Transcriptional Profiling of Young-of-the-Year Winter Flounder in Long Island Bays

Inshore winter flounder (Pseudopleuronectes americanus) populations have reached record low numbers in recent years, and recruitment into the fishery appears to be limited by survival of post-settlement juvenile populations.  As part of a larger project examining factors influencing survival of young-of–the-year (YOY) winter flounder in Long Island bays, we are examining    differential gene expression between populations.  Pooled cDNA libraries were created from livers obtained from YOY flounder collected at two sites (Shinnecock and Moriches Bays), and paired-end Illumina sequencing performed to identify differentially expressed genes between these populations.  Over 180,000 contigs (>100 bp) were found with a mean size of 579 bp, and differential analysis was performed using DESeq. Reads were mapped back to the assembled transcripts using tophat and counts coverage for each transcript. There were 253 differentially expressed transcripts (57% with functional annotation, all from teleost genomes), of which 180 were significantly overexpressed at Moriches as compared to Shinnecock.  A high proportion of genes involved in wound healing, contaminant and sugar/carbohydrate metabolism were observed in these differential groupings.  Select genes from these groups will be further evaluated for use as biomarkers in individual fish across six different Long Island bays.