Chromosome-level assembly of the Hypophthalmichthys molitrix (Cypriniformes: Cyprinidae) genome provides insights into its ecological adaptation.
Hypophthalmichthys molitrix (silver carp) is phytoplanktivorous and is an economically and ecologically important fish species. As a well-known invasive species, a number of factors associated with the ecological adaptations of this species are largely unknown. Here, we present a chromosomal-level assembly of the species based on the PacBio Sequel II platform and Hi-C scaffolding technology. Based on the high-quality genome sequences and previous genome sequencing projects, a number of genes that were probably subject to positive selection reside in the genome of H. molitrix, and the last common ancestors of H. molitrix and H. nobilis were identified. Some of these genes may partially explain the mechanisms of H. molitrix for surviving damage due to toxic algae. Demographic history estimation suggests that the effective population size (EPS) of the species may have constantly increased along with the uplift of the Qinghai-Tibet Plateau, started to decline when quaternary glaciation started, and further declined during the Younger Dryas Period. Moreover, the introgression from H. nobilis to H. molitrix in North America was corroborated based on the whole-genome sequencing data, and the proportion of introgressed regions was estimated to be approximately 5.8%. Based on the high-quality assembly, the possible mechanisms by which H. molitrix adapts to its endemic and invaded locations were profiled.