Limits...
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.

Show MeSH

Related in: MedlinePlus

The comparison of genomic organization between the DEV Clone-03 strain and the published VAC strain, together with the PCR strategy. The upper part shows the genomic organization of sequences corresponding to those in the present study in the published sequences of the genome of the DEV VAC strain. The genomic organization of the presented fragment in the DEV Clone-03 is listed below. The red and blank arrows indicate the ORFs, with different colours to make two adjacent ORFs evident. The pink arrows indicate the ORFs that were not detected in other heprsviruses but were detected in DEV. The dark blue indicates the UL region; the dashed gray boxes in the genome of DEV Clone-03 indicate uncertain regions. The PCR strategy used to obtain the fragment is depicted at the bottom. The blue arrows indicate the twelve overlapping fragments that were obtained to form a continuous DNA fragment; the primer positions and amplification directions are also shown. The arrows indicate the genes and the interval shows the relative position of the two adjacent ORFs. The confirmation PCR strategy is depicted in the centre. The bars indicate the PCR product with the primers embedded. The green ellipse indicates the predicted origins of replication (oriS).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3113978&req=5

Figure 1: The comparison of genomic organization between the DEV Clone-03 strain and the published VAC strain, together with the PCR strategy. The upper part shows the genomic organization of sequences corresponding to those in the present study in the published sequences of the genome of the DEV VAC strain. The genomic organization of the presented fragment in the DEV Clone-03 is listed below. The red and blank arrows indicate the ORFs, with different colours to make two adjacent ORFs evident. The pink arrows indicate the ORFs that were not detected in other heprsviruses but were detected in DEV. The dark blue indicates the UL region; the dashed gray boxes in the genome of DEV Clone-03 indicate uncertain regions. The PCR strategy used to obtain the fragment is depicted at the bottom. The blue arrows indicate the twelve overlapping fragments that were obtained to form a continuous DNA fragment; the primer positions and amplification directions are also shown. The arrows indicate the genes and the interval shows the relative position of the two adjacent ORFs. The confirmation PCR strategy is depicted in the centre. The bars indicate the PCR product with the primers embedded. The green ellipse indicates the predicted origins of replication (oriS).

Mentions: A fragment of 42,897 bp downstream of the LORF11 gene was amplified from the genome of the Clone-03 strain of DEV in this study. The genome structure and the gene layout of this fragment are depicted in Figure 1. The fragment contained part of the sequence of the LORF11 gene [12], the rightmost part of the L region, the US region and its flanking sequences, and inverted repeats of the short region (IRS and TRS). The L region and IRS were interrupted by a set of tandem repeat sequences designated as α-type-like sequences [13], as in the case of the two regions in herpes simplex virus (HSV) [19]. Another α-type-like sequence was also found at the end of the TRS in the DEV genome. The overall G plus C ratio of the region sequenced was 46.09%.


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)

The comparison of genomic organization between the DEV Clone-03 strain and the published VAC strain, together with the PCR strategy. The upper part shows the genomic organization of sequences corresponding to those in the present study in the published sequences of the genome of the DEV VAC strain. The genomic organization of the presented fragment in the DEV Clone-03 is listed below. The red and blank arrows indicate the ORFs, with different colours to make two adjacent ORFs evident. The pink arrows indicate the ORFs that were not detected in other heprsviruses but were detected in DEV. The dark blue indicates the UL region; the dashed gray boxes in the genome of DEV Clone-03 indicate uncertain regions. The PCR strategy used to obtain the fragment is depicted at the bottom. The blue arrows indicate the twelve overlapping fragments that were obtained to form a continuous DNA fragment; the primer positions and amplification directions are also shown. The arrows indicate the genes and the interval shows the relative position of the two adjacent ORFs. The confirmation PCR strategy is depicted in the centre. The bars indicate the PCR product with the primers embedded. The green ellipse indicates the predicted origins of replication (oriS).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: The comparison of genomic organization between the DEV Clone-03 strain and the published VAC strain, together with the PCR strategy. The upper part shows the genomic organization of sequences corresponding to those in the present study in the published sequences of the genome of the DEV VAC strain. The genomic organization of the presented fragment in the DEV Clone-03 is listed below. The red and blank arrows indicate the ORFs, with different colours to make two adjacent ORFs evident. The pink arrows indicate the ORFs that were not detected in other heprsviruses but were detected in DEV. The dark blue indicates the UL region; the dashed gray boxes in the genome of DEV Clone-03 indicate uncertain regions. The PCR strategy used to obtain the fragment is depicted at the bottom. The blue arrows indicate the twelve overlapping fragments that were obtained to form a continuous DNA fragment; the primer positions and amplification directions are also shown. The arrows indicate the genes and the interval shows the relative position of the two adjacent ORFs. The confirmation PCR strategy is depicted in the centre. The bars indicate the PCR product with the primers embedded. The green ellipse indicates the predicted origins of replication (oriS).
Mentions: A fragment of 42,897 bp downstream of the LORF11 gene was amplified from the genome of the Clone-03 strain of DEV in this study. The genome structure and the gene layout of this fragment are depicted in Figure 1. The fragment contained part of the sequence of the LORF11 gene [12], the rightmost part of the L region, the US region and its flanking sequences, and inverted repeats of the short region (IRS and TRS). The L region and IRS were interrupted by a set of tandem repeat sequences designated as α-type-like sequences [13], as in the case of the two regions in herpes simplex virus (HSV) [19]. Another α-type-like sequence was also found at the end of the TRS in the DEV genome. The overall G plus C ratio of the region sequenced was 46.09%.

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