Genomic Characterization and Phylogenetic Relationships of Procypris rabaudi Revealed by Whole-Genome Survey Analysis

<i>Procypris rabaudi</i>, a member of the Cyprinidae family and genus <i>Procypris</i>, has been designated as a national second-class protected wildlife species in China due to a significant decline in its wild populations. Understanding its genomic characteristics and mitochondrial genome structure is crucial for germplasm conservation and systematic classification. In this study, we utilized high-throughput sequencing to investigate the genome of <i>P. rabaudi</i>. The genome size was 1.5 Gb, with a heterozygosity rate of 0.44% and 61.47% of repetitive sequences. We identified 1,151,980 simple sequence repeats (SSRs), with mononucleotide repeats being the most abundant at 55.34%. The complete mitochondrial genome was assembled with 16,595 bp length. A phylogenetic tree constructed from 13 mitochondrial protein-coding genes indicated that genus <i>Procypris</i> was most closely related to genus <i>Luciocyprinus</i> and formed a monophyletic group with <i>Cyprinus</i>, <i>Carassioides</i>, and <i>Carassius</i>. Pairwise Sequentially Markovian Coalescent (PSMC) analysis revealed a rapid population expansion prior to the Last Interglacial Period, followed by a decline after reaching its peak during Last Glacial Period. Notably, <i>P. rabaudi</i> exhibited a two-peak demographic pattern during both the Last Glacial Period. These genomic data provide valuable resources for the conservation of <i>P. rabaudi</i> germplasm and for future studies on cyprinid classification and evolution.