Transcriptional profiles of heat stress response in Yellowtail Kingfish

Predicting the capacity of organisms to adjust to the pressures posed by climate change is a topic of much current research effort, particularly for species we harvest. To explore one measure of capacity to adapt, the physiological compensations in response to heat stress as might be experienced in a marine heatwave, we exposed Yellowtail Kingfish (Seriola lalandi) to sublethal heat stress, and used the transcriptome in gill and muscle, benchmarked against heat shock proteins and oxidative stress indicators, to characterise the acute heat stress response (6 hours after the initiation of stress), and the physiological compensation to that response (24 and 72 hours after the initiation of stress). RNA was extracted from each tissue and sequenced using Illumina NextSeq protocols. A de novo assembly was created using the Trinity pipeline, reads were mapped to the assembly using the Salmon algorithm, and differential expression calculated using DESeq. SuperTranscripts were constructed using the Trinity pipeline, and differential exon usage was measured using DexSeq. The transcriptome was operationally annotated by using a Diamond search, both against the nr database and against the closely related Yellowtail Amberjack (Serioloa lalandi dorsalis), for which an Ensembl genome is available. The heat stress experiments induced elevations in heat shock proteins but not protein thiols, demonstrating the sublethal stress level. The initial response (6 hours) to heat stress included the expected cellular stress response. Exposure of more than 12 hours led to altered transcriptomic patterns for protein degradation, membrane transporters, and primary metabolism. In the muscle, numerous transcripts with mitochondrial function had altered abundance. There was a profound change to the regulation of transcription, as well as numerous transcripts with differential exon usage, suggesting that this may be a mechanism for conferring physiological resilience to heat stress. These results demonstrate the processes involved in acclimation to heat stress in this species. Future work should investigate the role of genome regulation, and alternative splicing in particular, on conferring resilience to temperature changes.