Identification and classification of feline endogenous retroviruses in the cat genome using degenerate PCR and in silico data analysis

Abstract

The purpose of this study was to identify and classify endogenous retroviruses (ERVs) in the cat genome. Pooled DNA from five 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 c and b elements from cat genome contigs, which were classified into 42 ERV c and 4 b families and further analysed. Among them, 99 c and 5 b 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 (FcERV) and providing advanced insights into their structural characteristics, localization in the genome, and diversity.

Endogenous Retroviruses in Domestic Animals

“…Recently, a genome-wide search of ERVs in the cat genome using degenerative PCR of the pro - pol complex and BLAST searches was carried out, and 219 ERVs were detected [36]. In an approach using degenerate PCR, 9 families of class I (FcERV γ1 to γ9) and 1 family of class II (FcERVβ1) were identified.…”

“…In an approach using degenerate PCR, 9 families of class I (FcERV γ1 to γ9) and 1 family of class II (FcERVβ1) were identified. In in silico analysis, where the Felis catus -6.2 assembly was analyzed, 33 more families of class I (FcERV γ10 to γ42) and 3 more families of class II (FcERVβ2 to β4) were identified, although 24 of those families comprised one or two members [36]. Of the detected ERVs, 51 were full-length retroviruses with a complete structure [36].…”

“…In in silico analysis, where the Felis catus -6.2 assembly was analyzed, 33 more families of class I (FcERV γ10 to γ42) and 3 more families of class II (FcERVβ2 to β4) were identified, although 24 of those families comprised one or two members [36]. Of the detected ERVs, 51 were full-length retroviruses with a complete structure [36]. In addition, 757 putative ERVs from Class III were detected, but their classification into families was difficult [36].…”

“…Of the detected ERVs, 51 were full-length retroviruses with a complete structure [36]. In addition, 757 putative ERVs from Class III were detected, but their classification into families was difficult [36]. The most abundant families were γ6 (35 members) and γ1 (18 members), and their integration times were estimated to be 3.8-16 MYA and 8.2-30 MYA, respectively.…”

“…The most abundant families were γ6 (35 members) and γ1 (18 members), and their integration times were estimated to be 3.8-16 MYA and 8.2-30 MYA, respectively. On the whole, the feline ERVs were inserted between 2.3 and 41.7 MYA [36]. …”