Generation of Genomic Resources for Atlantic Sturgeon Using Next Generation Sequencing

Caviar producing sturgeon is a high-value species and over the past decade sturgeon aquaculture has grown. However, market demand and growth may have negative impacts on production due to the need for higher throughput, which can strain the physiological limits of the fish and lead to greater susceptibility to pathogens and external stressors. A broader knowledge of sturgeon biology and genetics will be required to maximize culture and to fulfill the market demand for sturgeon products. Unfortunately, there is a paucity of genomic information available for sturgeon species, and thus the generation of these resources may help to identify high-quality broodstock and facilitate optimization of culture conditions. RNA-seq was used to identify Atlantic sturgeon (Acipenser oxyrhynchus) genes that respond to lipopolysaccharide (LPS) stimulation. A reference transcriptome assembly for Atlantic sturgeon spleen was using over 750,000,000 pair-end Illumina reads. The reference assembly was comprised of ~ 400,000 cDNAs, and ~ 70% of the 750,000,000 pair-end reads re-mapped properly to the reference. This transcriptome was used for the identification of sturgeon LPS-responsive genes such as interleukin-8, cathelicidin, major histocompatibility complex (MHC) I and II. In addition, existing pipelines were used to identify 3 million single-nucleotide polymorphisms (SNPs) for this emerging aquaculture species. Due to the duplicated nature of the Atlantic sturgeon, following read mapping, consensus calling and SNP identification, we used an in-house custom filtering algorithm and reduced the SNPs to a collection of ~ 50,000 high-quality markers. Further studies are under way to validate the LPS-responsive genes and SNPs.