Identification of Novel Transcribed Regions in Zebrafish (Danio rerio) Using RNA-Sequencing.

Jingwen Wang,Liselotte Vesterlund,Hong Jiao,Juha Kere

doi:10.1371/journal.pone.0160197

Abstract

Zebrafish (Danio rerio) has emerged as a model organism to investigate vertebrate development and human genetic diseases. However, the zebrafish genome annotation is still ongoing and incomplete, and there are still new gene transcripts to be found. With the introduction of massive parallel sequencing, whole transcriptome studies became possible. In the present study, we aimed to discover novel transcribed regions (NTRs) using developmental transcriptome data from RNA sequencing. In order to achieve this, we developed an in-house bioinformatics pipeline for NTR discovery. Using the pipeline, we detected 152 putative NTRs that at the time of discovery were not annotated in Ensembl and NCBI gene database. Four randomly selected NTRs were successfully validated using RT-PCR, and expression profiles of 10 randomly selected NTRs were evaluated using qRT-PCR. The identification of these 152 NTRs provide new information for zebrafish genome annotation as well as new candidates for studies of zebrafish gene function.

Highlights

Transcriptome analysis has become a key tool for understanding functional roles of genes involved in a variety of biological processes including early development [1]
We have identified 152 putative novel transcribed regions (NTRs) that at the time of discovery were not annotated in Ensembl and NCBI gene database using an in-house bioinformatics pipeline to systematically in zebrafish early development by reanalyzing our previously obtained RNA sequencing technologies (RNA-Seq) data [8]
With the increasing number of RNA-Seq data from a large variety of species, there is a vast amount of novel information that can be found using relatively simple in-house bioinformatics pipelines

Summary

Introduction

Transcriptome analysis has become a key tool for understanding functional roles of genes involved in a variety of biological processes including early development [1]. In 2005 Mathavan et al [2] published a genome-wide microarray analysis of the embryonic zebrafish transcriptome using 12 different embryonic time points. The study revealed a highly dynamic and diverse transcriptional profile during embryogenesis and identified a previously unknown set of very early genes transcribed prior to the mid-blastula transition (MBT). Technologies for transcriptome analysis have improved dramatically, and high throughput RNA sequencing technologies (RNA-Seq) have revolutionized transcriptomics by detailed examination of cellular transcriptomes with high sensitivity, high dynamic range, and expression at a single-cell resolution [3, 4]. PLOS ONE | DOI:10.1371/journal.pone.0160197 July 27, 2016

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