Jellyfish, such as Chrysaora quinquecirrha, hold an important evolutionary position and have great ecological value. However, limited genomic resources are currently available for studying their basic genetic and development processes. Here, we de novo assembled the first high-quality reference genome of C. quinquecirrha, and successfully annotated 21,606 protein-coding genes. Codon usage analysis identified the frequent use of low-GC-content codons during protein-coding gene translation. Analysis of the relative evolution rate indicated that jellyfish had a faster evolution rate than sea anemones but slower rate than the species in Hydra. Phylogenetic analysis with two other species of jellyfish indicated that Aurelia aurita and Nemopilema nomurai have a closer relationship with each other than with C. quinquecirrha, with divergence from their common ancestor occurring ≈475.7 million years ago. Our study not only showed the genomic characteristics and molecular adaptive evolution of C. quinquecirrha, but also provides valuable genomic resources for further study on complex developmental processes and environmental adaptations.

The Atlantic sea nettle (Chrysaora quinquecirrha) has an important evolutionary position due to its high ecological value. However, due to limited sequencing technologies and complex jellyfish genomic sequences, the current C. quinquecirrha genome assembly is highly fragmented. Here, we used the most advanced high-throughput chromosome conformation capture (Hi-C) technology to obtain high-coverage sequencing data of the C. quinquecirrha genome. We then anchored these data to the previously published contig-level assembly to improve the genome. Finally, a high-continuity genome sequence of C. quinquecirrha was successfully assembled, which contained 1 882 scaffolds with a N50 length of 3.83 Mb. The N50 length of the genome assembly was 5.23 times longer than the previously released one, and additional analysis revealed that it had a high degree of genomic continuity and accuracy. Acquisition of the high-continuity genome sequence of C. quinquecirrha not only provides a basis for the study of jellyfish evolution through comparative genomics but also provides an important resource for studies on jellyfish growth and development.

Background: Mobile antimicrobial resistance genes (ARGs) on plasmids or other elements enable Salmonella Typhimurium to spread resistance across hosts and environments. The emergence of multi-drug resistance (MDR) Salmonella Typhimurium has raised global concern, yet little is reported about these mobile elements from the Thailand pork supply chain, where this risk of transfer to humans remains largely uncharacterized. Methods: Between March 2023 and February 2024, 25 S. Typhimurium isolates were collected from pig carcasses in slaughterhouses and pork swabs from retail markets in northeastern Thailand. Nine representative isolates, sampled across three seasons, were subjected to Illumina whole-genome sequencing. Assemblies were analyzed for sequence types, phylogenetic relationships, antimicrobial resistance (AMR) determinants, plasmid replicons and mobilization features, functional annotation based on COG (Clusters of Orthologous Groups of proteins) classification, and comparative genomics against a reference strain. Results: Genome assemblies ranged from 4.76 to 5.00 Mb with consistent GC (guanine-cytosine) content (52.0–52.2%). Phylogenetic analysis revealed three sequence types: ST34 (77.8%), ST19, and ST1543. ST34 isolates displayed the broadest AMR gene repertoires, carrying tetracycline (tetA/tetB), sulfonamide (sul1/sul2/sul3), aminoglycoside (aadA, aph(6)-Id, aph(3″)-Ib), phenicol (floR, catA1), and β-lactam (bla_TEM-1B) genes, whereas non-ST34 isolates harbored fewer determinants. ARGs frequently co-localized with IncQ1 and Col-type plasmid replicons, MOB_H/MobA relaxases (enzymes that initiate plasmid transfer), and conjugation modules (type IV secretion and coupling proteins), often alongside virulence loci and metal resistance operons. Functional annotation showed highly conserved metabolic and housekeeping functions, while comparative genomics confirmed >90% core genome conservation, with variability concentrated in genomic islands encoding hypothetical proteins. These genomic patterns were inferred from a limited WGS dataset (nine isolates) and should therefore be considered exploratory and require confirmation in larger collections. Conclusions: Multi-drug resistant ST34 Salmonella Typhimurium predominated in the northeastern Thailand pork supply chain, with diverse resistance genes carried on IncQ1/Col-type plasmids linked to MOB_H relaxases and conjugation modules. The stability of these mobilizable elements underscores their role in sustaining MDR traits and highlights the risk of foodborne AMR transmission, reinforcing the need for continuous genomic surveillance under a One Health framework.

Background: Pancreatic adenocarcinoma (PAAD) is an aggressive and invasive tumor with poor prognosis. Identifying prognostic biomarkers of PAAD will provide crucial information for developing treatment plans. Methods: In this analysis, a gene-expression dataset, containing RNA-sequencing data recalculated into transcripts per million, was obtained from the UCSC Xena platform. Three thousand nine hundred and seventy six differentially expressed genes were obtained with analysis of variance. Using these data a co-expression network was constructed using weighted gene co-expression network analysis, from which we obtained eight modules. Results: The blue module included 497 genes and demonstrated significant negative correlation with overall survival. Furthermore, pathway analyses demonstrated the involvement of many of these genes in the tight junction pathway, which plays a critical role in PAAD. In addition, we identified six genes in common (i.e., ANXA2 [annexin A2], EPHA2 [erythropoietin-producing hepatocellular class A2], ITGB4 [integrin beta 4], KRT19 [keratin type I cytoskeletal 19], LGALS3 [galectin-3], and S100A14 [S100 calcium binding protein A14]) between the protein-protein interaction and gene co-expression networks that may have critical functions in PAAD. These hub genes were not only highly expressed at the RNA level but also exhibited high expression in the immunohistological data in the Human Protein Atlas Database. Conclusion: Thus, this research clarified the framework of co-expressed gene modules in PAAD and highlighted potential prognostic biomarkers for the clinical diagnosis of PAAD.

In this study, the complete mitochondrial genome (mitogenome) of Cotylorhiza tuberculata (Scyphozoa; Rhizostomeae; Cepheidae) was assembled by the next-generation sequencing data. The complete mitogenome spanned 16,590 bp and contained 14 protein-coding genes, two transfer RNA genes, and two ribosomal RNA genes. Total AT% content was 67.7%, comprising A 30.22%, C 16.16%, G 17.05%, and T 36.56%. The gene arrangement exhibited consistency with the known mitogenomes of other jellyfish species. Furthermore, the phylogenetic relationship of C. tuberculata was investigated based on analysis of the 13 common protein-coding genes. Results indicated a close relationship between C. tuberculata and both Cassiopea xamachana and Cassiopea andromeda. These findings provide a valuable reference for advancing understanding of the phylogenetic relationships, taxonomic classification, and phylogeography of jellyfish species.

Triple-negative breast cancer (TNBC) poses significant challenges due to its high aggressiveness, poor prognosis, and the lack of effective targeted therapies. Paclitaxel (PTX) is a chemotherapeutic agent commonly used in the treatment of TNBC; however, its efficacy is often compromised by drug resistance mediated by autophagy. This study investigated the synergistic effects of the autophagy inhibitor 3-methyladenine (3-MA) and PTX in a TNBC nude mouse model. Monitoring tumor volume and employing HE staining, immunofluorescence, and transmission electron microscopy revealed that PTX monotherapy induced tumor autophagy, characterized by the accumulation of LC3B/VPS34 proteins and an increase in autophagosomes. However, the co-administration of 3-MA reversed this process, significantly decreasing the tumor growth rate. Immunofluorescence and qPCR demonstrated that the combination group had fewer Ki-67-positive cells and more Caspase-3-positive cells, along with upregulated expression of autophagy-related genes and Caspase-family apoptosis genes. Consequently, this study suggests that inhibiting autophagy with 3-MA disrupts the autophagy-mediated protective mechanism of tumor cells, promoting the activation of apoptotic signals and enhancing the antitumor activity of PTX. These findings may offer new molecular mechanistic insights and potential therapeutic strategies for overcoming PTX resistance in TNBC.