Xuezhu Lee

In 2025, a severe mass mortality outbreak struck captive Geochelone sulcata at a zoo in Guangdong Province, China. To trace the causative agent, identify the viral strain and characterize associated pathological lesions, respiratory tract samples collected from diseased tortoises were subjected to a combined technical workflow. Metagenomic high-throughput sequencing was first applied to screen for potential pathogens, followed by virus isolation via cell culture. Transmission electron microscopy (TEM) was used to observe viral morphology. The major capsid protein (MCP) gene was amplified by PCR for molecular identification, and whole-genome sequencing together with phylogenetic analysis was performed to clarify the genetic features of the isolate. The results verified that ranavirus was the primary pathogen responsible for the mortality. Pathological examination demonstrated acute necrosis, hemorrhage and inflammatory infiltration in multiple organs including the liver, spleen, lung, and pancreas. TEM observation revealed typical iridovirus-like particles with an average diameter of approximately 70 nm. Molecular and genomic analyses confirmed the pathogen as Tiger Frog Virus (TFV) of the genus Ranavirus, designated TFV-CN2025, which shared 99.8% nucleotide sequence homology with known TFV reference strains. To our knowledge, this is the first report of lethal TFV infection in G. sulcata, which provides detailed pathological evidence for this cross-species transmission event from amphibian hosts to terrestrial chelonians. Our findings indicate that TFV poses considerable risks to the tortoise breeding industry and ecological security in China. We therefore suggest incorporating TFV detection into routine quarantine and disease surveillance programs for captive tortoises.

Long noncoding RNAs (lncRNAs) constitute an emerging group of ncRNAs that modulate gene expression at the transcriptional or translational level. Koi herpesvirus (KHV), also known as Cyprinus herpesvirus type 3 (CyHV-3) and characterized by high pathogenicity and high mortality, has caused substantial economic losses in the common carp and koi carp fisheries industry. In this work, we sequenced the lncRNA and mRNA of host koi carp infected with KHV. A total of 20,178 DEmRNAs were obtained, of which 5021 mRNAs were upregulated and 15,157 mRNAs were downregulated. Both KEGG pathways and GO terms were enriched in many important immune pathways. The KEGG analysis showed that DEGs were significantly enriched in many important immune pathways, such as apoptosis, NOD-like receptor signaling pathway, Jak-STAT signaling pathway, TNF signaling pathway, IL-17 signaling pathway, NF-kappa B signaling pathway, and so on. Furthermore, a total of 32,697 novel lncRNA transcripts were obtained from koi carp immune tissues; 9459 of these genes were differentially expressed. Through antisense, cis-acting, and trans-acting analyses, the target genes of differentially expressed lncRNAs (DElncRNAs) were predicted. Gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that the DElncRNA expression pattern was consistent with the differential mRNA expression pattern. The lncRNA–mRNA network analysis, which included many immune pathways, showed that after KHV infection, the expression of most lncRNAs and their target mRNAs were downregulated, suggesting that these lncRNAs engage in a positive regulatory relationship with their target mRNAs. Considering that many studies have shown that herpesviruses can escape the immune system by negatively regulating these immune pathways, we speculated that these lncRNAs play a significant role in KHV’s escape from host immunity. Furthermore, 10 immune-related genes and 20 lncRNAs were subsequently verified through RT–qPCR, to confirm the accuracy of the high-throughput sequencing results. In this study, we aimed to explore lncRNA functions in the immune response of lower vertebrates and provide a theoretical basis for the study of noncoding RNAs in teleosts. Therefore, exploring lncRNA expression in KHV-infected koi carp helped us better understand the biological role played by lncRNA-dependent pathways in aquaculture animal viral infection.

The spotted catfish, Arius maculatus (Siluriformes), is an important economical aquaculture species inhabiting the Indian Ocean, as well as the western Pacific Ocean. The bioinformatics data in previous studies about the phylogenetic reconstruction of Siluriformes were insufficient and incomplete. In the present study, we presented a newly sequenced A. maculatus mitochondrial genome (mtDNA). The A. maculatus mtDNA was 16,710 bp in length and contained two ribosomal RNA (rRNA) genes, thirteen protein-coding genes (PCGs), twenty-two transfer RNA (tRNA) genes, and one D-loop region. The composition and order of these above genes were similar to those found in most other vertebrates. The relative synonymous codon usage (RSCU) of the 13 PCGs in A. maculatus mtDNA was consistent with that of PCGs in other published Siluriformes mtDNA. Furthermore, the average non-synonymous/synonymous mutation ratio (Ka/Ks) analysis, based on the 13 PCGs of the four Ariidae species, showed a strong purifying selection. Additionally, phylogenetic analysis, according to 13 concatenated PCG nucleotide and amino acid datasets, showed that A. maculatus and Netuma thalassina (Netuma), Occidentarius platypogon (Occidentarius), and Bagre panamensis (Bagre) were clustered as sister clade. The complete mtDNA of A. maculatus provides a helpful dataset for research on the population structure and genetic diversity of Ariidae species.

The complete mitochondrial DNA sequence of Apogonichthyoides taeniatus (Cuvier, 1828) is determined. The mitochondrial genome is 17,050 in length and has the same composition and gene order like most other vertebrates. The phylogenetic analysis based on 13 concatenated PCGs nucleotide sequences among 20 species showed that this species has high support with the sister branch Jaydia lineata. Our findings provide useful information for phylogenetic and evolutionary research of Kurtiformes species.