a Collaborative Travel Fund to TB made by King Abdullah University of Science and Technology. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
dc.eprint.versionPublisher's Version/PDF
dc.identifier.citationBayer T, Aranda M, Sunagawa S, Yum LK, DeSalvo MK, et al. (2012) Symbiodinium Transcriptomes: Genome Insights into the Dinoflagellate Symbionts of Reef-Building Corals. PLoS ONE 7: e35269. doi:10.1371/journal.pone.0035269.
dc.identifier.doi10.1371/journal.pone.0035269
dc.identifier.issn1932-6203
dc.identifier.journalPLoS ONE
dc.identifier.pmcidPMC3329448
dc.identifier.pmid22529998
dc.identifier.urihttp://hdl.handle.net/10754/323516
dc.language.isoen
dc.publisherPublic Library of Science (PLoS)
dc.relation.urlhttp://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0035269
dc.relation.urlhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329448/
dc.rightsArchived with thanks to PloS one
dc.subject.meshAnimals
dc.subject.meshAnthozoa
dc.subject.meshBase Composition
dc.subject.meshCodon
dc.subject.meshCoral Reefs
dc.subject.meshDinoflagellida
dc.subject.meshExpressed Sequence Tags
dc.subject.meshGenome
dc.subject.meshHistones
dc.subject.meshMolecular Sequence Annotation
dc.subject.meshNucleosomes
dc.subject.meshOxidative Stress
dc.subject.meshPhylogeny
dc.subject.meshSymbiosis
dc.subject.meshTranscription Factors
dc.subject.meshTranscriptome
dc.subject.meshAnimals
dc.subject.meshAnthozoa
dc.subject.meshBase Composition
dc.subject.meshCodon
dc.subject.meshCoral Reefs
dc.subject.meshDinoflagellida
dc.subject.meshExpressed Sequence Tags
dc.subject.meshGenome
dc.subject.meshHistones
dc.subject.meshMolecular Sequence Annotation
dc.subject.meshNucleosomes
dc.subject.meshOxidative Stress
dc.subject.meshPhylogeny
dc.subject.meshSymbiosis
dc.subject.meshTranscription Factors
dc.subject.meshTranscriptome
dc.titleSymbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals.
dc.typeArticle
display.details.left<span><h5>Type</h5>Article<br><br><h5>Authors</h5><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Bayer, Till,equals">Bayer, Till</a><br><a href="https://repository.kaust.edu.sa/search?query=orcid.id:0000-0001-6673-016X&spc.sf=dc.date.issued&spc.sd=DESC">Aranda, Manuel</a> <a href="https://orcid.org/0000-0001-6673-016X" target="_blank"><img src="https://repository.kaust.edu.sa/server/api/core/bitstreams/82a625b4-ed4b-40c8-865a-d6a5225a26a4/content" width="16" height="16"/></a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Sunagawa, Shinichi,equals">Sunagawa, Shinichi</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Yum, Lauren,equals">Yum, Lauren</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Desalvo, Michael K,equals">Desalvo, Michael K</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Lindquist, Erika,equals">Lindquist, Erika</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Coffroth, Mary Alice,equals">Coffroth, Mary Alice</a><br><a href="https://repository.kaust.edu.sa/search?query=orcid.id:0000-0003-4555-3795&spc.sf=dc.date.issued&spc.sd=DESC">Voolstra, Christian R.</a> <a href="https://orcid.org/0000-0003-4555-3795" target="_blank"><img src="https://repository.kaust.edu.sa/server/api/core/bitstreams/82a625b4-ed4b-40c8-865a-d6a5225a26a4/content" width="16" height="16"/></a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Medina, Mónica,equals">Medina, Mónica</a><br><br><h5>KAUST Department</h5><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.department=Biological and Environmental Sciences and Engineering (BESE) Division,equals">Biological and Environmental Sciences and Engineering (BESE) Division</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.department=Marine Science Program,equals">Marine Science Program</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.department=Red Sea Research Center (RSRC),equals">Red Sea Research Center (RSRC)</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.department=Reef Genomics Lab,equals">Reef Genomics Lab</a><br><br><h5>Date</h5>2012-04-18</span>
display.details.right<span><h5>Abstract</h5>Dinoflagellates are unicellular algae that are ubiquitously abundant in aquatic environments. Species of the genus Symbiodinium form symbiotic relationships with reef-building corals and other marine invertebrates. Despite their ecologic importance, little is known about the genetics of dinoflagellates in general and Symbiodinium in particular. Here, we used 454 sequencing to generate transcriptome data from two Symbiodinium species from different clades (clade A and clade B). With more than 56,000 assembled sequences per species, these data represent the largest transcriptomic resource for dinoflagellates to date. Our results corroborate previous observations that dinoflagellates possess the complete nucleosome machinery. We found a complete set of core histones as well as several H3 variants and H2A.Z in one species. Furthermore, transcriptome analysis points toward a low number of transcription factors in Symbiodinium spp. that also differ in the distribution of DNA-binding domains relative to other eukaryotes. In particular the cold shock domain was predominant among transcription factors. Additionally, we found a high number of antioxidative genes in comparison to non-symbiotic but evolutionary related organisms. These findings might be of relevance in the context of the role that Symbiodinium spp. play as coral symbionts.Our data represent the most comprehensive dinoflagellate EST data set to date. This study provides a comprehensive resource to further analyze the genetic makeup, metabolic capacities, and gene repertoire of Symbiodinium and dinoflagellates. Overall, our findings indicate that Symbiodinium possesses some unique characteristics, in particular the transcriptional regulation in Symbiodinium may differ from the currently known mechanisms of eukaryotic gene regulation.<br><br><h5>Citation</h5>Bayer T, Aranda M, Sunagawa S, Yum LK, DeSalvo MK, et al. (2012) Symbiodinium Transcriptomes: Genome Insights into the Dinoflagellate Symbionts of Reef-Building Corals. PLoS ONE 7: e35269. doi:10.1371/journal.pone.0035269.<br><br><h5>Acknowledgements</h5>This study was supported through NSF (National Science Foundation) awards IOS 0644438 and IOS 0926906 (MM), OCE 0424994 (MAC), a KAUST AEA (King Abdullah University of Science and Technology) 3 Joint Collaborative Research award (CRV), and through a Collaborative Travel Fund to TB made by King Abdullah University of Science and Technology. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.<br><br><h5>Publisher</h5><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.publisher=Public Library of Science (PLoS),equals">Public Library of Science (PLoS)</a><br><br><h5>Journal</h5><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.journal=PLoS ONE,equals">PLoS ONE</a><br><br><h5>DOI</h5><a href="https://doi.org/10.1371/journal.pone.0035269">10.1371/journal.pone.0035269</a><br><br><h5>PubMed ID</h5><a href="https://www.ncbi.nlm.nih.gov/pubmed/22529998">22529998</a><br><br><h5>PubMed Central ID</h5><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329448">PMC3329448</a><br><br><h5>Additional Links</h5>http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0035269http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329448/</span>
kaust.personBayer, Till
kaust.personAranda, Manuel
kaust.personYum, Lauren
kaust.personVoolstra, Christian R.
orcid.authorBayer, Till
orcid.authorAranda, Manuel::0000-0001-6673-016X
orcid.authorSunagawa, Shinichi
orcid.authorYum, Lauren
orcid.authorDesalvo, Michael K
orcid.authorLindquist, Erika
orcid.authorCoffroth, Mary Alice
orcid.authorVoolstra, Christian R.::0000-0003-4555-3795
orcid.authorMedina, Mónica
orcid.id0000-0003-4555-3795
orcid.id0000-0001-6673-016X
refterms.dateFOA2018-06-13T14:32:41Z
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