The Genome of Aiptasia and the Role of MicroRNAs in Cnidarian-Dinoflagellate Endosymbiosis

Handle URI:
http://hdl.handle.net/10754/595368
Title:
The Genome of Aiptasia and the Role of MicroRNAs in Cnidarian-Dinoflagellate Endosymbiosis
Authors:
Baumgarten, Sebastian ( 0000-0003-2646-7699 )
Abstract:
Coral reefs form marine-biodiversity hotspots of enormous ecological, economic, and aesthetic importance that rely energetically on a functional symbiosis between the coral animal and a photosynthetic alga. The ongoing decline of corals worldwide due to anthropogenic influences heightens the need for an experimentally tractable model system to elucidate the molecular and cellular biology underlying the symbiosis and its susceptibility or resilience to stress. The small sea anemone Aiptasia is such a model organism and the main aims of this dissertation were 1) to assemble and analyze its genome as a foundational resource for research in this area and 2) to investigate the role of miRNAs in modulating gene expression during the onset and maintenance of symbiosis. The genome analysis has revealed numerous features of interest in relation to the symbiotic lifestyle, including the evolution of transposable elements and taxonomically restricted genes, linkage of host and symbiont metabolism pathways, a novel family of putative pattern-recognition receptors that might function in host-microbe interactions and evidence for horizontal gene transfer within the animal-alga pair as well as with the associated prokaryotic microbiome. The new genomic resource was used to annotate the Aiptasia miRNA repertoire to illuminate the role of post-transcriptional regulatory mechanisms in regulating endosymbiosis. Aiptasia encodes a majority of species-specific miRNAs and first evidence is presented that even evolutionary conserved miRNAs are undergoing recent differentiations within the Aiptasia genome. The analysis of miRNA expression between different states of Symbiodinium infection further revealed that species-specific and conserved miRNAs are symbiotically regulated. In order to detect functional miRNA-mRNA interactions and to investigate the downstream effects of such miRNA action, a protocol for cross-linking immunoprecipitations of Argonaute, the central protein of the miRNA-induced silencing complex, was developed. This method identified binding sites of miRNAs on a transcriptome-wide scale and revealed target genes of symbiotically regulated miRNAs that were identified previously to be involved in the symbiosis. In summary, this dissertation provides novel insights into miRNA-mediated post-transcriptional modulation of the host transcriptome and by presenting a critically needed genomic resource, lays the foundation for the continued development of Aiptasia as a model for coral symbiosis.
Advisors:
Voolstra, Christian R. ( 0000-0003-4555-3795 )
Committee Member:
Aranda, Manuel ( 0000-0001-6673-016X ) ; Pain, Arnab ( 0000-0002-1755-2819 ) ; Pringle, John R.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Marine Science Program
Program:
Marine Science
Issue Date:
Feb-2016
Type:
Dissertation
Appears in Collections:
Marine Science Program; Dissertations; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.advisorVoolstra, Christian R.en
dc.contributor.authorBaumgarten, Sebastianen
dc.date.accessioned2016-02-01T12:31:31Zen
dc.date.available2016-02-01T12:31:31Zen
dc.date.issued2016-02en
dc.identifier.urihttp://hdl.handle.net/10754/595368en
dc.description.abstractCoral reefs form marine-biodiversity hotspots of enormous ecological, economic, and aesthetic importance that rely energetically on a functional symbiosis between the coral animal and a photosynthetic alga. The ongoing decline of corals worldwide due to anthropogenic influences heightens the need for an experimentally tractable model system to elucidate the molecular and cellular biology underlying the symbiosis and its susceptibility or resilience to stress. The small sea anemone Aiptasia is such a model organism and the main aims of this dissertation were 1) to assemble and analyze its genome as a foundational resource for research in this area and 2) to investigate the role of miRNAs in modulating gene expression during the onset and maintenance of symbiosis. The genome analysis has revealed numerous features of interest in relation to the symbiotic lifestyle, including the evolution of transposable elements and taxonomically restricted genes, linkage of host and symbiont metabolism pathways, a novel family of putative pattern-recognition receptors that might function in host-microbe interactions and evidence for horizontal gene transfer within the animal-alga pair as well as with the associated prokaryotic microbiome. The new genomic resource was used to annotate the Aiptasia miRNA repertoire to illuminate the role of post-transcriptional regulatory mechanisms in regulating endosymbiosis. Aiptasia encodes a majority of species-specific miRNAs and first evidence is presented that even evolutionary conserved miRNAs are undergoing recent differentiations within the Aiptasia genome. The analysis of miRNA expression between different states of Symbiodinium infection further revealed that species-specific and conserved miRNAs are symbiotically regulated. In order to detect functional miRNA-mRNA interactions and to investigate the downstream effects of such miRNA action, a protocol for cross-linking immunoprecipitations of Argonaute, the central protein of the miRNA-induced silencing complex, was developed. This method identified binding sites of miRNAs on a transcriptome-wide scale and revealed target genes of symbiotically regulated miRNAs that were identified previously to be involved in the symbiosis. In summary, this dissertation provides novel insights into miRNA-mediated post-transcriptional modulation of the host transcriptome and by presenting a critically needed genomic resource, lays the foundation for the continued development of Aiptasia as a model for coral symbiosis.en
dc.language.isoenen
dc.subjectAiptasiaen
dc.subjectGenomeen
dc.subjectDinoflagellateen
dc.subjectmiRNAen
dc.subjectEndosymbiosisen
dc.subjectGene regulationen
dc.titleThe Genome of Aiptasia and the Role of MicroRNAs in Cnidarian-Dinoflagellate Endosymbiosisen
dc.typeDissertationen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentMarine Science Programen
thesis.degree.grantorKing Abdullah University of Science and Technologyen_GB
dc.contributor.committeememberAranda, Manuelen
dc.contributor.committeememberPain, Arnaben
dc.contributor.committeememberPringle, John R.en
thesis.degree.disciplineMarine Scienceen
thesis.degree.nameDoctor of Philosophyen
dc.person.id121376en
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