WGS-based de novo genome assemblies and comparative functional annotations on genomic architecture and molecular variation in Oecophylla smaragdina (Formicidae: Hymenoptera)

Oecophylla smaragdina, the Asian weaver ant, is a socially complex arboreal species with three distinct morphological castes queen, drone, and worker. Despite its pronounced caste differentiation, the genomic basis underlying these phenotypic distinctions remains less understood. In this study, we present caste-specific draft genome assemblies and functional annotations to investigate the genomic architecture and diversity among castes. Whole-genome sequencing was performed using the Illumina NovaSeq 6000 platform. GenomeScope analysis estimated genome sizes ranging from 210-227 Mb, with low repeat content (0.6–1.4%). Assemblies generated via SPAdes revealed that the worker genome was the most contiguous (N50: 16 kb; scaffolds: 120,615). BUSCO assessments (Hymenoptera_odb10) indicated the highest completeness in the worker genome (84.2%), followed by the queen (74.8%) and drone (72.3%). QUAST comparisons against the reference genome (GCA_048542515.1) supported these findings, with the worker genome showing the largest genome fraction (95.47%). Structural annotation using AGAT identified 32,485 genes in the queen, 17,904 in the drone, and 17,723 in the worker. Functional annotation through InterProScan and eggNOG-mapper revealed enrichment in transcription and signal transduction categories across all castes. Gene ontology analysis highlighted caste-specific pathways like reproductive functions in queens, metabolic processes in workers, and neural functions in drones. Phylogenetic reconstruction confirmed close clustering of all three castes within O. smaragdina and the broader Formicidae lineage. All sequencing data have been deposited in the NCBI Sequence Read Archive under BioProject ID PRJNA1078118. These draft genome assemblies provide a foundational resource for future investigations into caste differentiation, eusociality, and evolutionary genomics in ants.