AUTHOR=Mohamed Amin R. , King Harry , Evans Bradley , Reverter Antonio , Kijas James W. 

TITLE=Multi-Tissue Transcriptome Profiling of North American Derived Atlantic Salmon

JOURNAL=Frontiers in Genetics

VOLUME=9

YEAR=2018

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2018.00369

DOI=10.3389/fgene.2018.00369

ISSN=1664-8021

ABSTRACT=<p>The availability of a reference genome assembly for Atlantic salmon, <italic>Salmo salar</italic>, SNP genotyping platforms and low cost sequencing are enhancing the understanding of both life history and production-related traits in this important commercial species. We collected and analyzed transcriptomes from selected tissues of Atlantic salmon to inform future functional and comparative genomics studies. Messenger RNA (mRNA) was isolated from pituitary gland, brain, ovary, and liver before Illumina sequencing produced a total of 640 million 150-bp paired-end reads. Following read mapping, feature counting, and normalization, cluster analysis identified genes highly expressed in a tissue-specific manner. We identified a cluster of 508 tissue specific genes for pituitary gland, 3395 for brain, 2939 for ovary, and 539 for liver. Functional profiling identified gene clusters describing the unique functions of each tissue. Moreover, highly-expressed transcription factors (TFs) present in each tissue-specific gene cluster were identified. TFs belonging to <italic>homeobox</italic> and <italic>bhlh</italic> families were identified for pituitary gland, <italic>pou</italic> and <italic>zf-c2h2</italic> families for brain, <italic>arid</italic>, and <italic>zf-c2h2</italic> for ovary and <italic>rxr</italic>-like family for liver. The data and analysis presented are relevant to the emerging Functional Annotation of All Salmonid Genomes (FAASG) initiative that is seeking to develop a detailed understanding of both salmonid evolution and the genomic elements that drive gene expression and regulation.</p>