A reference genome for Acanthamoeba of genotype T6 assembled from an isolate from a UK patient with Acanthamoeba keratitis

Free-living amoebae of the genus Acanthamoeba can cause Acanthamoeba keratitis (AK), a sight-threatening infection of the cornea. Morphological and genotypic species delimitation within this genus remains controversial, underscoring the need for a deeper understanding of the relationship between Acanthamoeba diversity and clinical outcome. Genomic approaches are increasingly used to investigate infection dynamics. Using a hybrid assembly strategy that combined long- and short-read sequencing to improve assembly contiguity and lower errors, we generated the first complete nuclear and mitochondrial genome sequences for a rare genotype T6 Acanthamoeba isolate obtained from an AK patient in the United Kingdom. The isolate, GP39, most closely matches the description of Acanthamoeba palestinensis based on morphological features and growth characteristics. Phylogenetic analyses of rRNA genes demonstrated a close relationship with other genotype T6 isolates. Whole-genome sequence comparison showed that the available genotype T2 genome assembly (CDFA01), also nominally A. palestinensis , is more similar to our T6 assembly than to T4 assemblies. However, these were still approximately 10% divergent. These findings suggest a species-level divergence between these isolates and further highlight the limited resolution of morphological characteristics for species-level identification within Acanthamoeba spp.