De novo assembly and transcriptome analysis of Atlantic salmon macrophage/dendritic-like TO cells following type I IFN treatment and Salmonid alphavirus subtype-3 infection

BMC Genomics
Cheng XuHetron Mweemba Munang'andu

Abstract

Interferons (IFN) are cytokines secreted by vertebrate cells involved in activation of signaling pathways that direct the synthesis of antiviral genes. To gain a global understanding of antiviral genes induced by type I IFNs in salmonids, we used RNA-seq to characterize the transcriptomic changes induced by type I IFN treatment and salmon alphavirus subtype 3 (SAV-3) infection in TO-cells, a macrophage/dendritic like cell-line derived from Atlantic salmon (Salmo salar L) head kidney leukocytes. More than 23 million reads generated by RNA-seq were de novo assembled into 58098 unigenes used to generate a total of 3149 and 23289 differentially expressed genes (DEGs) from TO-cells exposed to type I IFN treatment and SAV-3 infection, respectively. Although the DEGs were classified into genes associated with biological processes, cellular components and molecular function based on gene ontology classification, transcriptomic changes reported here show upregulation of genes belonging to the canonical type I IFN signaling pathways together with a broad spectrum of antiviral genes that block virus replication in host cells. In addition, the transcriptome shows a profile of genes associated with apoptosis as well as genes that activate a...Continue Reading

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Citations

Sep 18, 2015·Frontiers in Immunology·Hetron Mweemba Munang'anduØystein Evensen
Jun 13, 2015·Journal of Immunology Research·Hetron Mweemba Munang'andu, Øystein Evensen
May 28, 2016·Biology·Jun Zou, Christopher J Secombes
Nov 8, 2016·Developmental and Comparative Immunology·Mehrdad SobhkhezJorunn B Jørgensen
Apr 5, 2018·International Journal of Molecular Sciences·Hetron Mweemba Munang'anduLior David
Oct 2, 2019·European Journal of Cancer Care·Jon Arne SandmaelAnne-Sofie Helvik
Apr 7, 2017·Frontiers in Microbiology·Hetron M Munang'anduØystein Evensen
Nov 12, 2015·Frontiers in Immunology·Hetron Mweemba Munang'anduØystein Evensen
Feb 22, 2017·BMC Genomics·UNKNOWN Aquaculture Genomics, Genetics and Breeding WorkshopTao Zhou
May 27, 2020·Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics·Xue LuJian-Fang Gui

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Datasets Mentioned

BETA
JQ799139
GSE64095

Methods Mentioned

BETA
RNA-seq
PCR
electrophoresis
GTPases

Software Mentioned

cells
Trinity
Trans
Blast2GO
BlastX
Oasis
ESTScan
illumina
AbySS
SOAP2denovo

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