Tuana Öğretici

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.

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.

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.