Sea stickleback genome reveals repeated chromosomal rearrangements in sticklebacks
- 1Department of Biology, University of Copenhagen, Denmark
Abstract
Sticklebacks (Gasterosteidae) encompass model organisms which are of particular interest for evolutionary and ecological genomics. Within Gasterosteidae, chromosome number is variable (2n=40-46) and independent fusions of homologous chromosomes have been proposed. The sea stickleback (or fifteen-spined stickleback, Spinachia spinachia ) has the lowest known number of chromosomes (2n=40) and hence is crucial in understanding chromosome evolution among sticklebacks, but is so far missing in genomic datasets. Here, we present a high-quality diploid genome assembly of S. spinachia. PacBio HiFi and Hi-C reads were assembled into a genome of 407.5 Mb in size, consisting of 20 chromosomes, with an N50 of 6.6 Mb and 98.96% complete single-copy BUSCO genes. A phylogenetic tree inferred across five stickleback species and four outgroup genomes from 19,156 genes, alongside synteny analyses and ancestral chromosome reconstructions, confirms S. spinachia as the sister species to the four-spined stickleback (Apeltes quadracus) and not as the sister group to all other sticklebacks as once thought. It has one species-specific chromosome fusion and shares two fusions with the three-spined stickleback (Gasterosteus aculeatus), none of which are present in its sister species. One of these fusions is also present in Pungitius, leading to reinterpretion of this fusion as ancestral to Gasterosteidae, with subsequent fission in Apeltes. This implies a lower ancestral chromosome number in Gasterosteidae (2n=44) than previously thought. The other fusion shared with G. aculeatus presents a case of convergence. Our results suggest that karyotype evolution in Gasterosteidae has been shaped by ancestral chromosome fusion, convergent fusion, and secondary fission.
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BibTeX
@misc{drewalowski2026stickleback,
title = {{Sea stickleback genome reveals repeated chromosomal rearrangements in sticklebacks}},
author = {J. Drewalowski and S. Kliver and L. Hilgers and P. R. Moller and S. S. Mak and I. Kovacic and B. Petersen and J. Nesme and A. M. Mc Cartney and A. Mouton and G. Formenti and H. Svardal and G. Diedericks and H. G. Leitao and R. Fernandez and N. Escudero and J. Salces-Ortiz and C. Ciofi and C. Natali and M. A. Diroma and A. Iannucci and M. Sollitto and M. Hiller and M. T. P. Gilbert and J. Stiller},
howpublished = {bioRxiv},
year = {2026},
month = aug,
doi = {10.64898/2026.08.30.747834},
url = {https://www.biorxiv.org/content/10.64898/2026.08.30.747834v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Sea stickleback genome reveals repeated chromosomal rearrangements in sticklebacks
AU - J. Drewalowski
AU - S. Kliver
AU - L. Hilgers
AU - P. R. Moller
AU - S. S. Mak
AU - I. Kovacic
AU - B. Petersen
AU - J. Nesme
AU - A. M. Mc Cartney
AU - A. Mouton
AU - G. Formenti
AU - H. Svardal
AU - G. Diedericks
AU - H. G. Leitao
AU - R. Fernandez
AU - N. Escudero
AU - J. Salces-Ortiz
AU - C. Ciofi
AU - C. Natali
AU - M. A. Diroma
AU - A. Iannucci
AU - M. Sollitto
AU - M. Hiller
AU - M. T. P. Gilbert
AU - J. Stiller
PY - 2026
DA - 2026/08/30
PB - bioRxiv
DO - 10.64898/2026.08.30.747834
UR - https://www.biorxiv.org/content/10.64898/2026.08.30.747834v1
AB - Sticklebacks (Gasterosteidae) encompass model organisms which are of particular interest for evolutionary and ecological genomics. Within Gasterosteidae, chromosome number is variable (2n=40-46) and independent fusions of homologous chromosomes have been proposed. The sea stickleback (or fifteen-spined stickleback, Spinachia spinachia ) has the lowest known number of chromosomes (2n=40) and hence is crucial in understanding chromosome evolution among sticklebacks, but is so far missing in genomic datasets. Here, we present a high-quality diploid genome assembly of S. spinachia. PacBio HiFi and Hi-C reads were assembled into a genome of 407.5 Mb in size, consisting of 20 chromosomes, with an N50 of 6.6 Mb and 98.96% complete single-copy BUSCO genes. A phylogenetic tree inferred across five stickleback species and four outgroup genomes from 19,156 genes, alongside synteny analyses and ancestral chromosome reconstructions, confirms S. spinachia as the sister species to the four-spined stickleback (Apeltes quadracus) and not as the sister group to all other sticklebacks as once thought. It has one species-specific chromosome fusion and shares two fusions with the three-spined stickleback (Gasterosteus aculeatus), none of which are present in its sister species. One of these fusions is also present in Pungitius, leading to reinterpretion of this fusion as ancestral to Gasterosteidae, with subsequent fission in Apeltes. This implies a lower ancestral chromosome number in Gasterosteidae (2n=44) than previously thought. The other fusion shared with G. aculeatus presents a case of convergence. Our results suggest that karyotype evolution in Gasterosteidae has been shaped by ancestral chromosome fusion, convergent fusion, and secondary fission.
ER -