Palliyath Gangaraj Karyath, Jangam Ashok Kumar, Katneni Vinaya Kumar, Kaikkolante Nimisha, Panjan Nathamuni Suganya, Jayaraman Roja, Jagabattula Syamadayal, Moturi Muralidhar, Shekhar Mudagandur Shashi
ICAR-Central Institute of Brackishwater Aquaculture, Chennai, India.
Biochem Genet. 2025 Apr;63(2):1459-1478. doi: 10.1007/s10528-024-10772-y. Epub 2024 Apr 3.
Shrimp farming, a dominant economic activity in coastal areas, is affected by different abiotic and biotic stress factors. These stressors, under poor management conditions, could affect growth and health of farmed animals. Understanding the common gene expressions in response to stress, regardless of the specific stress factor, holds significant importance in the field of functional genomics. Scope of this study is to identify the core transcriptomic responses in the shrimp species Penaeus vannamei exposed to various abiotic and biotic stress conditions and to decipher their functional importance. To achieve our objective, we gathered and analyzed multiple RNA-seq datasets related to twelve abiotic and nine biotic stress conditions. Through the in silico meta-analysis, we predicted 961 differentially expressed genes (meta-DEGs) for abiotic stress conditions and 517 meta-DEGs for biotic stress conditions, respectively. These meta-DEGs represent genes that are commonly expressed across different stress factors and are indicative of the organism's general response to stress. The annotation of nineteen core up-regulated meta-DEGs revealed their diverse functions in detoxification, cell adhesion, metal ion binding, and oxidative phosphorylation. These genes play a crucial role in stress response and immune defense. For abiotic stress, significant pathways associated with the stress response include tryptophan metabolism, starch and sucrose metabolism, fatty acid degradation, carbohydrate digestion and absorption, phenylalanine metabolism, drug metabolism-other enzymes, arachidonic acid metabolism, and fatty acid elongation. Similarly, for biotic stress, metabolism of xenobiotics by cytochrome P450, pentose and glucuronate interconversions, steroid hormone biosynthesis, and drug metabolism-cytochrome P450 were found to be significant pathway associations. In addition, the study also predicted 17 stress regulatory motifs present in the identified meta-DEGs. These motifs have significance in identifying the stress responses of the organism. The metabolic pathways and regulatory motifs associated with abiotic and biotic stress factors identified through this study could be a valuable resource for developing stress management approaches in shrimp aquaculture.
对虾养殖是沿海地区的一项主要经济活动，受到不同的非生物和生物应激因素影响。在管理不善的情况下，这些应激源会影响养殖动物的生长和健康。了解无论具体应激因素如何，对压力作出反应时的常见基因表达，在功能基因组学领域具有重要意义。本研究的范围是确定凡纳滨对虾在暴露于各种非生物和生物应激条件下的核心转录组反应，并解读其功能重要性。为实现我们的目标，我们收集并分析了与十二种非生物和九种生物应激条件相关的多个RNA测序数据集。通过计算机元分析，我们分别预测了非生物应激条件下的961个差异表达基因（元DEG）和生物应激条件下的517个元DEG。这些元DEG代表了在不同应激因素中普遍表达的基因，表明了生物体对压力的一般反应。对19个核心上调元DEG的注释揭示了它们在解毒、细胞粘附、金属离子结合和氧化磷酸化方面的多种功能。这些基因在应激反应和免疫防御中起着关键作用。对于非生物应激，与应激反应相关的重要途径包括色氨酸代谢、淀粉和蔗糖代谢、脂肪酸降解、碳水化合物消化和吸收、苯丙氨酸代谢、药物代谢-其他酶、花生四烯酸代谢和脂肪酸延长。同样，对于生物应激，细胞色素P450对外源生物的代谢、戊糖和葡糖醛酸的相互转化、类固醇激素生物合成以及药物代谢-细胞色素P450被发现是重要的途径关联。此外，该研究还预测了在所鉴定的元DEG中存在17个应激调节基序。这些基序在识别生物体的应激反应方面具有重要意义。通过本研究确定的与非生物和生物应激因素相关的代谢途径和调节基序，可能是开发对虾养殖应激管理方法的宝贵资源。
