Near-complete genome assembly of the African turquoise killifish enables locus-level profiling of transposable element expression

An improved chromosome-scale assembly of the African turquoise killifish, Nothobranchius furzeri, resolves tandem repeats occupying up to 28.0% of the whole genome and matches the experimentally estimated genome size and chromosome number. Using this and other complete vertebrate assemblies, the authors show that choices in tandem repeat detection reshape the apparent transposable element landscape, with different TE workflows recovering complementary sets of age- and sex-associated TE loci in a sex-balanced multi-tissue aging cohort. Combinatorial use of repeat detection programs supports robust, locus-level profiling of TEs.