ESTABLISHING A MODEL: AMPHIDINIUM CARTERAE AS A TEMPLATE FOR DINOFLAGELLATE GENOMICS & EXPRESSION

Abstract

Dinoflagellates are globally important protists that underpin marine food webs, drive coral symbioses, and generate harmful algal blooms, yet their unique genomic architecture has hindered their adoption as tractable model systems. This dissertation advances Amphidinium carterae as a reference dinoflagellate by combining ecological, molecular, and genomic approaches to address key barriers in the field.First, the long-term laboratory microbiome of A. carterae was characterized, assembling 15 complete bacterial genomes with long-read sequencing. These analyses revealed antibiotic-resistant taxa, metabolic pathways linked to nutrient cycling, and potential interactions with host physiology, underscoring the importance of defining the microbiome when developing experimental models. Next, a functional genomics tool was established by delivering antisense morpholinos targeting the translation initiation factor eIF4E-1a. This knockdown system reduced protein abundance without severely impacting viability, providing proof-of-principle for genetic manipulation in dinoflagellates. The dinoflagellate approach to transcription was described using synchronized cultures, integrating Nanopore direct RNA sequencing, ribosome profiling, and translation assays over a diel cycle. Results showed that gene regulation is dominated by post-transcriptional mechanisms, including dynamic translational control and pervasive RNA modifications (m⁶A, m⁵C, and pseudouridine). Distinct functional enrichments were observed across Growth, Synthesis, and Division phases, highlighting translational orchestration as the primary driver of cellular rhythms. Finally, a 1.25 Gb long-read genome assembly for A. carterae was produced with curated annotation of tandemly duplicated genes, nested gene structures, and extensive repetitive regions. Tandem gene arrays were found to strongly correlate with transcript abundance, suggesting a dosage-based regulatory strategy in lieu of conventional transcriptional control. Across different genome regions there were strong differences in expression of different transcripts. Comparative analyses confirmed these features as conserved across dinoflagellates, while also highlighting the prevalence of lineage-specific “dark genes” with unknown function. Together, these studies expand genomic resources, functional tools, and expression analyses for A. carterae, establishing it as a tractable system for probing dinoflagellate biology. More broadly, they illuminate alternative strategies of genome organization and regulation in eukaryotes, providing a foundation for future work on dinoflagellate ecology, evolution, and the mechanisms underlying their environmental impacts.