Transcriptome analysis of Sparidentex hasta larvae exposed to water-accommodated fraction of Kuwait crude oil.

Anthropogenic activities have been shown to significantly affect marine life. Water pollution and oil spills are particularly deleterious to the fish population, especially during their larval stage. In this study, Sobaity-sea bream Sparidentex hasta (Valenciennes, 1830) larvae were exposed to serial dilutions of water-accommodated fraction of Kuwait crude oil (KCO-WAF) for varying durations (3, 6, 24, 48, 72 or 96 h) in acute exposure regime. Gene expression was assessed using RNA sequencing and validated through RT-qPCR. The RNA sequencing data were aligned to the sequenced genome, and differentially expressed genes were identified in response to treatment with or without KCO-WAF at various exposure times. The highest number of differentially expressed genes was observed at the early time point of 6 h of post-exposure to KCO-WAF. The lowest number of differentially expressed genes were noticed at 96 h of treatment indicating early response of the larvae to KCO-WAF contaminant. The acquired information on the differentially expressed genes was then used for functional and pathway analysis. More than 90% of the differentially expressed genes had a significant BLAST match, with the two most common matching species being Acanthopagrus latus and Sparus aurata. Approximately 65% of the differentially expressed genes had Gene Ontology annotations, whereas > 35% of the genes had KEGG pathway annotations. The differentially expressed genes were found to be enriched for various signaling pathways (e.g., MAPK, cAMP, PI3K-Akt) and nervous system-related pathways (e.g., neurodegeneration, axon guidance, glutamatergic synapse, GABAergic synapse). Early exposure modulated the signaling pathways, while KCO-WAF exposure of larvae for a longer duration affected the neurodegenerative/nervous system-related pathways. RT-qPCR analysis confirmed the differential expression of genes at each time point. These findings provide insights into the underlying molecular mechanisms of the deleterious effects of acute exposure to oil pollution-on marine fish populations, particularly at the early larval stage of Sparidentex hasta.

De-novo genome assembly and annotation of sobaity seabream Sparidentex hasta.

Sparidentex hasta (Valenciennes, 1830) of the Sparidae family, is an economically important fish species. However, the genomic studies on S. hasta are limited due to the absence of its complete genome. The goal of the current study was to sequence, assemble, and annotate the genome of S. hasta that will fuel further research related to this seabream. The assembled draft genome of S. hasta was 686 Mb with an N50 of 80 Kb. The draft genome contained approximately 22% repeats, and 41,201 genes coding for 44,555 transcripts. Furthermore, the assessment of the assembly completeness was estimated based on the detection of ∼93% BUSCOs at the protein level and alignment of >99% of the filtered reads to the assembled genome. Around 68% of the predicted proteins (n = 30,545) had significant BLAST matches, and 30,473 and 13,244 sequences were mapped to Gene Ontology annotations and different enzyme classes, respectively. The comparative genomics analysis indicated S. hasta to be closely related to Acanthopagrus latus. The current assembly provides a solid foundation for future population and conservation studies of S. hasta as well as for investigations of environmental adaptation in Sparidae family of fishes. Value of the Data: This draft genome of S. hasta would be very applicable for molecular characterization, gene expression studies, and to address various problems associated with pathogen-associated immune response, climate adaptability, and comparative genomics. The accessibility of the draft genome sequence would be useful in understanding the pathways and functions at the molecular level, which may further help in improving the economic value and their conservation.