development of genomic resources for the spotted seatrout Cynoscion nebulosus  

The spotted seatrout (Cynoscion nebulosus) is a popular recreational fish commonly found in coastal waters of the northern Gulf of Mexico and Southeastern United States. Aquaculture of this species is being developed along the gulf coast primarily for fisheries stock enhancement. Genetic management is an essential component of stocking programs and aims to minimize the negative genetic impacts of releases on wild populations. Knowledge of population structure and of the degree of genetic adaptations of local populations is essential in order to design appropriate management units for these programs. High-density genome scans allow in-depth characterization of genetic variation as needed to assess reliably population structure and gene flow and to identify genomic regions affected by selection and local adaptation. These genome scans can now be produced using cost-effective approaches based on next generation sequencing but their exploitation is greatly enhanced when a reference genome is available for the species of interest. The objective of this work is to initiate the development of a reference genome for spotted seatrout by generating a draft sequence assembly and a linkage map. These tools will be applied to monitor and manage genetic resources of captive and wild spotted seatrout.

The DNA of one outbred spotted seatrout specimen was sequenced using the PAC-BIO SMRT technology (7 SMRT cells) and the Illumina®HiSeq2500 platform (v4 paired-end sequencing, one sequencing lane). A total of 402M paired-end Illumina raw reads with 92% bases showing quality scores greater than 30 were obtained. Hybrid assembly of the datasets obtained using the two platforms is currently in progress. The assembly will be used as a reference to map Restriction Site Associated DNA (RAD) Tags and characterize associated Single Nucleotide Polymorphisms (SNPs). SNPs discovery and mapping via RAD-sequencing of the DNA from parents and offspring from one full-sib outbred family is in progress. The family was produced by fertilizing in vitro the eggs of one wild-caught female with the sperm of one wild-caught male on June 2^nd 2015. Progeny were sampled at 14 days post hatch (n = 132) and then at 195 days post hatch (n = 105). To date, libraries generated using the double-digest RAD-sequencing protocol for 79 of the progeny sampled was sequenced in multiplex on one lane of the Illumina®HiSeq2500 platform producing an average 2.3 M filtered reads per individual. Sequencing of the remaining 158 offspring is in progress. The SNPs identified in the mapping family will be used to construct a high-resolution linkage map, which will facilitate orienting and ordering scaffolds of the draft genome assembly, studying population structure and gene flow in particular mapping genomic regions impacted by natural selection, localizing genes impacting phenotypic traits in spotted seatrout, and assessing effective population size and demographic parameters of wild and captive stocks.