Onur Obut

Orosanga japonica (Hemiptera: Ricaniidae) is an invasive, polyphagous planthopper established in Türkiye since 2007 that threatens economically important perennial and field crops across the Black Sea region. Although its establishment and rapid spread suggest considerable adaptive capacity, the genomic basis of this potential remains unexplored. We combined whole-genome sequencing with RNA-Seq data to generate a functionally annotated genome, recovering 92.5% of conserved single-copy orthologs. Utilizing these resources, we performed comparative genomic analyses across 20 additional hemipteran and thysanopteran species, investigating gene family dynamics and genome-wide positive selection. These analyses revealed 52 gene families with statistically significant, lineage-specific size changes (24 expansions and 28 contractions): expanded families were enriched for C2H2 zinc-finger transcription factors, α/β-hydrolases, major facilitator transporters, serpins, and chemosensory proteins, whereas contracted families included a cytochrome P450 family. Additionally, branch site tests identified 122 candidate genes under lineage-specific positive selection. These loci fall into three functional categories potentially associated with invasion-related traits: host detection and neuronal excitability, stress tolerance (xenobiotic, oxidative, and proteostatic), and barrier remodeling. Together, these genomic signatures highlight candidate molecular mechanisms that may contribute to host detection, xenobiotic tolerance, and ecological plasticity, providing a framework for evolutionary analysis and the targeted management of this emerging agricultural pest.

The European anchovy is a keystone forage species in the Mediterranean and Northeast Atlantic, yet a chromosome-scale reference genome has been lacking. Here, we present a 1.4 Gb assembly anchored to 24 chromosomes (scaffold N50 = 56.4 Mb; BUSCO 96.6%) with 27,663 annotated protein-coding genes and 44.6% repetitive content dominated by DNA transposons, which likely account for the near doubling of genome size relative to Atlantic herring. Comparative analyses across 11,755 orthogroups revealed a net contractive trend in Clupeidae, superimposed on conspicuous expansions of antiviral and innate-immune gene families (TRIM16, GTPase IMAP member 8, IFI44, Toll-like receptors), with GO enrichment exceeding 400-fold for antiviral regulatory processes. Branch-site analyses identified 216 positively selected genes in E. encrasicolus, 81 of which map to innate signaling, epigenetic regulation, ubiquitin-mediated immunity, and selective autophagy. Multitissue RNA-Seq further demonstrated that expanded, positively selected, and epithelial barrier-associated genes, including 11 claudin paralogues, zonula-occludens scaffolds, and tricellular junction components, are coordinately enriched in the gill. Together, these findings highlight a gill-enriched immune landscape potentially shaped by filter-feeding ecology, providing a genomic framework for clupeid immunogenomics and aquaculture applications.

Microbial cell-free supernatants (CFS) produced by lactic acid bacteria represent complex bioactive metabolite mixtures with potential applications in food safety and microbiota-targeted interventions. However, the biological safety and the capacity of Latilactobacillus sakei-derived CFS to modulate the intestinal microbiome remain insufficiently characterized. Here, we investigated the chemical composition, antimicrobial activity, cytotoxicity, systemic safety, and potential to modulate the intestinal microbiota of a freeze-dried CFS of L. sakei ATCC 15521. The characterization analyses showed that the CFS contained a diverse array of bioactive compounds, including organic acids, phenolic compounds, free amino acids, volatile metabolites, and antioxidant activities. The CFS exhibited broad-spectrum antimicrobial activity against major foodborne pathogens. In vitro analyses using Caco-2 cells revealed concentration-dependent cytotoxicity with an IC₅₀ value of 9.37 mg/mL, whereas sub-cytotoxic concentrations maintained high epithelial cell viability. Gastric administration of the freeze-dried CFS in BALB/c mice did not cause significant systemic toxicity, as assessed by serum biochemical markers and histopathological evaluations. Furthermore, 16S rRNA-based microbiome analyses showed that CFS administration altered the intestinal microbial community composition, differentially enriching specific bacterial taxa and predicting altered microbial metabolic pathways in duodenal and cecal samples. Linear discriminant analysis effect size (LEfSe) analyses identified enrichment of Limosilactobacillus and Lactobacillaceae-associated taxa in the treatment groups, suggesting that the CFS has microbiota-modulatory activity. Collectively, these findings demonstrate that L. sakei-derived CFS constitutes a chemically diverse and biologically active metabolite preparation that modulates the intestinal microbiota without inducing detectable systemic toxicity in vivo.

Sex determination in teleost fishes exhibits remarkable evolutionary plasticity; however, the underlying mechanisms remain largely elusive for many species of high economic importance. Herein, we provide the first genome-wide investigation of the genetic basis of sex determination in the European anchovy (Engraulis encrasicolus), an ecologically and commercially vital clupeiform fish. Using low-pass whole-genome resequencing of 100 sexually mature individuals (50 females and 50 males), we conducted a genome-wide association study (GWAS) and F_ST scans to identify sex-linked loci and characterize sex-determining regions (SDRs). Our analyses revealed two major candidate SDRs located on chromosomes 14 and 18, encompassing multiple sex-associated single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). Among these, the amhr2 (anti-Müllerian hormone type 2 receptor) gene on Chr14 displayed the strongest and most consistent association with phenotypic sex, marked by several male-specific missense SNPs and InDel variants. Comparative and transcriptomic analyses confirmed sex-biased expression of amhr2 and other SDR-linked genes, potentially indicating a male heterogametic (XY-like) genetic sex determination system. These results provide the first molecular evidence for a candidate SDR in E. encrasicolus, raise the possibility of involvement of amhr2 and additional loci in sex determination, and highlight rapid sex chromosome turnover within Clupeiformes. Our findings not only expand the understanding of teleost sex determination evolution but also establish a genomic foundation for developing molecular tools for sex identification and population management in anchovy fisheries.

Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related mortality, underscoring the need to elucidate molecular mechanisms that regulate tumor cell state and behavior. Leucine zipper–like post-translational regulator 1 (LZTR1) regulates RAS/mitogen-activated protein kinase (MAPK) signaling, yet LZTR1-dependent transcriptional alterations in HCC cells remain poorly defined. To address this gap and determine how LZTR1 loss reshapes signaling, transcriptional programs, and cellular phenotypes, we established a LZTR1 knockout (KO) Hep3B model and combined pathway profiling with transcriptomic and functional analyses. Immunoblotting revealed increased phosphorylation across the RAF–MEK–ERK–RSK cascade in LZTR1 KO cells. Transcriptome-wide RNA sequencing (RNA-Seq) identified differentially expressed genes, and selected findings were validated by qRT-PCR. Gene set enrichment analysis indicated that the epithelial–mesenchymal transition (EMT) gene set was enriched in control cells. At the protein level, LZTR1 loss remodeled EMT-associated markers in a hybrid epithelial–mesenchymal pattern consistent with epithelial–mesenchymal plasticity (EMP). Vimentin was suppressed at transcript and protein levels. Functionally, LZTR1 KO cells exhibited impaired wound closure and reduced transwell migration and invasion. Collectively, these findings define an EMP-related molecular and phenotypic state associated with LZTR1 deficiency in Hep3B cells, providing insight into how LZTR1 loss reshapes tumor cell behavior in HCC.

Bumblebees are ubiquitous, cold-adapted, primitively eusocial bees and important pollinators for crops and vegetation. However, many species are declining worldwide due to multiple factors, including human-induced habitat loss, agricultural chemicals, global warming, and climate change. In particular, future climate scenarios predict a shift in the spatial distribution of bumblebees under global warming, with some species declining and others potentially expanding. Here, we report a de novo genome assembly and annotation for Bombus lapidarius and Bombus niveatus to decipher species-specific potential genomic capacity against such environmental stressors. With harboring more than 23,000 protein-coding genes, the assembled genomes of B. lapidarius and B. niveatus are 244.44 Mb (scaffold N50 of 9.45 Mb) and 259.84 Mb (scaffold N50 of 10.94 Mb), respectively, which exhibit similar trends in terms of genome size and composition with other bumblebees. Gene family analysis reveals differences in species-specific expanded gene families. B. lapidarius exhibits expanded genes related to pre/postsynaptic organization, while B. niveatus shows a distinct expansion in gene families regulating cellular growth, aging, and responses to abiotic and biotic stressors, such as those containing SCAN domains, WD-repeats, and Ras-related proteins. Our genome-wide screens revealed positive selection on environmental stress-responsive genes such as dip2, yme1l, and spg7 in B. lapidarius, whereas positive selection signatures were found in genes such as myd88, mybbp1A, and rhau, which are involved in environmental stress resistance for B. niveatus. These high-quality genome assemblies and comparative genome analysis unveil potential drivers that underlie genome evolution in bumblebees, offering valuable insights into environmental adaptation and conservation efforts.