Abstract
Leafcutter ants are ecologically important insects that cultivate fungal gardens for sustenance, playing crucial roles in Neotropical ecosystems. Due to their ecological and evolutionary significance, high-quality genomic assemblies for the species in this fascinating group can provide a foundation for understanding their evolution. Here, we present a chromosome-scale, haplotype-resolved genome assembly for Acromyrmex octospinosus, a common leafcutter ant species broadly distributed in the Neotropics. Using PacBio HiFi sequencing (99x coverage) and Hi-C scaffolding (51x coverage), we generated both haplotype-resolved assemblies (312-314 Mb) and a haplotype-collapsed assembly (320 Mb), each containing 19 chromosomes. One hundred percent of the assembly is anchored to chromosome-level scaffolds, and the assemblies exhibit high contiguity (contig N50: 6.13-8.28 Mb), base accuracy (QV 61.5-61.8), and gene completeness (BUSCO scores: 98.3% to 98.4%). Synteny analysis between haplotypes revealed high concordance (96.0% to 96.8%) with minor structural variations, consistent with expectations for a diploid individual. Combining transcriptomic and homology-based protein evidence with ab initio predictions, we annotated 12,123 genes, achieving a near-complete BUSCO gene completeness of 99.6%. The high-quality assemblies significantly enhance the current genomic resources available for leafcutter ants, providing a foundation for future comparative genomic studies within Acromyrmex and across fungus-farming ants.