Poropuntius huangchuchieni is a diploid species in the family cyprinid, widely distributed in Mekong and Red River basins. Previous study suggested that it is one of the most closely related diploid ancestral species to common carp, which has allotetraploidized genome generated by merging two diploid genomes during evolution. Therefore, P. huangchuchieni is an ideal diploid model for polyploid evolution study in Cyprinidae. Here, we report a high-quality chromosome-level genome assembly of P. huangchuchieni by the integrating of the Oxford Nanopore Technology and Hi-C technology. The assembled genome size was 1021.38 Mb with a scaffold N50 of 32.93 Mb. More than 47.61% of the genome was identified as repetitive elements, and 895.66 Mb sequences were anchored onto 25 chromosomes. Of the 24,099 predicted protein-coding genes, 97.57% were functional annotated. Approximately 95.9% of complete BUSCOs were detected in the genome.The high-quality genomic data of P. huangchuchieni provides an ancestral diploid reference for the evolution and adaptation of allotetraploid carps.

Here, we report a high-quality chromosome-level genome assembly of P. huangchuchieni by the integrating of the Oxford Nanopore Technology and Hi-C technology. A total of 76.06 Gb of Nanopore long reads and 247.72 Gb Illumina data were used for high-accuracy assembly and annotation.