RNA-Seq Technology and Its Application in Fish Transcriptomics

Abstract

High-throughput sequencing technologies, also known as next-generation sequencing (NGS) technologies, have revolutionized the way that genomic research is advancing. In addition to the static genome, these state-of-art technologies have been recently exploited to analyze the dynamic transcriptome, and the resulting technology is termed RNA sequencing (RNA-seq). RNA-seq is free from many limitations of other transcriptomic approaches, such as microarray and tag-based sequencing method. Although RNA-seq has only been available for a short time, studies using this method have completely changed our perspective of the breadth and depth of eukaryotic transcriptomes. In terms of the transcriptomics of teleost fishes, both model and non-model species have benefited from the RNA-seq approach and have undergone tremendous advances in the past several years. RNA-seq has helped not only in mapping and annotating fish transcriptome but also in our understanding of many biological processes in fish, such as development, adaptive evolution, host immune response, and stress response. In this review, we first provide an overview of each step of RNA-seq from library construction to the bioinformatic analysis of the data. We then summarize and discuss the recent biological insights obtained from the RNA-seq studies in a variety of fish species.

De novo Assembly, Characterization and Functional Annotation of Southern Hake (Merluccius australis) Transcriptome

“…Of these, approximately 75% (2401) of the unigenes had significant BLAST matches with fish species, such as Nile tilapia, zebrafish, Atlantic salmon and spotted green pufferfish, among others ( Table 3). The remaining 7143 (69.26%) unigenes resulted in non-significant hits, a result similar to other studies of non-model fish species (Shin et al, 2012;Qian et al, 2014). Normally this happens either due to incomplete gene information on non-model species in public database or because sequences of non-coding RNAs among the unigenes are included (Hou et al, 2011).…”

RNA-Seq as an Emerging Tool for Marine Dinoflagellate Transcriptome Analysis: Process and Challenges

“…This method has been employed extensively for both eukaryotic and prokaryotic organisms [10,[22][23][24]. Thus, in this review, we provide an overview of the process and technical aspect of dinoflagellates transcriptomics technology using RNA-seq and highlight the considerations and challenges using RNA-seq.…”

“…This process is important to fragmentize the long RNA into short sizes of fragments, according to the NGS sequencing platform. In most cases, RNA is fragmented prior to the reverse transcription to cDNA molecules allowing a more uniform fragment across the transcript and allowing for a more comprehensive analysis of transcriptome, but resulting in depleted transcript ends [10]. However, when using the Roche 454 platform, the fragmentation is done after the reverse transcription to cDNA molecules, but rendering the sequencing depth lower than Illumina or SOLiD platform [24].…”

“…Unlike genome, which is relatively stable and unchanged, transcriptomes tend to change under different environmental conditions and growth stages [10]. Thus, transcriptomic acts as a powerful tool to unravel the complexity of dinoflagellates physiology and gene regulation.…”

Harnessing Next Generation Sequencing in Climate Change: RNA-Seq Analysis of Heat Stress-Responsive Genes in Wheat (Triticum aestivum L.)

“…Plant omics and new biotechnologies such as massively parallel sequencing and microarray analysis were preferred tools to identify and characterize the differentially expressed genes (DEGs) under HS in different modal species (Gong et al 2014;Qian et al 2014;Rabara et al 2014), but NextGeneration Sequencing (NGS) is now the most preferred technique used for transcriptome study. The transcriptome data generated through NGS provide very useful information on the regulatory pathway networks operating in plants under different conditions (Rensink and Buell, 2005).…”