Near-complete genome assembly of the African turquoise killifish enables locus-level profiling of transposable element expression
- 1National Institute of Genetics
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.
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BibTeX
@misc{ogawa2026nearcomplete,
title = {{Near-complete genome assembly of the African turquoise killifish enables locus-level profiling of transposable element expression}},
author = {Y. Ogawa and A. Kawaguchi and K. Abe and T. Ishitani and S. Kuraku},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.12.757905},
url = {https://www.biorxiv.org/content/10.64898/2026.10.12.757905v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Near-complete genome assembly of the African turquoise killifish enables locus-level profiling of transposable element expression
AU - Y. Ogawa
AU - A. Kawaguchi
AU - K. Abe
AU - T. Ishitani
AU - S. Kuraku
PY - 2026
DA - 2026/10/12
PB - bioRxiv
DO - 10.64898/2026.10.12.757905
UR - https://www.biorxiv.org/content/10.64898/2026.10.12.757905v1
AB - 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.
ER -