Fu Yuanshuai, Jia Liang, Shi Zhiyi, Zhang Junling, Li Wenjuan
Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Ministry of Agriculture, China.
Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Ministry of Agriculture, China.
Comp Biochem Physiol Part D Genomics Proteomics. 2017 Jun;22:58-66. doi: 10.1016/j.cbd.2017.01.003. Epub 2017 Jan 25.
The Japanese flounder (Paralichthys olivaceus) is one of the most important commercial and biological marine fishes. However, the molecular biology involved during embryogenesis and early development of the Japanese flounder remains largely unknown due to a lack of genomic resources. A comprehensive and integrated transcriptome is necessary to study the molecular mechanisms of early development and to allow for the detailed characterization of gene expression patterns during embryogenesis; this approach is critical to understanding the processes that occur prior to mesectoderm formation during early embryonic development. In this study, more than 117.8 million 100bp PE reads were generated from pooled RNA extracted from unfertilized eggs to 41dph (days post-hatching) embryos and were sequenced using Illumina pair-end sequencing technology. In total, 121,513 transcripts (≥200bp) were obtained using de novo assembly. A sequence similarity search indicated that 52,338 transcripts show significant similarity to 22,462 known proteins from the NCBI non-redundant database and the Swiss-Prot protein database and were annotated using Blast2GO. GO terms were assigned to 44,627 transcripts with 12,006 functional terms, and 10,024 transcripts were assigned to 133 KEGG pathways. Furthermore, gene expression differences between the unfertilized egg and the gastrula embryo were analysed using Illumina RNA-Seq with single-read sequencing technology, and 24,837 differentially and specifically expressed transcripts were identified and included 5,286 annotated transcripts and 19,569 non-annotated transcripts. All of the expressed transcripts in the unfertilized egg and gastrula embryo were further classified as maternal, zygotic, or maternal-zygotic transcripts, which may help us to understand the roles of these transcripts during the embryonic development of the Japanese flounder. Thus, the results will contribute to an improved understanding of the gene expression patterns and signalling pathways that control the molecular mechanisms of early embryonic development.
牙鲆（Paralichthys olivaceus）是最重要的商业和生物学海洋鱼类之一。然而，由于缺乏基因组资源，牙鲆胚胎发生和早期发育过程中的分子生物学仍 largely unknown。一个全面且整合的转录组对于研究早期发育的分子机制以及详细表征胚胎发生过程中的基因表达模式是必要的；这种方法对于理解早期胚胎发育中中胚层形成之前发生的过程至关重要。在本研究中，从不受精卵到孵化后41天（dph）的胚胎提取的混合RNA中产生了超过1.178亿条100bp的双端读数，并使用Illumina双端测序技术进行测序。使用从头组装总共获得了121,513个转录本（≥200bp）。序列相似性搜索表明，52,338个转录本与来自NCBI非冗余数据库和Swiss-Prot蛋白质数据库的22,462个已知蛋白质显示出显著相似性，并使用Blast2GO进行注释。GO术语被分配给44,627个转录本，具有12,006个功能术语，并且10,024个转录本被分配到133条KEGG途径。此外，使用Illumina RNA-Seq单端测序技术分析了未受精卵和原肠胚之间的基因表达差异，鉴定出24,837个差异和特异性表达的转录本，包括5,286个注释转录本和19,569个未注释转录本。未受精卵和原肠胚中的所有表达转录本进一步被分类为母体、合子或母体 - 合子转录本，这可能有助于我们了解这些转录本在牙鲆胚胎发育过程中的作用。因此，这些结果将有助于更好地理解控制早期胚胎发育分子机制的基因表达模式和信号通路。
