Identification and classification of endogenous retroviruses in the canine genome using degenerative PCR and in-silico data analysis

Abstract

Pooled genomic DNA from 10 dogs was subjected to polymerase chain reaction with primers targeting the retroviral pro/pol region. Sequence analysis of 120 clones obtained by PCR revealed 81 of retroviral origin. Subsequent analysis of the dog genome (CanFam 2.0) by BLAST investigation using degenerate PCR products and previously identified retroviral sequences permitted the identification of additional retroviral γ and β sequences. A phylogenetic analysis using the retroviral protease (PR) and reverse transcriptase (RT) sequences in the dog genome resulted in identification of 17 γ and 7 β families. In addition, we also identified 167 spuma-like ERV elements from CanFam 2.0 based on sequence homology to murine (Mu)ERV-L and human (H)ERV-L. Our results could contribute to the understanding of the influence of retroviruses in shaping the genome structure and altering gene expression by providing quantitative and locational information of ERV loci and their diversity in the dog genome.

Endogenous Retroviruses in Domestic Animals

“…In a more recent work based on the use of degenerative PCR of the pro-pol complex and BLAST searches, more ERVs were discovered in the canine genome [32]. In this experimental approach, 81 unique sequences were detected, all of which belonged to Class I ERVs, and they were classified into 4 groups: CfERV γ1 to γ4 [32].…”

“…In this experimental approach, 81 unique sequences were detected, all of which belonged to Class I ERVs, and they were classified into 4 groups: CfERV γ1 to γ4 [32]. The number of sequences that clustered in each group and their lengths were variable [32], with CfERV γ1 being the most abundant (48 sequences clustered in this group), and sequences from CfERV γ2 being slightly shorter. These sequences and retroviral sequences of other species were used to carry out an in silico analysis using BLAST against the canine genome.…”

“…These sequences and retroviral sequences of other species were used to carry out an in silico analysis using BLAST against the canine genome. On the whole, 168 sequences were identified as ERVs: 160 from Class I and 8 from Class II [32]. The elements from Class I clustered into 17 subgroups (CfERV γ1 to γ17), while the elements from Class II clustered into 7 groups (CfERV β1 to β7) [32].…”

“…On the whole, 168 sequences were identified as ERVs: 160 from Class I and 8 from Class II [32]. The elements from Class I clustered into 17 subgroups (CfERV γ1 to γ17), while the elements from Class II clustered into 7 groups (CfERV β1 to β7) [32]. However, some concerns have been raised regarding this classification [33].…”

“…However, some concerns have been raised regarding this classification [33]. Their insertion could have occurred between 2.35-25.63 MYA according to conservative estimates, or, if the criteria were relaxed, it could have occurred between 0.83-42.97 MYA [32]. An additional BLAST search was performed for ERVs from Class III using sequences from human and mice ERVs, and 167 elements were detected in the canine genome [32].…”