Wang Jingwen, Vesterlund Liselotte, Kere Juha, Jiao Hong
Department of Biosciences and Nutrition, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.
Clinical Research Centre, Karolinska University Hospital, Huddinge, Sweden.
PLoS One. 2016 Jul 27;11(7):e0160197. doi: 10.1371/journal.pone.0160197. eCollection 2016.
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.
斑马鱼（Danio rerio）已成为研究脊椎动物发育和人类遗传疾病的模式生物。然而，斑马鱼基因组注释仍在进行中且不完整，仍有新的基因转录本有待发现。随着大规模平行测序技术的引入，全转录组研究成为可能。在本研究中，我们旨在利用RNA测序的发育转录组数据发现新的转录区域（NTRs）。为实现这一目标，我们开发了一个用于发现NTRs的内部生物信息学流程。使用该流程，我们检测到152个推定的NTRs，在发现时它们未在Ensembl和NCBI基因数据库中注释。随机选择的4个NTRs通过RT-PCR成功验证，随机选择的10个NTRs的表达谱通过qRT-PCR进行评估。这152个NTRs的鉴定为斑马鱼基因组注释提供了新信息，也为斑马鱼基因功能研究提供了新的候选对象。
