Supporting data for "Telomere-to-telomere genome and resequencing of 254 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis"

The Asian icefish, Protosalanx chinensis, has undergone extensive colonization in various waters across China for decades due to its ecological and physiological significance as well as its economic importance in the fishery resource. Here, we decoded a telomere-to-telomere (T2T) genome of P. chinensis combining PacBio HiFi long reads, ultra-long ONT (nanopore) reads and Hi-C data. The telomere was identified in both ends of the contig/chromosome. The expanded gene associated with circadian entrainment suggests that P. chinensis may exhibit high sensitivity to photoperiod. The contracted genes of immune-related families and DNA repair associated with positive selection in P. chinensis suggests there is selective pressure during adaptive evolution. The population genetic analysis reveals the genetic diversity and genomic footprints in 254 individuals from eight different locations. The natural seawater samples result in the highest diversity compared with other freshwater and introduced populations. The genes associated with divergent regions were found to be related to the osmotic pressure system, suggesting adaptations to alkalinity and salinity. Thus, this T2T genome and genetic variation findings are a valuable resource for genomic footprints in P. chinensis, shedding light on its evolution, comparative genomics, as well as the genetic differences between natural and introduced populations.