Near complete assembly of Drosophila melanogaster Canton S strain genome

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The fruit fly Drosophila melanogaster is a pivotal model organism, yet its reference genome (ISO-1 strain) retains unresolved gaps in complex regions. Here, we present a near-complete telomere-to-telomere genome assembly (Dm.nT2T) of the Canton S strain (male), generated using an integrative approach combining PacBio HiFi, Oxford Nanopore ultra-long reads, and Hi-C data. This assembly spans 161.63 Mb, closes 93.28% of gaps in the current reference genome, and improves contiguity (contig N50 of 21.93 Mb). We identify centromeric and telomeric regions, yielding a more complete genome map. Comparative analysis with the ISO-1 reference identifies 7989 structural variants, including large insertions/deletions enriched in telomeric and centromeric regions. Notably, we detect SINE transposable elements, and identify 92 genes via multi-strategy annotation. Functional validation of two genes shows that Chr3L.2449, expressed in olfactory tissues, is critical for olfactory sensitivity. Dm.nT2T provides a high-quality resource for exploring genomic complexity, strain diversity, and gene function in Drosophila. The fruit fly Drosophila melanogaster is an important model organism, but its reference genome retains unresolved gaps. Here, the authors report a near-complete telomere-to-telomere genome of the D. melanogaster S strain closing many remaining gaps.

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