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

## TL;DR

This study provides genomic insights into the endangered Procypris rabaudi fish, revealing its genome size, structure, and evolutionary relationships to aid conservation and classification.

## Contribution

The study presents the first whole-genome survey and mitochondrial genome of Procypris rabaudi, revealing its unique demographic history and phylogenetic position.

## Key findings

- The genome of Procypris rabaudi is 1.5 Gb with 61.47% repetitive sequences and 0.44% heterozygosity.
- Phylogenetic analysis shows Procypris is closely related to Luciocyprinus and clusters with Cyprinus and Carassius.
- PSMC analysis reveals a two-peak demographic pattern during the Last Glacial Period.

## Abstract

Procypris rabaudi is an endangered cyprinid fish under national protection in China. This study performed its genome survey analysis, revealing a 1.5 Gb size with 0.44% heterozygosity and 61.47% repetitive sequences. The mitochondrial genome is 16,595 bp. Phylogenetic analysis shows Procypris is closest to Luciocyprinus and clusters with Cyprinus and Carassius. PSMC analysis indicates population expansion before the Last Interglacial, and then decline after a peak in the Last Glacial Period, featuring a unique two-peak demographic pattern. These genomic insights aid conservation and evolutionary studies of cyprinids.

Procypris rabaudi, a member of the Cyprinidae family and genus Procypris, 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 P. rabaudi. 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 Procypris was most closely related to genus Luciocyprinus and formed a monophyletic group with Cyprinus, Carassioides, and Carassius. 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, P. rabaudi exhibited a two-peak demographic pattern during both the Last Glacial Period. These genomic data provide valuable resources for the conservation of P. rabaudi germplasm and for future studies on cyprinid classification and evolution.