Chromosome-level genome of Poropuntius huangchuchieni provides a diploid
progenitor-like reference genome for the allotetraploid Cyprinus carpio
The diploid Poropuntius huangchuchieni in the cyprinid family, which is
widely distributed in the Mekong and Red River basins, is one of the
most closely related diploid progenitor-like species of allotetraploid
common carp, which was generated by merging of two diploid genomes
during evolution. Therefore, the P. huangchuchieni genome is essential
for polyploidy evolution studies in Cyprinidae. Here, we report a
high-quality chromosome-level genome assembly of P. huangchuchieni by
integrating Oxford Nanopore and Hi-C technology. The assembled genome
size was 1021.38 Mb, 895.66 Mb of which was anchored onto 25 chromosomes
with a N50 of 32.93 Mb. The genome contained 486.28 Mb repetitive
elements and 24,099 protein-coding genes. Approximately 95.9% of the
complete BUSCOs were detected, suggesting a high completeness of the
genome. Evolutionary analysis revealed that P. huangchuchieni diverged
from Cyprinus carpio at approximately 12 Mya. Genome comparison between
P. huangchuchieni and the B subgenome of C. carpio provided insights
into chromosomal rearrangements during the allotetraploid speciation.
With the complete gene set, 17,474 orthologous genes were identified
between P. huangchuchieni and C. carpio, providing a broad view of the
gene component in the allotetraploid genome, which is critical for
future genetic analyses. The high-quality genomic dataset created for P.
huangchuchieni provides a diploid progenitor-like reference for the
evolution and adaptation of allotetraploid carps.