A Haplotype-resolved Chromosome-scale Genome Assembly and Annotation for the Leafcutter Ant, Acromyrmex octospinosus

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.

Keywords: diploid assembly; fungus-farming ants; hymenoptera; insect genomics.

Fig. 1.

a) Hi-C density map for the haplotype-collapsed assembly of A. octospinosus. b) Synteny and structural rearrangements between 2 haplotypes of the A. octospinosus genome. The scaffolds presented on the y-axis are those of hap1.