Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Academy of Fishery Sciences, Nanning, Guangxi 530021, China.
Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Academy of Fishery Sciences, Nanning, Guangxi 530021, China.
Gene. 2018 Nov 30;677:24-31. doi: 10.1016/j.gene.2018.07.042. Epub 2018 Jul 24.
The Litopenaeus vannamei (L. vannamei) is one of the most widely cultured shrimp species in the world, with low temperature being one of the most serious threats to its growth and survival. To examine the potential regulatory mechanism of cold adaptation, we conducted a microRNAs (miRNAs) analysis on the hepatopancreas of L. vannamei under normal temperature 28 °C (M28), cold acclimation 16 °C for 6 days (M16), and recovered under normal temperature (MR). In total 14,754,823, 14,945,246 and 15,880,093 raw reads representing 10,690,259, 8,587,144, and 11,512,941 unique sequences of 18-32 nt length were obtained from the M28, M16 and MR libraries, respectively. After comparing the miRNA sequences with the miRBase database, 68 known mature miRNAs and 47 novel miRNAs were identified. Expression analysis showed that 34 miRNAs were significantly differential expressed in response to cold adaptation. Compared to the M28 library, 21 miRNAs were upregulated and 13 miRNAs were downregulated significantly in the M16 library. After recovery to normal temperature, there are 16 miRNAs upregulated and 15 miRNAs downregulated significantly compared to M28 library. Then, five significantly differential expressed miRNAs under cold acclimation including three known miRNAs (mja-miR-6491, mja-miR-6494, and Bta-miR-2478) and two newly-identified miRNAs (novel_68 and novel_5) were selected for validation by RT-qPCR in the hepatopancreas and muscle tissues of cold treated shrimps. The expression trend of most the miRNAs from RT-qPCR were consistent with the next-generation sequencing data. Further, the Gene Ontology (GO) annotation showed that the metabolic process GO term was significantly enriched with target genes of the differentially expressed miRNAs. Additionally, KEGG pathway analysis suggested that the fatty acid degradation and glycerolipid metabolism pathways etc. are significantly enriched with the target genes. These findings may contribute to a better understanding of the molecular mechanisms governing the responses to low temperature in L. vannamei.
凡纳滨对虾（L. vannamei）是世界上养殖最广泛的虾类之一，低温是对其生长和生存最严重的威胁之一。为了研究低温适应的潜在调控机制，我们对正常温度 28°C（M28）、低温适应 6 天 16°C（M16）和恢复正常温度（MR）下的凡纳滨对虾肝胰腺进行了 microRNAs（miRNAs）分析。分别从 M28、M16 和 MR 文库中获得了代表 18-32 nt 长度的 10,690,259、8,587,144 和 11,512,941 个独特序列的 14,754,823、14,945,246 和 15,880,093 条原始reads。将 miRNA 序列与 miRBase 数据库进行比较后，鉴定出 68 个已知成熟 miRNA 和 47 个新的 miRNA。表达分析显示，34 个 miRNA 对低温适应有显著差异表达。与 M28 文库相比，M16 文库中有 21 个 miRNA 上调，13 个 miRNA 显著下调。恢复到正常温度后，与 M28 文库相比，有 16 个 miRNA 上调，15 个 miRNA 下调。然后，选择在冷适应下表达差异显著的五个 miRNA 进行验证，包括三个已知 miRNA（mja-miR-6491、mja-miR-6494 和 Bta-miR-2478）和两个新鉴定的 miRNA（novel_68 和 novel_5），在冷处理虾的肝胰腺和肌肉组织中通过 RT-qPCR 进行验证。大多数 miRNA 的 RT-qPCR 表达趋势与下一代测序数据一致。此外，GO 注释显示，代谢过程 GO 术语显著富集了差异表达 miRNA 的靶基因。此外，KEGG 通路分析表明，脂肪酸降解和甘油脂代谢途径等显著富集了靶基因。这些发现可能有助于更好地理解凡纳滨对虾低温响应的分子机制。
