Identification and Classification of Endogenous Retroviruses in the Cat Genome Using Degenerate PCR and in silico Data Analysis

The purpose of this study was to identify and classify endogenous retroviruses (ERV) in the cat genome. Pooled DNA from 5 domestic cats was subjected to degenerate PCR with primers specific to the conserved retroviral pro-pol region. The 59 amplified retroviral sequences were used for in silico analysis of the cat genome (Felis_catus-6.2). We identified 219 ERV γ and β elements from cat genome contigs, which were classified into 42 ERV γ and 4 β families and further analyzed. Among them, 99 γ and 5 β ERV elements contained the complete retroviral structure. Furthermore, we identified 757 spuma-like ERV elements based on the sequence homology to murine (Mu)ERV-L and human (H)ERV-L. To the best of our knowledge, this is the first detailed genome scale analysis examining Felis catus endogenous retroviruses (FERV) and providing advanced insights into their structural characteristics, localization in the genome, and diversity.