title: Identification of Novel Transcribed Regions in Zebrafish (Danio rerio) Using RNA-Sequencing.
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.
authors.affiliation: Department of Biosciences and Nutrition, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.
authors.forename: Jingwen
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Biosciences and Nutrition, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.
authors.forename: Liselotte
authors.initials: L
authors.lastname: Vesterlund
authors.affiliation: Department of Biosciences and Nutrition, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.|Clinical Research Centre, Karolinska University Hospital, Huddinge, Sweden.|Department of Medical Genetics, Hartman Institute, University of Helsinki, Finland.|Folkhälsan Institute of Genetics, Helsinki, Finland.
authors.forename: Juha
authors.initials: J
authors.lastname: Kere
authors.affiliation: Department of Biosciences and Nutrition, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.|Clinical Research Centre, Karolinska University Hospital, Huddinge, Sweden.
authors.forename: Hong
authors.initials: H
authors.lastname: Jiao
mesh_terms: D000818:Animals; D018507:Gene Expression Regulation, Developmental; D058977:Molecular Sequence Annotation; D059467:Transcriptome; D015027:Zebrafish / Q000235:genetics* / Q000254:growth & development