RNA-seq analysis of the Atlantic sturgeon gill response to the "sturgeon-louse" (Dichelesthium oblongum)  

Atlantic sturgeon (Acipenser Oxyrhynchus) is one of the caviar producing sturgeon species native to North America. Due to declining natural stocks of this species and other sturgeons (25/27 acipenserids are endangered), aquaculture has emerged as a promising alternative to supply the market with caviar without further harvest pressure on natural stocks. Intensive culture operations can strain the physiological limits of fish species we have little knowledge on and lead to greater susceptibility to pathogens and external stressors. Clearly, a more comprehensive knowledge of sturgeon biology and genetics will be required in order to maximize culture and to fulfill the market demand for sturgeon products including caviarThe gill is an important immune tissue as it serves as an external barrier to pathogens/parasites and an important compartment of mucosal immunity. However, there is an unclear role for the gill as an immune tissue, especially in non-model species. Therefore, the goal of this study was to study the response of the sturgeon gill transcriptome to infection with the sturgeon-louse in order to generate a better understanding of the role of the gill as an immune tissue.

The Acipenserid family represents a challenge for genomic studies given the highly duplicated nature and size of the genome. To overcome this challenge, a large number of reads (~1 billion) were used in a custom assembly pipeline using digital normalization and multiple state of the art assemblers. Pair-end stranded Illumina libraries where produced from gill mRNA of fish infected with different louse life-stages and sequenced with the Illumina HiSeq 2000. A reference transcriptome assembly for Atlantic sturgeon was generated, to which nearly 70% of the pair-end reads can be properly mapped. Analysis of differentially expressed transcripts using edgeR and DESeq has enabled identification of sturgeon lice-responsive transcripts such as MH class I/II, IRF7, IL17/18, TNFaP, MCSF, Calmodulin. These transcripts indicate that there is both an inflammatory and antigen processing response in the gill and also a potential conserved role of Calmodulin in the response to parasitic copepods. Taken together, these data contribute to the characterization of the gills immunological role and the first line of defense against parasites in Atlantic sturgeon.