Sex chromosome turnover in African annual killifishes of the genus Nothobranchius

Sex chromosomes of teleost fishes undergo frequent turnovers. Annual Nothobranchius killifishes provide a suitable system to study sex chromosome turnover as they comprise the XY sex chromosome system in the model turquoise killifish, N. furzeri, and X1X2Y multiple sex chromosomes in six other representatives scattered across the Nothobranchius phylogeny, nested within species without cytologically detectable sex chromosomes. We combined molecular cytogenetics and genomic analyses to examine the X1X2Y systems in four Nothobranchius spp. and their outgroup Fundulosoma thierryi. Fluorescence in situ hybridization with painting probes specific for three sex chromosome systems and N. furzeri bacterial artificial chromosomes (BAC) bearing orthologues of eight genes repeatedly co-opted as master sex determining (MSD) genes in fishes suggests at least four independent origins of sex chromosomes in the genus Nothobranchius. The synteny block carrying the amhr2 gene was shared by X1X2Y systems o..., Genome de novo assembly and its quality evaluation
The F. thierryi long reads were first corrected using the Illumina short reads. Then, several options were used for genome assembly using Flye v2.8 (Kolmogorov et al. 2019) with the \"––nano-raw\" and \"--min-overlap 5000“ option giving the best assembly in terms of contiguity and BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness. The assembly underwent one round of long read polishing via medaka (https://github.com/nanoporetech/medaka) followed by a round of short read polishing using NextPolish (Hu et al. 2020) with Illumina reads. Haplotypic duplicates were then removed using the purge_dups v1.0.1 tool (Guan et al. 2020). Assembly quality was assessed using BUSCO v5 with the Actinopterygii database (odb_10) (Manni et al. 2021). Contamination checks were performed using BlobTools v1.0 (Laetsch & Blaxter 2017), and any contigs associated with non-target organisms were eliminated using the \"seqfilter\" function. The best..., , # Description of the data and file structure

**README for the Dryad repository**: [https://doi.org/10.1111/mec.70029](https://doi.org/10.1111/mec.70029)

**Study:**

Hospodářská M, Mora P, Chung Voleníková A, Al-Rikabi A, Altmanová M, Simanovsky SA, Tolar N, Pavlica T, Janečková K, Štundlová J, Bobryshava K, Jankásek M, Hiřman M, Liehr T, Reichard M, Krysanov EY, Ráb P, Englert C, Nguyen P, Sember A (2025) *Multiple Origins of Sex Chromosomes in *Nothobranchius* Killifishes*. **Molecular Ecology**, 34:e70029. [https://doi.org/10.1111/mec.70029](https://doi.org/10.1111/mec.70029)

Last updated: August 11, 2025

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## Data provided

### *Fundulosoma thierryi*

#### Genome assembly

* `Nthi_Corr-Uncor_Strict_Meta_Min5000_assembly_Medaka_Long_Next_Short_Purged.fasta`: FASTA format of the *Fundulosoma thierryi* female genome assembly.
* `FTHI_NFU_ragoo.fasta`: FASTA of Fundulosoma thierryi pseudochromosomes scaffolded by RaGOO using *Nothobranchius furzeri* as reference.

#### Gene annota...,