Yongyao Yu’s research while affiliated with Huazhong Agricultural University and other places

Euchiloglanis kishinouyei is a typical endemic torrent catfish found in the Jinsha River system of the upper Yangtze River in China. It inhabits fast-flowing streams with steep elevation gradients and has evolved unique biological adaptations to thrive in these extreme environments. A high-quality genome provides key insights into the adaptive mechanisms driving its evolution in these harsh conditions. In this study, we successfully assembled the first telomere-to-telomere (T2T) genome of E. kishinouyei, marking the first T2T genome assembly of torrent catfish. The genome spans 886.74 Mb, anchored to 27 chromosomes, with over 99% coverage. The quality value (QV) and Benchmarking Universal Single-Copy Ortholog (BUSCO) scores were 46.96 and 98.50%, respectively, reflecting the high quality of the assembly. We identified repetitive elements accounting for 45.59% (404.23 Mb) of the genome and predicted 24,403 protein-coding genes, 94.37% of which were annotated. This high-fidelity genome assembly provides a valuable resource for future research and lays the foundation for exploring the ecological adaptation mechanisms and evolutionary biology of torrent catfish.

The genus Triplophysa exhibits remarkable adaptability to the unique environment found at the Qinghai-Tibet Plateau (QTP). Higher quality genomes are helpful to the study of the adaptability to the extreme environment in the plateau. This study utilized PacBio HiFi, Ultra-long ONT, and Hi-C sequencing of Triplophysa yaopeizhii to construct the first telomere-to-telomere (T2T) gapless genome assembly of the genus Triplophysa. The genome size is 671.58 Mb, with a contig N50 length of 26.04 Mb. The sequences were anchored onto 25 chromosomes with all centromeres and telomeres. Furthermore, 293.98 Mb (43.77%) of repetitive sequences and 26,487 protein-coding genes were identified. Comparative analyses with the genomes of closely related species demonstrated high completeness, continuity, and accuracy of the genome. The genomic quality was further substantiated by the QV of 31.82 with 96.60% of BUSCO. This study provides a valuable genetic resource of the genus Triplophysa and serves as an essential reference for elucidating the adaptive genetic mechanisms of plateau fish to the high altitude.

The polymeric immunoglobulin (Ig) receptor-like (pIgRL) molecules have been identified in teleost fish. However, compare to the functional studies of their related genes (mammalian CD300 family, et al) in eliminating pathogen invasion while preserving homeostasis, the roles of pIgRL in teleost fish remain unclear. In this study, we demonstrated that a pair of pIgRL molecules in zebrafish, pIgRL3.5 and pIgRL4.2, were highly expressed in the intestine and immune cells. Moreover, we constructed an Edwardsiella piscicida infection model, which induced strong inflammatory responses in the zebrafish intestine. Interestingly, pIgRL3.5 and pIgRL4.2 exhibited opposite inducible expression patterns in response to bacterial infection, suggesting that they perform different roles. More importantly, by conducting overexpression and knockdown experiments, our findings demonstrated that zebrafish pIgRL3.5 played a protective role in the host defense against E. piscicida infection by inhibiting excessive inflammatory responses. In contrast, pIgRL4.2 facilitated pathogen growth and dissemination in zebrafish intestine. Collectively, our findings were the first to demonstrate that a pair of pIgRL molecules in teleost fish play opposite roles in mucosal immune response to bacterial infection. Therefore, our results provide crucial insights into the conserved role of pIgRL molecules in immune regulatory functions throughout vertebrate evolution.

Simple Summary Strong ultraviolet radiation is an extreme environmental characteristic of the Tibetan Plateau. Melanin is the most important light-protective substance that allows fish to resist ultraviolet radiation. In order to explore the melanin protection mechanism of fish in the Tibetan Plateau against strong ultraviolet radiation, Triplophysa stenura distributed in high elevation areas was selected as the research object. Transcriptome differences were compared between skin and peritoneal wall layers with different melanin contents to explore the regulatory genes related to melanin synthesis. This provides basic data for analyzing the molecular mechanism of melanin protection in plateau fish against strong ultraviolet radiation. The results indicate that a total of twenty-three DEGs are enriched in the melanin synthesis pathway by a local Blast comparison, of which nine DEGs are significantly upregulated in the peritoneal wall layer and six DEGs are significantly upregulated in the dorsal and lateral skin. The results suggest that these genes may be associated with the molecular mechanism of melanin synthesis in T. stenura, and the differential regulation of genes may be related to the differences in the UVR intensity and tissue sites of melanin synthesis. Further investigation is needed to determine how these genes specifically regulate melanin synthesis. Abstract A total of 81,868 All-Unigenes were sequenced and assembled by the transcriptome in the dorsal skin, the lateral skin, and the peritoneal wall layer of Triplophysa stenura with a total assembly length of 123,827,585 bp, and 68,750 unigenes were annotated to seven functional databases. A total of 588 DEGs were screened between the dorsal and lateral skin, 17,097 DEGs were screened between the dorsal skin and the peritoneal wall layer, and 16,598 DEGs were screened between the lateral skin and the peritoneal wall layer. Most of DEGs in three tissues were annotated to GO terms related to cellular structures, binding, cellular processes, and catalytic activity. They were also annotated to KEGG pathways such as the MAPK signaling pathway, PI3K-Akt signaling pathway, Wnt signaling pathway, melanogenesis, tyrosine metabolism, and cell cycle. A total of twenty-three DEGs were found to be enriched in the melanin synthesis pathway by a local Blast comparison, of which nine DEGs were significantly upregulated in the peritoneal wall layer and six DEGs were significantly upregulated in the dorsal and lateral skin. The results suggest that these genes may be associated with the molecular mechanism of melanin synthesis in T. stenura, and the differential regulation of genes may be related to the differences in UVR intensity and tissue sites of melanin synthesis. Further investigation is needed on how these genes specifically regulate melanin synthesis.

Respiratory structures are crucial for vertebrate survival, as they serve not only to perform gas-exchange processes but also as entry points for opportunistic pathogens. Previous studies have demonstrated that fish contain gill mucosal-associated lymphoid tissue, and harbor a large number of commensal bacteria on their surface and contribute to maintaining fish health. However, by far, very limited information is known regarding the effects of viral infection on gill mucosal immunity and microbiota homeostasis. In this study, we conducted an infection model by bath with infectious hematopoietic necrosis virus (IHNV) and revealed a 27 % mortality rate among rainbow trout in the first two weeks after infection. Moreover, we found that diseased fish with the highest IHNV loads in gills exhibiting severe damage, as well as increased goblet cell counts in both primary lamellae (PL) and secondary lamellae (SL). Additionally, RT-qPCR and RNA-seq analyses revealed that IHNV infection induced a strong innate and adaptive antiviral immune responses. Interestingly, an antibacterial immune response was also observed, suggesting that a secondary bacterial infection occurred in trout gills after viral infection. Furthermore, 16S rRNA analysis of trout gills revealed a profound dysbiosis marked by a loss of beneficial taxa and expansion of pathobionts following IHNV infection. Overall, our finding demonstrates that IHNV infection induces significant changes of the microbial community in the fish respiratory surface, thus triggering local antiviral and bacterial mucosal immunity.

T and B lymphocytes (T and B cells) are immune effector cells that play critical roles in adaptive immunity and defend against external pathogens in most vertebrates, including teleost fish. In mammals, the development and immune response of T and B cells is associated with cytokines including chemokines, interferons, interleukins, lymphokines, and tumor necrosis factors during pathogenic invasion or immunization. Given that teleost fish have evolved a similar adaptive immune system to mammals with T and B cells bearing unique receptors (B-cell receptors (BCRs) and T-cell receptors (TCRs)) and that cytokines in general have been identified, whether the regulatory roles of cytokines in T and B cell-mediated immunity are evolutionarily conserved between mammalians and teleost fish is a fascinating question. Thus, the purpose of this review is to summarize the current knowledge of teleost cytokines and T and B cells as well as the regulatory roles of cytokines on these two types of lymphocytes. This may provide important information on the parallelisms and dissimilarities of the functions of cytokines in bony fish versus higher vertebrates, which may aid in the evaluation and development of adaptive immunity-based vaccines or immunostimulants.