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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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Related in: MedlinePlus

Comparison of genes in the DEV and alphaherpesvirus US regions. The comparison was based on the published sequences (37, 21, 20, 49). The red and blank arrows indicate the ORFs that were homologous in different alphaherpesviruses. The gray arrows indicate the ORFs that not exist in all the selected viruses. The green bars in the leftmost and rightmost parts indicate the sequences of the genomes, except for the US region. The targeted regions compared in this study are boxed.
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Figure 6: Comparison of genes in the DEV and alphaherpesvirus US regions. The comparison was based on the published sequences (37, 21, 20, 49). The red and blank arrows indicate the ORFs that were homologous in different alphaherpesviruses. The gray arrows indicate the ORFs that not exist in all the selected viruses. The green bars in the leftmost and rightmost parts indicate the sequences of the genomes, except for the US region. The targeted regions compared in this study are boxed.

Mentions: A comparison of the genetic organization of selected alphaherpesvirus US segment genes is presented in Figure 6. Despite obvious similarities, there were marked differences in gene content, organization and localization between DEV and other alphaherpesviruses. Nevertheless, these overall gene layouts are consistent with a model that accounts for the divergence of alphaherpesvirus from a common ancestor by a number of homologous and semihomologous recombination events, which resulted in concomitant loss or gain of US genes [23].


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)

Comparison of genes in the DEV and alphaherpesvirus US regions. The comparison was based on the published sequences (37, 21, 20, 49). The red and blank arrows indicate the ORFs that were homologous in different alphaherpesviruses. The gray arrows indicate the ORFs that not exist in all the selected viruses. The green bars in the leftmost and rightmost parts indicate the sequences of the genomes, except for the US region. The targeted regions compared in this study are boxed.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Comparison of genes in the DEV and alphaherpesvirus US regions. The comparison was based on the published sequences (37, 21, 20, 49). The red and blank arrows indicate the ORFs that were homologous in different alphaherpesviruses. The gray arrows indicate the ORFs that not exist in all the selected viruses. The green bars in the leftmost and rightmost parts indicate the sequences of the genomes, except for the US region. The targeted regions compared in this study are boxed.
Mentions: A comparison of the genetic organization of selected alphaherpesvirus US segment genes is presented in Figure 6. Despite obvious similarities, there were marked differences in gene content, organization and localization between DEV and other alphaherpesviruses. Nevertheless, these overall gene layouts are consistent with a model that accounts for the divergence of alphaherpesvirus from a common ancestor by a number of homologous and semihomologous recombination events, which resulted in concomitant loss or gain of US genes [23].

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