In order to identify potential growth markers for monitoring growth patterns in Pacific halibut, the IPHC has embarked on transcriptome sequencing of growth-relevant tissues, namely skeletal muscle (white and red) and liver. Growth transcriptome sequencing involves the generation of a large collection of sequences representing the transcripts (expressed genes) in a particular or set of tissues that participate in growth responses in Pacific halibut. For the identification of potential growth markers, the IPHC set out to sequence expressed genes in white and red skeletal muscle as well as in liver of adult Pacific halibut by RNA sequencing. Total RNA purified from each of the three growth-related tissues was sequenced separately using an Illumina HiSeq 2500 platform at the 2 X 100 base pairs (bp) paired end mode. Coverage per tissue was set at 30 million reads. Reads were assembled de novo into contigs using the Trinity software. Contigs were then annotated using an iterative blast strategy by performing, as a first step, blastx against the zebrafish (Danio rerio) protein database. As a second step, non-annotated transcripts were then subjected to blast against the vertebrate Uniprot protein database. The resulting contig N50 metric for white skeletal muscle, red skeletal muscle and liver were 1,198, 1,096 and 2,322 bp, respectively. The resulting percentage of annotated contigs for white skeletal muscle, red skeletal muscle and liver were 41.7, 38.6, 35.5%, respectively. A set of genes expressed in white skeletal muscle that change their expression levels in response to temperature-induced growth manipulations under laboratory conditions have been selected as potential molecular growth markers. Real time quantitative PCR assays have been developed for each of these markers to test their utility in describing the effects of size and diet availability in wild Pacific halibut. This set of molecular growth markers could be used to investigate temporal and/or spatial variation of growth patterns in Pacific halibut.
