Transcriptomics of coral-algal interactions: novel insights into the establishment of symbiosis

Mohamed, Amin Roushdy (2016) Transcriptomics of coral-algal interactions: novel insights into the establishment of symbiosis. PhD thesis, James Cook University.

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Abstract

Reef-building corals are considered as meta-organisms where the coral animal lives in symbiosis with a wide array of microorganisms. While mutualistic association between corals and Symbiodinium is crucial for the functioning and success of the coral reef ecosystems, surprisingly little is currently known about its molecular basis and this is especially true of the events leading to establishment of the relationship. A morphologically similar alga to Symbiodinium was discovered in Australian corals and has been identified as Chromera. The discovery of Chromera is very significant as it holds a unique position in evolution, between the photosynthetic dinoflagellates and the parasitic apicomplexans. The nature of the association between Chromera and corals is currently unclear. In this thesis, I used high throughput next generation sequencing technology (Illumina RNA-Seq) to explore the molecular mechanisms underlying establishment of coral-algal symbiosis between coral larvae and a competent strain of Symbiodinium. I examined also the nature of the poorly understood relationship between corals and the newly described photosynthetic apicomplexan alga Chromera using RNA-Seq. Finally, I present a functional genomic resource (transcriptome) for a Chromera strain isolated from a Great Barrier Reef coral, and use a comparative transcriptomic approach to examine sharing of functions and pathways among Chromera, Symbiodinium kawagutii and Plasmodium falciparum.

To better understand the molecular mechanisms underlying the initial coral- Symbiodinium interactions, Acropora digitifera larvae were inoculated with a competent Symbiodinium strain and the responses of the coral whole transcriptome were investigated 4, 12 and 48 h post-Symbiodinium infection using RNA-Seq. Although previous studies (based on use of cDNA microarrays) did not detect host signals during establishment of coral-Symbiodinium symbiosis, using the RNA-Seq approach, transient changes in gene expression, involving 1073 differentially expressed genes (DEGs), were observed early in the Symbiodinium uptake (infection) process. This is the first report of differential expression of a significant number of genes during Symbiodinium uptake by corals. The list of DEGs allowed the construction of a model for the molecular mechanisms that operate during onset and establishment of coral- Symbiodinium symbiosis, including suppression of host immunity, protein synthesis and oxidative metabolism. More importantly, the data provided support for the formation of the symbiosome as an arrested early phagosome, a mechanism thought also to apply to the process by which Symbiodinium colonises some sea anemones.

To determine the nature of the relationship between corals and Chromera "the closest relative to apicomplexan parasites", A. digitifera larvae were inoculated with Chromera CCMP2878 strain and the coral whole transcriptome responses were investigated at 4, 12 and 48 h post-Chromera infection using RNA-Seq. Stress, disease and immune challenge (in corals) have distinct transcriptomic signatures as does the process of infection by a competent Symbiodinium strain. Analysis of the transcriptomic impact of Chromera infection shed some light on the nature of the coral-Chromera association and provided novel insights into host-parasite/pathogen interactions. Based on the transcriptomic data, I suggest that the coral-Chromera relationship may be parasitic, thus the assumption that Chromera is a coral symbiont requires re-evaluation.

In order to provide a functional genomic resource for a chromerid alga and explore its gene catalogue, a de novo transcriptome assembly was generated for a Chromera strain isolated from Montipora digitata on the GBR and the obtained contigs were annotated. This novel dataset was compared with coding sequence data for another Chromera strain (isolated from different host and geographic location) and 664 orthologous gene pairs were identified. The overwhelming majority of these orthologs were under purifying selection, only one pair being under positive selection; this gene encoded a homolog of the human tetratricopeptide TTC21B. Overall KEGG pathway distributions were very similar between Chromera and Symbiodinium the largest proportion of genes in both cases being assigned to metabolism. Comparing KEGG pathways involved in glycan biosynthesis and transcription machinery, revealed the genetic uniqueness of the symbiotic dinoflagellate Symbiodinium.

In conclusion, coral-algal symbioses are the basis for coral reef ecosystems thus understanding these relationships at a molecular level is very important especially for reef management and fighting against coral bleaching. The work presented in this thesis provides novel insights into the molecular events occurring during onset of coral- Symbiodinium symbiosis that enabled better mechanistic understanding of algal symbioses in corals. Knowledge derived from the thesis contributes to better understanding of the symbiont infection process and that will help in coral reef management especially when engineering coral symbioses towards increased coral thermotolerance/resilience and better understanding how symbiosis breakdown (coral bleaching) occurs, thus understanding the mechanisms of coral symbiosis is a step forward in order to combat coral bleaching. In addition, the thesis showed that coral responses to Chromera have similarities to the responses of vertebrates to parasites and provided insights into host-pathogen/parasite interactions that will enhance our understanding how host cells defend them selves against infectious organisms. Moreover, the thesis provided a genomic resource for a Chromera strain that can be used as a reference for large-scale gene expression and comparative analyses to better understand the biology of these newly discovered algae and suggested the potential use of Chromera as a model organism in developing anti-malarial drugs.

Item ID: 49900
Item Type: Thesis (PhD)
Keywords: Acropora, Chromera, coral-algal symbiosis, dinoflagellates, gene expression, host-parasite interactions, next generation sequencing, nucleotide sequence, parasites, Plasmodium, RNA-Seq, Symbiodinium, symbiosome, transcriptome, transcriptomics
Additional Information:

Publications arising from this thesis are available from the Related URLs field. The publications are:

Chapter 2: Mohamed, A.R., Cumbo, V., Harii, S., Shinzato, C., Chan, C.X., Ragan, M.A., Bourne, D.G., Willis, B.L., Ball, E.E., Satoh, N., and Miller, D.J. (2016) The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome. Molecular Ecology, 25 (13). pp. 3127-3141.

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Date Deposited: 18 Aug 2017 02:54
FoR Codes: 06 BIOLOGICAL SCIENCES > 0608 Zoology > 060802 Animal Cell and Molecular Biology @ 40%
06 BIOLOGICAL SCIENCES > 0604 Genetics > 060405 Gene Expression (incl Microarray and other genome-wide approaches) @ 40%
06 BIOLOGICAL SCIENCES > 0603 Evolutionary Biology > 060307 Host-Parasite Interactions @ 20%
SEO Codes: 97 EXPANDING KNOWLEDGE > 970106 Expanding Knowledge in the Biological Sciences @ 100%
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