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

Handle URI:
http://hdl.handle.net/10754/323516
Title:
Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals.
Authors:
Bayer, Till; Aranda, Manuel ( 0000-0001-6673-016X ) ; Sunagawa, Shinichi; Yum, Lauren K; Desalvo, Michael K; Lindquist, Erika; Coffroth, Mary Alice; Voolstra, Christian R. ( 0000-0003-4555-3795 ) ; Medina, Mónica
Abstract:
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.
KAUST Department:
Red Sea Research Center (RSRC)
Citation:
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.
Publisher:
Public Library of Science (PLoS)
Journal:
PLoS ONE
Issue Date:
18-Apr-2012
DOI:
10.1371/journal.pone.0035269
PubMed ID:
22529998
PubMed Central ID:
PMC3329448
Type:
Article
ISSN:
1932-6203
Sponsors:
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.
Additional Links:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0035269; http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329448/
Appears in Collections:
Articles; Red Sea Research Center (RSRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorBayer, Tillen
dc.contributor.authorAranda, Manuelen
dc.contributor.authorSunagawa, Shinichien
dc.contributor.authorYum, Lauren Ken
dc.contributor.authorDesalvo, Michael Ken
dc.contributor.authorLindquist, Erikaen
dc.contributor.authorCoffroth, Mary Aliceen
dc.contributor.authorVoolstra, Christian R.en
dc.contributor.authorMedina, Mónicaen
dc.date.accessioned2014-07-21T12:53:49Z-
dc.date.available2014-07-21T12:53:49Z-
dc.date.issued2012-04-18en
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.en
dc.identifier.issn1932-6203en
dc.identifier.pmid22529998en
dc.identifier.doi10.1371/journal.pone.0035269en
dc.identifier.urihttp://hdl.handle.net/10754/323516en
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.en
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.en
dc.language.isoenen
dc.publisherPublic Library of Science (PLoS)en
dc.relation.urlhttp://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0035269en
dc.relation.urlhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329448/en
dc.rightsArchived with thanks to PloS oneen
dc.subject.meshAnimalsen
dc.subject.meshAnthozoaen
dc.subject.meshBase Compositionen
dc.subject.meshCodonen
dc.subject.meshCoral Reefsen
dc.subject.meshDinoflagellidaen
dc.subject.meshExpressed Sequence Tagsen
dc.subject.meshGenomeen
dc.subject.meshHistonesen
dc.subject.meshMolecular Sequence Annotationen
dc.subject.meshNucleosomesen
dc.subject.meshOxidative Stressen
dc.subject.meshPhylogenyen
dc.subject.meshSymbiosisen
dc.subject.meshTranscription Factorsen
dc.subject.meshTranscriptomeen
dc.subject.meshAnimalsen
dc.subject.meshAnthozoaen
dc.subject.meshBase Compositionen
dc.subject.meshCodonen
dc.subject.meshCoral Reefsen
dc.subject.meshDinoflagellidaen
dc.subject.meshExpressed Sequence Tagsen
dc.subject.meshGenomeen
dc.subject.meshHistonesen
dc.subject.meshMolecular Sequence Annotationen
dc.subject.meshNucleosomesen
dc.subject.meshOxidative Stressen
dc.subject.meshPhylogenyen
dc.subject.meshSymbiosisen
dc.subject.meshTranscription Factorsen
dc.subject.meshTranscriptomeen
dc.titleSymbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals.en
dc.typeArticleen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.identifier.journalPLoS ONEen
dc.identifier.pmcidPMC3329448en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionEuropean Molecular Biology Laboratory, Heidelberg, Germanyen
dc.contributor.institutionDepartment of Anesthesia, UCSF School of Medicine, University of California San Francisco, San Francisco, CA, United Statesen
dc.contributor.institutionDepartment of Energy Joint Genome Institute, Walnut Creek, CA, United Statesen
dc.contributor.institutionGraduate Program in Evolution, Ecology and Behavior, Department of Geology, State University of New York at Buffalo, Buffalo, NY, United Statesen
dc.contributor.institutionSchool of Natural Sciences, University of California Merced, Merced, CA, United Statesen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorBayer, Tillen
kaust.authorAranda, Manuelen
kaust.authorYum, Laurenen
kaust.authorVoolstra, Christian R.en

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