High temperatures are considered one of the most significant limitations to subtropical fishery production. Largemouth bass (Micropterus salmoides) is an economically important freshwater species grown in subtropical areas, which are extremely sensitive to heat stress (HS). However, comprehensive transcriptomic data for the livers of largemouth bass in response to HS are still lacking. In this study, a comparative transcriptomic analysis was performed to investigate the gene expression profiles of the livers of largemouth bass under HS treatment. As a result, 6114 significantly differentially expressed genes (DEGs), which included 2645 up-regulated and 3469 down-regulated genes, were identified in response to HS. Bioinformatics analyses demonstrated that the ‘ECM-receptor interaction’ pathway was one of the most dramatically changed pathways in response to HS, and eight DEGs assigned to this pathway were taken as hub genes. Furthermore, the expression of these eight hub genes was determined by quantitative reverse transcription PCR, and all of them showed a significant change at the transcriptional level, suggesting a crucial role of the ‘ECM-receptor interaction’ pathway in the response of largemouth bass to HS. These findings may improve our understanding of the molecular mechanisms underlying the response of largemouth bass to HS.

Background: Chrysanthemum virus B (CVB), a key member of the genus Carlavirus, family Betaflexiviridae, causes severe viral diseases in chrysanthemum (Chrysanthemum morifolium) plants worldwide. However, information on the mechanisms underlying the response of chrysanthemum plants to CVB is scant. Methods: Here, an integrated next-generation sequencing and comparative transcriptomic analysis of chrysanthemum leaves was conducted to explore the molecular response mechanisms of plants to a Chinese isolate of CVB (CVB-CN) at the molecular level. Results: In total, 4934 significant differentially expressed genes (SDEGs) were identified to respond to CVB-CN, of which 4097 were upregulated and 837 were downregulated. Gene ontology and functional classification showed that the majority of upregulated SDEGs were categorized into gene cohorts involved in plant hormone signal transduction, phenylpropanoid and flavonoid biosynthesis, and ribosome metabolism. Enrichment analysis demonstrated that ethylene pathway-related genes were significantly upregulated following CVB-CN infection, indicating a strong promotion of ethylene biosynthesis and signaling. Furthermore, disruption of the ethylene pathway in Nicotiana benthamiana, a model plant, using virus-induced gene silencing technology rendered them more susceptible to cysteine-rich protein of CVB-CN induced hypersensitive response, suggesting a crucial role of this pathway in response to CVB-CN infection. Conclusion: This study provides evidence that ethylene pathway has an essential role of plant in response to CVB and offers valuable insights into the defense mechanisms of chrysanthemum against Carlavirus.

Chrysanthemum (Chrysanthemum morifolium) is an important ornamental and medicinal plant suffering from many viruses and viroids worldwide. In this study, a new carlavirus, tentatively named Chinese isolate of Carya illinoinensis carlavirus 1 (CiCV1-CN), was identified from chrysanthemum plants in Zhejiang Province, China. The genome sequence of CiCV1-CN was 8795 nucleotides (nt) in length, with a 68-nt 5′-untranslated region (UTR) and a 76-nt 3′-UTR, which contained six predicted open reading frames (ORFs) that encode six corresponding proteins of various sizes. Phylogenetic analyses based on full-length genome and coat protein sequences revealed that CiCV1-CN is in an evolutionary branch with chrysanthemum virus R (CVR) in the Carlavirus genus. Pairwise sequence identity analysis showed that, except for CiCV1, CiCV1-CN has the highest whole-genome sequence identity of 71.3% to CVR-X6. At the amino acid level, the highest identities of predicted proteins encoded by the ORF1, ORF2, ORF3, ORF4, ORF5, and ORF6 of CiCV1-CN were 77.1% in the CVR-X21 ORF1, 80.3% in the CVR-X13 ORF2, 74.8% in the CVR-X21 ORF3, 60.9% in the CVR-BJ ORF4, 90.2% in the CVR-X6 and CVR-TX ORF5s, and 79.4% in the CVR-X21 ORF6. Furthermore, we also found a transient expression of the cysteine-rich protein (CRP) encoded by the ORF6 of CiCV1-CN in Nicotiana benthamiana plants using a potato virus X-based vector, which can result in a downward leaf curl and hypersensitive cell death over the time course. These results demonstrated that CiCV1-CN is a pathogenic virus and C. morifolium is a natural host of CiCV1.

Within the context of global warming, understanding the molecular mechanisms behind physiological plasticity and local adaptation is essential for insect populations. This study performed an integrated miRNA and mRNA analysis on Aquatica leii larvae exposed to temperatures of 20 °C, 24 °C, 28 °C, and 32 °C. Under varying thermal conditions, 1983 genes exhibited differential expression (i.e., DEGs). These genes showed significant enrichment in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to carbohydrate metabolism, glycan biosynthesis and metabolism. Notably, we detected that the “neuroactive ligand–receptor interaction” signaling pathway, which is involved in environmental information processing, was significantly upregulated in the 28 °C and 32 °C treatment groups. This indicates that starting at 28 °C, A. leii needs to maintain normal cellular physiological functions by regulating ligand–receptor binding and signal transduction. Furthermore, 220 differentially expressed miRNAs (DEMs) were detected under the different temperature treatment conditions. An interaction network was constructed between key DEMs and DEGs, revealing 12 significant DEM-DEG regulatory pairs in A. leii under different temperature treatments. We found three miRNA-mRNA candidate modules that could be involved in A. leii’s response to high temperature, including ggo-miR-1260b and ptr-miR-1260b/RN001_010114, CM069438.1_43851/RN001_014852, and CM069438.1_43851/RN001_014877. Our data provide deeper insights into the molecular responses of A. leii to the high temperature at the miRNA and mRNA levels.

Widely used in humans and animals for bacterial infection management, antibiotics are poorly absorbed and persistent, being excreted into ecosystems and causing serious pollution. However, the effects of extended exposure to residual environmental levels of antibiotics in fireflies are currently unknown. In this study, we investigated Aquatica leii growth and development under chronic low-dose exposure to oxytetracycline (OTC) and levofloxacin (LEV) residues using physiology, transcriptomics, and metabolomics. The results showed that OTC and LEV treatments enhanced A. leii larval growth (increased body length and weight) and significantly altered SOD and CAT activities. Transcriptional analyses identified 1193 and 1669 differentially expressed genes from the LEV and OTC groups, respectively, compared to the control group, predominantly associated with insect hormone biosynthesis, digestive system, immune system, and signal transduction. The metabolomic results showed that 965 and 1094 endogenous metabolites (i.e., comprising mainly amino acids, organic acids, and carbohydrates) were affected by LEV and OTC treatments, respectively. These metabolites are mainly enriched in signal transduction, amino acid metabolism, and energy metabolism pathways. Further, a conjoint omics analysis highlighted the multifaceted regulatory roles of glutathione metabolism in the response of A. leii to OTC and LEV treatments. The study provides critical insights into the transcriptional and metabolic responses of A. leii to antibiotic treatment, informing dosage guidelines for sustainable A. leii farming.

The Gretchen Hagen 3 (GH3) gene family, a key component of the early auxin-responsive gene family, plays a pivotal role in regulating plant growth, development, and stress responses. However, to date, a comprehensive genome-wide analysis of the GH3 gene family and its potential role in plant defense against viruses, such as tomato yellow leaf curl virus (TYLCV), has not been conducted in Nicotiana benthamiana. Here, the GH3 gene family was thoroughly examined in N. benthamiana using a comprehensive genome-wide bioinformatic approach. A total of 25 potential GH3 genes were discovered in N. benthamiana. Phylogenetic analysis classified these NbGH3s into three different clades. Chromosomal distribution and synteny analyses revealed that NbGH3s are unevenly distributed across 14 chromosomes, with 20 segmental and one tandem duplication pairs. Promoter analysis suggested their involvement in phytohormone signaling and stress responses. Quantitative PCR showed that several NbGH3s are transcriptionally responsive to TYLCV infection, with five of them significantly upregulated in infected leaves. Furthermore, virus-induced gene silencing revealed that the suppression of NbGH3-3 and NbGH3-9 markedly increased host susceptibility to TYLCV, underscoring their critical roles in plant antiviral defense mechanisms. This research establishes a framework for understanding the functions of NbGH3s in plant growth and their response to TYLCV infection.