Chromosome-level genome assembly of the Poitevin stickleback (Pungitius vulgaris)
Abstract
The Poitevin stickleback ( Pungitius vulgaris ) is a Near Threatened freshwater fish endemic to France. Using PacBio HiFi long reads and Hi-C scaffolding, we generated the first chromosome-level reference genome for this species. The assembly spans 489.65 Mb across 21 chromosomes, with a scaffold N50 of 21.77 Mb and 99.5% BUSCO completeness. A total of 21,656 protein-coding genes were predicted, and approximately 25.65% of the genome was identified as repetitive sequences. Based on the enrichment of male-specific k-mers on chromosome 12 (chr12), we identified this chromosome as the putative sex chromosome, is consistent with an XY sex-determination system. A short male-specific region (~4 kb; chr12: 24,419,000-24,423,000 bp) was identified that is located in a highly repetitive region and contains one protein-coding gene ( gata1a -like). Although the exact boundary of the sex-determining region (SDR) can not be determined, this short male-specific region embedded in highly repetitive elements suggests a sex-determining architecture distinct from that reported in other sticklebacks. This reference genome provides a foundational resource for population genomics and for studies of sex chromosome evolution in the Poitevin stickleback.
Related
- Cold-water gut isolate from threespine stickleback (Gasterosteus aculeatus) reveals polypropylene surface oxidation and co-culture inhibition
- Recombination rate and efficiency of linked selection in small and large stickleback populations
- Effects of Rhizobium tropici inoculation and swine wastewater compost on common bean (Phaseolus vulgaris L.) growth and yield
- New Tonian-Ediacaran zircon U-Pb ages and Hf isotopes from arc-related magmatism with adakite-like signatures in the Araçuaí-Ribeira Orogenic System (SE-Brazil): Implications for early Western Gondwana assembly
- Fire modulates millennial plant community assembly
BibTeX
@article{wang2026chromosomelevel,
title = {{Chromosome-level genome assembly of the Poitevin stickleback (Pungitius vulgaris)}},
author = {Dandan Wang and Hongbo Wang and Gaël P.J. Denys and Juha Merilä},
journal = {Scientific Data},
year = {2026},
month = aug,
doi = {10.1038/s41597-026-08147-6},
url = {https://hal.science/hal-05732101v1},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Chromosome-level genome assembly of the Poitevin stickleback (Pungitius vulgaris)
AU - Dandan Wang
AU - Hongbo Wang
AU - Gaël P.J. Denys
AU - Juha Merilä
PY - 2026
DA - 2026/08/19
JO - Scientific Data
DO - 10.1038/s41597-026-08147-6
UR - https://hal.science/hal-05732101v1
AB - The Poitevin stickleback ( Pungitius vulgaris ) is a Near Threatened freshwater fish endemic to France. Using PacBio HiFi long reads and Hi-C scaffolding, we generated the first chromosome-level reference genome for this species. The assembly spans 489.65 Mb across 21 chromosomes, with a scaffold N50 of 21.77 Mb and 99.5% BUSCO completeness. A total of 21,656 protein-coding genes were predicted, and approximately 25.65% of the genome was identified as repetitive sequences. Based on the enrichment of male-specific k-mers on chromosome 12 (chr12), we identified this chromosome as the putative sex chromosome, is consistent with an XY sex-determination system. A short male-specific region (~4 kb; chr12: 24,419,000-24,423,000 bp) was identified that is located in a highly repetitive region and contains one protein-coding gene ( gata1a -like). Although the exact boundary of the sex-determining region (SDR) can not be determined, this short male-specific region embedded in highly repetitive elements suggests a sex-determining architecture distinct from that reported in other sticklebacks. This reference genome provides a foundational resource for population genomics and for studies of sex chromosome evolution in the Poitevin stickleback.
SN - 2052-4463
ER -