Transcriptome Profiling of Gene Expression in Atlantic Salmon (Salmo salar) at Early Stage of Development

IF 2.6 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Najib Abdellaoui, Min Sun Kim
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引用次数: 0

Abstract

For Atlantic salmon development, the most critical phase is the early development stage from egg to fry through alevin. However, the studies investigating the early development of Atlantic salmon based on RNA-seq are scarce and focus only on one stage of development. Therefore, using the RNA-seq technology, the assessment of different gene expressions of various early development stages (egg, alevin, and fry) was performed on a global scale. Over 22 GB of clean data was generated from 9 libraries with three replicates for each stage with over 90% mapping efficiency. A total of 5534 genes were differentially expressed, among which 19, 606, and 826 genes were specifically expressed in each stage, respectively. The transcriptome analysis showed that the number of differentially expressed genes (DEGs) increased as the Atlantic salmon progressed in development from egg to fry stage. In addition, gene ontology enrichment demonstrated that egg and alevin stages are characterized by upregulation of genes involved in spinal cord development, neuron projection morphogenesis, axonogenesis, and cytoplasmic translation. At the fry stage, upregulated genes were enriched in the muscle development process (muscle cell development, striated muscle cell differentiation, and muscle tissue development), immune system (defense response and canonical NF-kappaB signal transduction), as well as epidermis development. These results suggest that the early development of Atlantic salmon is characterized by a dynamic shift in gene expression and DEGs between different stages, which provided a solid foundation for the investigation of Atlantic salmon development.

Abstract Image

大西洋鲑(Salmo salar)早期发育阶段基因表达的转录组分析。
对于大西洋鲑的发育而言,最关键的阶段是从卵到鱼苗再到幼鱼的早期发育阶段。然而,基于 RNA-seq 对大西洋鲑早期发育的研究很少,而且只集中于一个发育阶段。因此,利用 RNA-seq 技术,在全球范围内对不同早期发育阶段(卵、幼鱼和鱼苗)的不同基因表达进行了评估。每个阶段有三个重复的 9 个文库产生了超过 22 GB 的纯净数据,其映射效率超过 90%。共有 5534 个基因有差异表达,其中每个阶段分别有 19、606 和 826 个基因特异表达。转录组分析表明,随着大西洋鲑鱼从卵到鱼苗阶段的发育,差异表达基因(DEGs)的数量有所增加。此外,基因本体富集表明,卵和幼鱼阶段的特点是脊髓发育、神经元投射形态发生、轴突生成和细胞质翻译相关基因的上调。在鱼苗阶段,上调基因富集于肌肉发育过程(肌肉细胞发育、横纹肌细胞分化和肌肉组织发育)、免疫系统(防御反应和典型 NF-kappaB 信号转导)以及表皮发育。这些结果表明,大西洋鲑的早期发育具有不同阶段之间基因表达和 DEGs 动态变化的特点,这为研究大西洋鲑的发育奠定了坚实的基础。
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来源期刊
Marine Biotechnology
Marine Biotechnology 工程技术-海洋与淡水生物学
CiteScore
4.80
自引率
3.30%
发文量
95
审稿时长
2 months
期刊介绍: Marine Biotechnology welcomes high-quality research papers presenting novel data on the biotechnology of aquatic organisms. The journal publishes high quality papers in the areas of molecular biology, genomics, proteomics, cell biology, and biochemistry, and particularly encourages submissions of papers related to genome biology such as linkage mapping, large-scale gene discoveries, QTL analysis, physical mapping, and comparative and functional genome analysis. Papers on technological development and marine natural products should demonstrate innovation and novel applications.
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