Exploring the First Draft Genome of the Oribatid Mite, Oppia nitens : A Standardized Model Invertebrate in Soil Ecotoxicology

Oribatid mites are among the most abundant groups of soil microarthropods. Oppia nitens (family Oppiidae), a member of one of the largest and most diverse oribatid mite families, has been developed as a standardized model organism for assessing soil contamination. However, limited genomic resources for this species hinder our understanding of its physiological adaptations and sensitivities to chemical and environmental stressors. Here, we present the annotated O. nitens draft genome, generated through a de novo hybrid assembly combining Oxford Nanopore Technologies and Illumina sequencing data, providing a foundation for identifying genes associated with adaptation to environmental and chemical stress. The assembled genome consists of 65 scaffolds spanning 125.4 Mb, with a GC content of 24.5% and an N50 of 4.41 Mb. Genome completeness, assessed using arthropod Benchmarking Universal Single-Copy Orthologs (BUSCO), revealed 99.1% BUSCO completeness, 98.0% complete single copy, 1.1% duplicated, 0.5% fragmented, and 0.4% missing orthologs (arachnida_odb12, n = 1123). Using the National Center for Biotechnology Information Eukaryotic Genome Annotation Pipeline, we annotated 15,291 genes, 16,969 mRNAs, and 14,938 proteins. This high-quality draft genome represents the first comprehensive genomic resource for O. nitens and provides a valuable foundation for future investigations into the molecular mechanisms underlying environmental adaptation, particularly tolerance to metal stress.