Department of Biological Sciences, Kongju National University, Gongju, 32588, South Korea.
Mar Biotechnol (NY). 2024 Oct;26(5):964-974. doi: 10.1007/s10126-024-10354-4. Epub 2024 Aug 7.
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.
对于大西洋鲑鱼的发育而言，最为关键的阶段是从卵到仔鱼再到稚鱼的早期发育阶段。然而，基于 RNA-seq 的大西洋鲑早期发育研究却相当匮乏，且仅聚焦于单一的发育阶段。因此，本研究利用 RNA-seq 技术，对不同早期发育阶段（卵、仔鱼和稚鱼）的各种基因表达进行了全面评估。通过 9 个重复的 3 个阶段（卵、仔鱼和稚鱼）的文库共生成了超过 22GB 的清洁数据，其映射效率超过 90%。共鉴定到 5534 个差异表达基因，其中 19、606 和 826 个基因分别在各阶段特异性表达。转录组分析表明，随着大西洋鲑从卵到稚鱼的发育进程，差异表达基因（DEGs）的数量逐渐增加。此外，GO 富集分析表明，卵和仔鱼阶段的特征是上调与脊髓发育、神经元投射形态发生、轴突发生和细胞质翻译相关的基因。在稚鱼阶段，上调的基因富集在肌肉发育过程（肌肉细胞发育、横纹肌细胞分化和肌肉组织发育）、免疫系统（防御反应和经典 NF-κB 信号转导）以及表皮发育过程中。这些结果表明，大西洋鲑的早期发育是以不同阶段之间基因表达和 DEGs 的动态转换为特征的，为大西洋鲑的发育研究奠定了坚实的基础。
