New tsetse ( <i>Glossina fuscipes fuscipes</i> ) genomes generated from wild and laboratory‐reared specimens

Tsetse (Glossina spp.) are vectors of African trypanosomes that cause devastating human and animal African trypanosomiases. While much of the research to better understand tsetse genetics and physiology relies on colony-reared flies, these flies may not represent the genetic diversity found in natural wild populations due to their long-term captivity. To enhance the translation of colony research into field applications, we utilized Nanopore sequencing to assemble genomes for a wild-caught female Glossina fuscipes fuscipes (Gff) from northwestern Uganda and for a female Gff from a laboratory line originally sourced from the Central African Republic in 1986. The new assemblies, from the wild-caught Gff (405.98 Mb, N50: 56.86 Mb) and the laboratory-derived Gff (398.22 Mb, N50: 47.811 Mb), demonstrate near-chromosomal level contiguity, high BUSCO scores (> 99.5%), high QV scores (> 37), and over 12 345 genes. Alignments between both new genomes reveal conserved synteny with only minor structural variants in the X, 1L, 1R, 2L, and 2R tsetse chromosomes. While most orthologs (10 730) were shared between both new genomes, we identified 381 unique orthologs and a small number of highly diverged shared single-copy homologs (3.84%). These gene-set differences could represent population-level variation due to the distinct geographic origin of these flies or adaptation to colony conditions. Our new high-quality genomes, with improvements in contiguity and completeness compared to the current NCBI RefSeq Gff genome, lay the foundation for advanced tsetse research, enabling robust lab-to-field translational applications to deepen our understanding of vector biology and disease transmission dynamics.