Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review

Abstract

In recent years, with the advent of next-generation sequencing along with the development of various bioinformatics tools, RNA sequencing (RNA-Seq)-based transcriptome analysis has become much more affordable in the field of biological research. This technique has even opened up avenues to explore the transcriptome of non-model organisms for which a reference genome is not available. This has made fish health researchers march towards this technology to understand pathogenic processes and immune reactions in fish during the event of infection. Recent studies using this technology have altered and updated the previous understanding of many diseases in fish. RNA-Seq has been employed in the understanding of fish pathogens like bacteria, virus, parasites, and oomycetes. Also, it has been helpful in unraveling the immune mechanisms in fish. Additionally, RNA-Seq technology has made its way for future works, such as genetic linkage mapping, quantitative trait analysis, disease-resistant strain or broodstock selection, and the development of effective vaccines and therapies. Until now, there are no reviews that comprehensively summarize the studies which made use of RNA-Seq to explore the mechanisms of infection of pathogens and the defense strategies of fish hosts. This review aims to summarize the contemporary understanding and findings with regard to infectious pathogens and the immune system of fish that have been achieved through RNA-Seq technology.

Acting locally - affecting globally: RNA sequencing of gilthead sea bream with a mild Sparicotyle chrysophrii infection reveals effects on apoptosis, immune and hypoxia related genes

“…To our knowledge, only one microarray study is available in the literature on the host response against a monogenean [33]. Thus far, RNA-seq has been used only recently to analyse the host reaction against some fish parasites [34][35][36][37][38] and no transcriptomic study on the response against a polyopistocothylean has been performed. Therefore, the current study on the reaction of GSB to S. chrysophrii is the first comprehensive transcriptomic analysis of a polyopistocothylean infection.…”

RNA Sequencing (RNA-Seq) Based Transcriptome Analysis in Immune Response of Holstein Cattle to Killed Vaccine against Bovine Viral Diarrhea Virus Type I

“…RNA sequencing is a developed method that uses deep sequencing technology for transcriptome profiling [16]; aside from providing a comprehensive picture of the transcriptome, it also reveals the activity and mechanism of the molecular structure and explores the biological function of a gene [17]. Furthermore, future works using this technology are considered, such as genetic linkage mapping, quantitative trait analysis, disease-resistant strains, effective vaccines, and therapies development [18].…”

Transcriptomics in aquaculture: current status and applications

“…A couple of recent studies review the application of transcriptome analysis in fish with response to bacterial and viral pathogens and parasites (Sudhagar et al . ; Ye et al . ).…”