The NCBI SRA database is constantly expanding due to the large amount of genomic and transcriptomic data from various organisms generated by next-generation sequencing, and re-searchers worldwide regularly deposit new data into the database. This high-coverage genomic and transcriptomic information can be re-evaluated regardless of the original research subject. The database-deposited NGS data can offer valuable insights into the genomes of organelles, particularly for non-model organisms. Here, we developed an automated bioinformatics workflow called “OrgaMiner”, designed to unveil high-quality mitochondrial and chloroplast genomes by data mining the NCBI SRA database. OrgaMiner, a Python-based pipeline, automatically orchestrates various tools to extract, assemble, and annotate organelle genomes for non-model organisms without available organelle genome sequences but with data in the NCBI SRA. To test the usability and feasibility of the pipeline, “mollusca” was selected as a keyword, and 76 new mitochondrial genomes were de novo assembled and annotated automatically without writing one single code. The applicability of the pipeline can be expanded to identify organelles in diverse invertebrate, vertebrate, and plant species by simply specifying the taxonomic name. OrgaMiner provides an easy-to-use, end-to-end solution for biologists mainly working with taxonomy and population genetics.

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.

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.