A near telomere-to-telomere genome assembly of the Amur stickleback (Pungitius sinensis) reveals structural variation and parallel evolution of sticklebacks

Fish species in the genus Pungitius exhibit substantial diversity in morphology and behavior. These species have undergone parallel evolution with three-spined sticklebacks, producing convergent traits. Pungitius genomes have a complex evolutionary history with extensive chromosomal rearrangements and structural variations, which is divided into two main clades: the pungitius clade, predominantly found in North America and Europe, and the sinensis clade endemic to Northeast Asia. While a genome reference has been available for the pungitius clade (i.e. ninespine stickleback Pungitius pungitius), genomic data for the sinensis clade remains lacking, which limits the exploration of genetic changes underlying their morphological diversity, geographic and ecological adaptation, and parallel evolution with the three-spined stickleback (Gasterosteus aculeatus). Here, we present a high-quality genome assembly for Amur stickleback (Pungitius sinensis) from the sinensis clade, which represents the first near telomere-to-telomere stickleback genome assembly using PacBio high-fidelity, Oxford Nanopore Technology ultra-long, and Hi-C sequencing data. Comparative chromosome-scale analyses indicate adaptive introgression from G. aculeatus into P. sinensis, and reveal shared genomic regions with the three-spined stickleback associated with dorsal spine and pelvic morphology. This genome also provides novel insights into chromosome rearrangements among sticklebacks and reveals unique characteristics in the evolution of sex chromosome systems within Gasterosteidae. Together, these results highlight the parallel evolutionary mechanisms shaping the morphology and behavior of Pungitius and Gasterosteus, offering a valuable resource for advancing research in ecological adaptation and genome evolution.