Work

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

Year: 2026

Type: preprint

Abstract: Tandem repeats (TRs) and transposable elements (TEs) occupy substantial fractions of eukaryotic genomes, yet how repeat detection programs affect downstream expression analyses remains poorly explored. Here, we present an improved chromosome-scale assembly of the African turquoise killifish, Nothobranchius furzeri . The assembly matches experimentally estimated genome size and chromosome number. It resolves highly expanded TRs that occupy up to 28.0% of the whole genome. Using this assembly and other complete vertebrate genome assemblies, we compared TR and TE-derived regions across combinations of TR detection programs and TE consensus library construction workflows under a standardized TE classification scheme. Choices in TR detection reshaped the apparent TE landscape. TE workflows shared a broad core of TE-derived regions but recovered complementary sets of age- and sex-associated TE loci, evaluated with a sex-balanced killifish multi-tissue aging cohort. Together, the combinatorial use of adaptable programs supports robust, locus-aware detection of complex repeats across genome assemblies.

Source: bioRxiv (Cold Spring Harbor Laboratory)

DOI: 10.64898/2026.10.12.757905

Authors: Yohey Ogawa, Akane Kawaguchi, Kota Abe, Tohru Ishitani, Shigehiro Kuraku

Institutions: National Institute of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Research Institute for Microbial Diseases, The University of Osaka, The University of Osaka, Center for Infectious Disease Education and Research, The University of Osaka

Language: English

Topic: Chromosomal and Genetic Variations

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green