摘要: No studies have systematically compared time-resolved and multi-tissue innate immune responses for European eels (Anguilla anguilla) with Aeromonas hydrophila infection by a high throughput method. Here, we challenged European eels with A. hydrophila (infected) or PBS (control). A low fatality rate (16.1%) was observed for the infected group at 2 d post-infection (dpi). Then we examined transcriptional profiles of intestines, livers and spleens from 12 European eels with/without infection by A. hydrophila at 6, 18 and 36 h post-infection (hpi). The results showed that the most differentially expressed genes (DEGs) were found in the spleen at 6 hpi (7569 DEGs), followed by the intestine at 6 hpi (3129 DEGs) and the liver at 18 hpi (2722 DEGs). Only 540, 41 and 130 DEGs were found in the spleen, liver, and intestine at 36 hpi, respectively. The comparison of DEG numbers and enriched KEGG pathways suggested a consistent time-course immune response in these tissues. A similar enrichment of pattern recognition receptors-related pathways including Toll-like receptors, NOD-like receptors and RIG-I-like receptors was found in the liver and spleen, but not in the intestine. Among immune-related DEGs, 62 paralogue pairs were found, and the expression trends of most paralogues were consistent. Some paralogues of immune-related DEGs had unique domains. Furthermore, large clusters representing similar tissue were shown for the intestine and spleen. A different co-expression network involved in cytokine signal transduction and inter-action existed between the liver and spleen. This study has provided time-resolved and multi-tissue transcriptome characteristics of A. anguilla in response to A. hydrophila infection.

摘要: Environmental DNA (eDNA) originates from cellular material shed by organisms into aquatic or terrestrial environments and can be sampled and monitored using metabarcoding technology, which is revolutionizing fish biodiversity monitoring. Several reviews concerning fish eDNA have focused on standard sampling methods and its applications, though a systematic review focused on marker genes, databases, and bioinformatic pipelines has not yet been published. Here, we present a comprehensive literature review of studies applying metabarcoding technology to fish eDNA for the purpose of fish biodiversity monitoring. We systematically provide the available universal primers used to amplify barcoding sequences from fish eDNA, and then discuss reference barcoding databases, relevant bioinformatic analyses, as well as developed pipelines. The performances of universal primers and their relevant reference databases are summarized. Combined use of multiple primer pairs targeted for more than one gene marker (e.g., 12S, 16S, Cytb, COI), and use of both local and public databases are recommended as approaches to improve the sensitivity and reliability of fish eDNA analyses. We also compare the effectiveness of eDNA metabarcoding to traditional approaches for monitoring fish biodiversity and highlight challenges and future perspectives associated with this new tool. Ultimately, we advocate for greater incorporation of eDNA analysis into fish biodiversity assessments to assist environmental managers.