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Different linkages in the long and short regions of the genomes of duck enteritis virus Clone-03 and VAC strains.

Liu X, Han Z, Shao Y, Li Y, Li H, Kong X, Liu S - Virol. J. (2011)

Bottom Line: The comparison of genomic organization in the fragment studied herein with those of other herpesviruses showed that DEV possesses some unique characteristics, such as the duplicated US1 at each end of the US region, and the US5, which showed no homology with those of other herpesviruses.In addition, the results of phylogenetic analysis of ORFs in the represented fragment indicated that DEV is closest to its counterparts VZV (Varicellovirus) and other avian herpesviruses.The phylogenetic analysis of genes in this region showed that DEV should be a separate member of the subfamily Alphaherpesvirinae.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Avian Infectious Diseases, National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150001, the People's Republic of China.

ABSTRACT

Background: Duck enteritis virus (DEV) is an unassigned member in the family Herpesviridae. To demonstrate further the evolutionary position of DEV in the family Herpesviridae, we have described a 42,897-bp fragment. We demonstrated novel genomic organization at one end of the long (L) region and in the entire short (S) region in the Clone-03 strain of DEV.

Results: A 42,897-bp fragment located downstream of the LOFR11 gene was amplified from the Clone-03 strain of DEV by using 'targeted gene walking PCR'. Twenty-two open reading frames (ORFs) were predicted and determined in the following order: 5'-LORF11-RLORF1-ORF1-ICP4-S1-S2-US1-US10-SORF3-US2-MDV091.5-like-US3-US4-US5-US6-US7-US8-ORFx-US1-S2-S1-ICP4 -3'. This was different from that of the published VAC strain, both in the linkage of the L region and S region, and in the length of the US10 and US7 proteins. The MDV091.5-like gene, ORFx gene, S1 gene and S2 gene were first observed in the DEV genome. The lengths of DEV US10 and US7 were determined to be 311 and 371 amino acids, respectively, in the Clone-03 strain of DEV, and these were different from those of other strains. The comparison of genomic organization in the fragment studied herein with those of other herpesviruses showed that DEV possesses some unique characteristics, such as the duplicated US1 at each end of the US region, and the US5, which showed no homology with those of other herpesviruses. In addition, the results of phylogenetic analysis of ORFs in the represented fragment indicated that DEV is closest to its counterparts VZV (Varicellovirus) and other avian herpesviruses.

Conclusion: The molecular characteristics of the 42,897-bp fragment of Clone-03 have been found to be different from those of the VAC strain. The phylogenetic analysis of genes in this region showed that DEV should be a separate member of the subfamily Alphaherpesvirinae.

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Hairpin-like secondary structure reflecting palindromic nature of sequences of oriS. The arrows and boxes at flanking the palindromes represented the two genes that flanked the oriS. The distances in nucleotides between the oriS sequence and the two genes are shown in brackets.
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Figure 7: Hairpin-like secondary structure reflecting palindromic nature of sequences of oriS. The arrows and boxes at flanking the palindromes represented the two genes that flanked the oriS. The distances in nucleotides between the oriS sequence and the two genes are shown in brackets.

Mentions: Two well-defined origins of replication were found in the IRS and TRS of the DEV genome, designated oriS. The two oriS were palindromic structures and contained the same sequence features: two inverted 9-bp sequences, which were identical to that recognized by the origin-binding protein (OBP) encoded by the UL9 binding sequence (GTTCGCAC), separated by a 43-bp AT-rich spacer sequence (76.75% A+T) (Figure 7). The features were the same as described for PRV (Pseudorabies virus) [24] and equine herpesvirus-1 (EHV-1) [25].


Different linkages in the long and short regions of the genomes of duck enteritis virus Clone-03 and VAC strains.

Liu X, Han Z, Shao Y, Li Y, Li H, Kong X, Liu S - Virol. J. (2011)

Hairpin-like secondary structure reflecting palindromic nature of sequences of oriS. The arrows and boxes at flanking the palindromes represented the two genes that flanked the oriS. The distances in nucleotides between the oriS sequence and the two genes are shown in brackets.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3113978&req=5

Figure 7: Hairpin-like secondary structure reflecting palindromic nature of sequences of oriS. The arrows and boxes at flanking the palindromes represented the two genes that flanked the oriS. The distances in nucleotides between the oriS sequence and the two genes are shown in brackets.
Mentions: Two well-defined origins of replication were found in the IRS and TRS of the DEV genome, designated oriS. The two oriS were palindromic structures and contained the same sequence features: two inverted 9-bp sequences, which were identical to that recognized by the origin-binding protein (OBP) encoded by the UL9 binding sequence (GTTCGCAC), separated by a 43-bp AT-rich spacer sequence (76.75% A+T) (Figure 7). The features were the same as described for PRV (Pseudorabies virus) [24] and equine herpesvirus-1 (EHV-1) [25].

Bottom Line: The comparison of genomic organization in the fragment studied herein with those of other herpesviruses showed that DEV possesses some unique characteristics, such as the duplicated US1 at each end of the US region, and the US5, which showed no homology with those of other herpesviruses.In addition, the results of phylogenetic analysis of ORFs in the represented fragment indicated that DEV is closest to its counterparts VZV (Varicellovirus) and other avian herpesviruses.The phylogenetic analysis of genes in this region showed that DEV should be a separate member of the subfamily Alphaherpesvirinae.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Avian Infectious Diseases, National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150001, the People's Republic of China.

ABSTRACT

Background: Duck enteritis virus (DEV) is an unassigned member in the family Herpesviridae. To demonstrate further the evolutionary position of DEV in the family Herpesviridae, we have described a 42,897-bp fragment. We demonstrated novel genomic organization at one end of the long (L) region and in the entire short (S) region in the Clone-03 strain of DEV.

Results: A 42,897-bp fragment located downstream of the LOFR11 gene was amplified from the Clone-03 strain of DEV by using 'targeted gene walking PCR'. Twenty-two open reading frames (ORFs) were predicted and determined in the following order: 5'-LORF11-RLORF1-ORF1-ICP4-S1-S2-US1-US10-SORF3-US2-MDV091.5-like-US3-US4-US5-US6-US7-US8-ORFx-US1-S2-S1-ICP4 -3'. This was different from that of the published VAC strain, both in the linkage of the L region and S region, and in the length of the US10 and US7 proteins. The MDV091.5-like gene, ORFx gene, S1 gene and S2 gene were first observed in the DEV genome. The lengths of DEV US10 and US7 were determined to be 311 and 371 amino acids, respectively, in the Clone-03 strain of DEV, and these were different from those of other strains. The comparison of genomic organization in the fragment studied herein with those of other herpesviruses showed that DEV possesses some unique characteristics, such as the duplicated US1 at each end of the US region, and the US5, which showed no homology with those of other herpesviruses. In addition, the results of phylogenetic analysis of ORFs in the represented fragment indicated that DEV is closest to its counterparts VZV (Varicellovirus) and other avian herpesviruses.

Conclusion: The molecular characteristics of the 42,897-bp fragment of Clone-03 have been found to be different from those of the VAC strain. The phylogenetic analysis of genes in this region showed that DEV should be a separate member of the subfamily Alphaherpesvirinae.

Show MeSH
Related in: MedlinePlus