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Species based synonymous codon usage in fusion protein gene of Newcastle disease virus.

Kumar CS, Kumar S - PLoS ONE (2014)

Bottom Line: Aromaticity, GC3s, and aliphatic index were not found responsible for species based synonymous codon usage bias in F gene of NDV.The phylogenetic analysis of isolates was found in corroboration with the relatedness of species based on codon usage bias.The relationship between the host species and the NDV isolates from the host does not represent a significant correlation in our study.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India.

ABSTRACT
Newcastle disease is highly pathogenic to poultry and many other avian species. However, the Newcastle disease virus (NDV) has also been reported from many non-avian species. The NDV fusion protein (F) is a major determinant of its pathogenicity and virulence. The functionalities of F gene have been explored for the development of vaccine and diagnostics against NDV. Although the F protein is well studied but the codon usage and its nucleotide composition from NDV isolated from different species have not yet been explored. In present study, we have analyzed the factors responsible for the determination of codon usage in NDV isolated from four major avian host species. The F gene of NDV is analyzed for its base composition and its correlation with the bias in codon usage. Our result showed that random mutational pressure is responsible for codon usage bias in F protein of NDV isolates. Aromaticity, GC3s, and aliphatic index were not found responsible for species based synonymous codon usage bias in F gene of NDV. Moreover, the low amount of codon usage bias and expression level was further confirmed by a low CAI value. The phylogenetic analysis of isolates was found in corroboration with the relatedness of species based on codon usage bias. The relationship between the host species and the NDV isolates from the host does not represent a significant correlation in our study. The present study provides a basic understanding of the mechanism involved in codon usage among species.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree illustrating relationship among the 201 Newcastle disease virus (NDV) strain (labelled as accession no/pathogenic/species) following the neighbour-joining method using MEGA6 software.Parameters include: pairwise deletion, 1000 replicates for bootstrap analysis and Jukes-Cantor substitution model, the rate variation among sites was modelled with a gamma distribution (shape parameter  =  5). L, M and V stands for lentogenic, mesogenic and velogenic strains. CH, PN, DK and GE stands for the chicken, pigeon, duck and goose, respectively.
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pone-0114754-g006: Phylogenetic tree illustrating relationship among the 201 Newcastle disease virus (NDV) strain (labelled as accession no/pathogenic/species) following the neighbour-joining method using MEGA6 software.Parameters include: pairwise deletion, 1000 replicates for bootstrap analysis and Jukes-Cantor substitution model, the rate variation among sites was modelled with a gamma distribution (shape parameter  =  5). L, M and V stands for lentogenic, mesogenic and velogenic strains. CH, PN, DK and GE stands for the chicken, pigeon, duck and goose, respectively.

Mentions: The phylogenetic tree of the 201 NDV isolates represents the relationship which can be categorized on two bases (Figure 6). The first basis is being species from which the strain was isolated and the second being virulence shown in that species based on the F protein cleavage site. It was observed that on the basis of species except one pigeon isolate (FJ986192) lying in region 3 all the pigeon isolates were seen to lie in region 2 (Figure 6). The region 1 and 5 consisted of isolates from chicken, duck and goose whereas; the region 4 consisted of isolates of only duck. It is evident from the phylogenetic tree that isolates from pigeon clearly out lies and is not found mixed as is seen in case of chicken, duck and goose. A group of isolates from duck is also seen in region 4 to out lie from the rest. On the basis of virulence the phylogenetic tree can be seen to represent a similar trend, all the isolates from duck species lying in region 4 are lysogenic. Most of the mesogenic isolates from chicken are seen to lie in region 3. Very few reported strains from pigeon are lentogenic and mesogenic whereas most are velogenic and seen to group together in region 2. The region 1 comprises of most of the velogenic isolates of chicken, goose and duck.


Species based synonymous codon usage in fusion protein gene of Newcastle disease virus.

Kumar CS, Kumar S - PLoS ONE (2014)

Phylogenetic tree illustrating relationship among the 201 Newcastle disease virus (NDV) strain (labelled as accession no/pathogenic/species) following the neighbour-joining method using MEGA6 software.Parameters include: pairwise deletion, 1000 replicates for bootstrap analysis and Jukes-Cantor substitution model, the rate variation among sites was modelled with a gamma distribution (shape parameter  =  5). L, M and V stands for lentogenic, mesogenic and velogenic strains. CH, PN, DK and GE stands for the chicken, pigeon, duck and goose, respectively.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4257736&req=5

pone-0114754-g006: Phylogenetic tree illustrating relationship among the 201 Newcastle disease virus (NDV) strain (labelled as accession no/pathogenic/species) following the neighbour-joining method using MEGA6 software.Parameters include: pairwise deletion, 1000 replicates for bootstrap analysis and Jukes-Cantor substitution model, the rate variation among sites was modelled with a gamma distribution (shape parameter  =  5). L, M and V stands for lentogenic, mesogenic and velogenic strains. CH, PN, DK and GE stands for the chicken, pigeon, duck and goose, respectively.
Mentions: The phylogenetic tree of the 201 NDV isolates represents the relationship which can be categorized on two bases (Figure 6). The first basis is being species from which the strain was isolated and the second being virulence shown in that species based on the F protein cleavage site. It was observed that on the basis of species except one pigeon isolate (FJ986192) lying in region 3 all the pigeon isolates were seen to lie in region 2 (Figure 6). The region 1 and 5 consisted of isolates from chicken, duck and goose whereas; the region 4 consisted of isolates of only duck. It is evident from the phylogenetic tree that isolates from pigeon clearly out lies and is not found mixed as is seen in case of chicken, duck and goose. A group of isolates from duck is also seen in region 4 to out lie from the rest. On the basis of virulence the phylogenetic tree can be seen to represent a similar trend, all the isolates from duck species lying in region 4 are lysogenic. Most of the mesogenic isolates from chicken are seen to lie in region 3. Very few reported strains from pigeon are lentogenic and mesogenic whereas most are velogenic and seen to group together in region 2. The region 1 comprises of most of the velogenic isolates of chicken, goose and duck.

Bottom Line: Aromaticity, GC3s, and aliphatic index were not found responsible for species based synonymous codon usage bias in F gene of NDV.The phylogenetic analysis of isolates was found in corroboration with the relatedness of species based on codon usage bias.The relationship between the host species and the NDV isolates from the host does not represent a significant correlation in our study.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India.

ABSTRACT
Newcastle disease is highly pathogenic to poultry and many other avian species. However, the Newcastle disease virus (NDV) has also been reported from many non-avian species. The NDV fusion protein (F) is a major determinant of its pathogenicity and virulence. The functionalities of F gene have been explored for the development of vaccine and diagnostics against NDV. Although the F protein is well studied but the codon usage and its nucleotide composition from NDV isolated from different species have not yet been explored. In present study, we have analyzed the factors responsible for the determination of codon usage in NDV isolated from four major avian host species. The F gene of NDV is analyzed for its base composition and its correlation with the bias in codon usage. Our result showed that random mutational pressure is responsible for codon usage bias in F protein of NDV isolates. Aromaticity, GC3s, and aliphatic index were not found responsible for species based synonymous codon usage bias in F gene of NDV. Moreover, the low amount of codon usage bias and expression level was further confirmed by a low CAI value. The phylogenetic analysis of isolates was found in corroboration with the relatedness of species based on codon usage bias. The relationship between the host species and the NDV isolates from the host does not represent a significant correlation in our study. The present study provides a basic understanding of the mechanism involved in codon usage among species.

No MeSH data available.


Related in: MedlinePlus