Multi-Tissue Transcriptome Profiling of North American Derived Atlantic Salmon

Overview

Journal Front Genet

Date 2018 Oct 2

PMID 30271423

Citations 6

Authors

Amin R Mohamed

Harry King

Bradley Evans

Antonio Reverter

James W Kijas

Affiliations

Soon will be listed here.

Abstract

The availability of a reference genome assembly for Atlantic salmon, , 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 and families were identified for pituitary gland, and families for brain, , and for ovary and -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.

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