Bioinformatics Approach to Determining Transcriptional and Translational Responses to Heat Stress in the Florida Red Tide Dinoflagellate <i> Karenia brevis </i>

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Fridey, Kelly Alayne
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The dinoflagellate <i>Karenia brevis</i> produces nearly annual harmful algal blooms in the Gulf of Mexico that can have deleterious effects on marine communities and can cause neurotoxic shellfish poisoning in humans. For over 60 years, the mechanisms of bloom formation and termination have been studied, but investigations of physiological changes at the molecular level in response to dynamic oceanographic conditions are still lacking. Previous studies in <i>K. brevis</i> have contributed to the current view that dinoflagellates regulate their gene expression post- transcriptionally, but the extent of this control is unknown. In the current study, RNA sequencing was used to determine both changes in transcript abundance and transcripts that are actively translated after exposure to a 6°C heat shock. Since there is not yet a consensus on what bioinformatic tools are the "best", <i>de novo</i> transcriptome assembly tools and algorithms to determine differential expression (DE) were first compared. The established pipeline was then utilized to investigate regulation at the level of transcription and translation and confirmed with RT qPCR. Little change in transcript abundance (3.5%) was seen following short term heat shock. Under the same conditions, 7.4% of transcripts changed in translation. The up-regulation of transcripts in with regulatory functions, including heat shock proteins, translation initiation factors, as well as some novel genes like death associated protein (DSP) and the dinoflagellate viral nucleoprotein (DVNP) suggest their involvement in the recovery from heat shock in <i>K. brevis.</i>
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