Symbiodinium microadriaticum is a dinoflagellate that lives in a mutualistic relationship with the coral Stylophora pistillata in the Red Sea. Symbiodinium microadriaticum is divided into several clades and the A1 clade of Symbiodinium microadriaticum lives in shallow waters and is resilient to thermal stress. The association between Symbiodinium microadriaticum A1 and Stylophora pistillata enables Stylophora pistillata to tolerate the rise in the sea surface temperature caused by global warming and climate change. Here, the first completely sequenced dinoflagellate genome is explored to answer two questions: The first question is whether self-extending symbiosis has a role in the ability of Symbiodinium microadriaticum A1 to adapt to thermal stress and other environmental perturbations. The second question is how endosymbiotic / horizontal gene transfer (E/HGT) affects dinoflagellates and the Tree of life (TOL). Using a large scale comparative and phylogenomic analysis, here I am addressing the extent of horizontal and endosymbiotic gene transfer in Symbiodinium microadriaticum A1 and in dinoflagellates in general. Two model organisms that do not live in mutualistic relationships with other organisms were used as controls for Stylophora pistillata and Symbiodinium microadriaticum. These two organisms are Nematostella vectensis and Alexandrium tamarense, respectively. Furthermore, because the monophyly of the chromalveolate, the eukaryotic supergroup the dinoflagellates belong to, is in controversy, this key relationship in the Tree of life is investigated in the second part of the thesis. The sequencing of the genome of Symbiodinium microadriaticum A1 (CCMP2467) provides a great opportunity to conduct a genome-wide analysis of the phylogenetic affiliation on a gene-by-gene basis. Trees that show monophyly of the stramenopile-alveolate-Rhizaria (SAR) clade were sorted out and the positions of cryptophytes and haptophytes in relation to the SAR clade were manually reviewed. In addition, trees were further sorted to address which clades are more highly involved in E/HGT to dinoflagellates and how E/HGT from these clades affects dinoflagellates. Results showed that most genes obtained from other unicellular eukaryotes encoded proteins that take part in: response to oxidative stress, signal transduction, cell adhesion, and arginine and proline metabolic pathway, besides other proteins that take part in other metabolic pathways. On the other hand, HGT genes from bacteria encoded proteins involved in signal transduction pathways such as the MepB permease, cyclic nucleotide binding domain. In addition, genes transferred to/from Symbiodiniummicroadriaticum A1and either Acropora digitifera or Stylophora pistillata mainly encoded transporters and proteins involved in cell adhesion and in peroxisome synthesis. Moreover, results showed that enzymes involved in the biosynthesis of essential amino Acids such as L-glutamate, glycine and threonine were missing from Stylophora pistillata although they are available, as expected, in Nematostella vectensis and other Metazoa species. Furthermore, contradicting the long-accepted chromalveolate hypothesis and the well-established monophyly of chromalveolates, my results suggest that cryptophytes and haptophytes are not in monophyly with the rest of the chromalveolate clade in most of the analyzed trees. Results also showed that E/HGT from bacteria to dinoflagellates transferred several methyltransferase genes, besides the RuBisCO encoding gene from proteobacteia and the Histone acetyltransferase HPA2 encoding gene that was also transferred from bacteria. To sum up, results identified the proteins that are putatively involved in adapting to environmental stress and where they have evolved from. Further studies can be done to understand their mechanisms of action and hence investigate if their actions can be enhanced to prevent the loss of the symbiont-host mutualistic relationship and to prevent coral bleaching. Also, this thesis challenges the monophyly of the chromalveolate clade and the position of cryptophytes and haptophytes in relation to this clade. .


School of Sciences and Engineering

Degree Name

MS in Biotechnology

First Advisor

Moustafa, Ahmed

Committee Member 1

ElGogary, Sawsan

Committee Member 2

Ferreira, Ari Jose Scattone

Committee Member 3

Voolstra, Christian

Document Type



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