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Genomic sequencing and analysis of Sucra jujuba nucleopolyhedrovirus.

Liu X, Yin F, Zhu Z, Hou D, Wang J, Zhang L, Wang M, Wang H, Hu Z, Deng F - PLoS ONE (2014)

Bottom Line: Seven homologous regions (hrs) were identified in the SujuNPV genome.SujuNPV contained several genes that were duplicated or copied multiple times: two copies of helicase, DNA binding protein gene (dbp), p26 and cg30, three copies of the inhibitor of the apoptosis gene (iap), and four copies of the baculovirus repeated ORF (bro).Phylogenetic analysis suggested that SujuNPV belongs to a subclade of group II alphabaculovirus, which differs from other baculoviruses in that all nine members of this subclade contain a second copy of dbp.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Virology, Virus Resource and Bioinformatics Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.

ABSTRACT
The complete nucleotide sequence of Sucra jujuba nucleopolyhedrovirus (SujuNPV) was determined by 454 pyrosequencing. The SujuNPV genome was 135,952 bp in length with an A+T content of 61.34%. It contained 131 putative open reading frames (ORFs) covering 87.9% of the genome. Among these ORFs, 37 were conserved in all baculovirus genomes that have been completely sequenced, 24 were conserved in lepidopteran baculoviruses, 65 were found in other baculoviruses, and 5 were unique to the SujuNPV genome. Seven homologous regions (hrs) were identified in the SujuNPV genome. SujuNPV contained several genes that were duplicated or copied multiple times: two copies of helicase, DNA binding protein gene (dbp), p26 and cg30, three copies of the inhibitor of the apoptosis gene (iap), and four copies of the baculovirus repeated ORF (bro). Phylogenetic analysis suggested that SujuNPV belongs to a subclade of group II alphabaculovirus, which differs from other baculoviruses in that all nine members of this subclade contain a second copy of dbp.

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Analysis of the duplicated gene p26.The tree was reconstructed based on protein sequences by MEGA5. The second copy was colored by purple branches and pink background and the number on the branch indicates a bootstrap value of 1000 randoms.
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pone-0110023-g008: Analysis of the duplicated gene p26.The tree was reconstructed based on protein sequences by MEGA5. The second copy was colored by purple branches and pink background and the number on the branch indicates a bootstrap value of 1000 randoms.

Mentions: SujuNPV contained an additional eight lepidoptera-conserved genes and 37 common genes with unknown functions (Table 2). P26 is an alphabaculovirus-specific gene. Among the 42 alphabaculoviruses previously sequenced, 19 contained a second copy of p26 and 16 of these belonged to group II. SujuNPV also contains two copies of p26, Suju10 (p26-1, 285 aa) and Suju56 (p26-2, 239 aa), which share 13.8% similarity. We name the one conserved in alphabaculoviruses as p26-1, and the second copy as p26-2. Phylogenetic analysis of p26 showed that the second copies of p26 could be classified into a unique subclade (colored pink in Fig. 8), with the exception of three group I baculoviruses (CfMNPV, ChocNPV and ChroNPV). Interestingly, the group II baculoviruses, except for LeseNPV, all specifically contain a conserved gene cluster that is p10, p26, ac29, lef-6 and dbp (dbp-2 in the 9 dbp-duplicated baculoviruses) in order. Although the significance of this gene cluster is unknown, it can provide us with more information for evolutionary analysis.


Genomic sequencing and analysis of Sucra jujuba nucleopolyhedrovirus.

Liu X, Yin F, Zhu Z, Hou D, Wang J, Zhang L, Wang M, Wang H, Hu Z, Deng F - PLoS ONE (2014)

Analysis of the duplicated gene p26.The tree was reconstructed based on protein sequences by MEGA5. The second copy was colored by purple branches and pink background and the number on the branch indicates a bootstrap value of 1000 randoms.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4201490&req=5

pone-0110023-g008: Analysis of the duplicated gene p26.The tree was reconstructed based on protein sequences by MEGA5. The second copy was colored by purple branches and pink background and the number on the branch indicates a bootstrap value of 1000 randoms.
Mentions: SujuNPV contained an additional eight lepidoptera-conserved genes and 37 common genes with unknown functions (Table 2). P26 is an alphabaculovirus-specific gene. Among the 42 alphabaculoviruses previously sequenced, 19 contained a second copy of p26 and 16 of these belonged to group II. SujuNPV also contains two copies of p26, Suju10 (p26-1, 285 aa) and Suju56 (p26-2, 239 aa), which share 13.8% similarity. We name the one conserved in alphabaculoviruses as p26-1, and the second copy as p26-2. Phylogenetic analysis of p26 showed that the second copies of p26 could be classified into a unique subclade (colored pink in Fig. 8), with the exception of three group I baculoviruses (CfMNPV, ChocNPV and ChroNPV). Interestingly, the group II baculoviruses, except for LeseNPV, all specifically contain a conserved gene cluster that is p10, p26, ac29, lef-6 and dbp (dbp-2 in the 9 dbp-duplicated baculoviruses) in order. Although the significance of this gene cluster is unknown, it can provide us with more information for evolutionary analysis.

Bottom Line: Seven homologous regions (hrs) were identified in the SujuNPV genome.SujuNPV contained several genes that were duplicated or copied multiple times: two copies of helicase, DNA binding protein gene (dbp), p26 and cg30, three copies of the inhibitor of the apoptosis gene (iap), and four copies of the baculovirus repeated ORF (bro).Phylogenetic analysis suggested that SujuNPV belongs to a subclade of group II alphabaculovirus, which differs from other baculoviruses in that all nine members of this subclade contain a second copy of dbp.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Virology, Virus Resource and Bioinformatics Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.

ABSTRACT
The complete nucleotide sequence of Sucra jujuba nucleopolyhedrovirus (SujuNPV) was determined by 454 pyrosequencing. The SujuNPV genome was 135,952 bp in length with an A+T content of 61.34%. It contained 131 putative open reading frames (ORFs) covering 87.9% of the genome. Among these ORFs, 37 were conserved in all baculovirus genomes that have been completely sequenced, 24 were conserved in lepidopteran baculoviruses, 65 were found in other baculoviruses, and 5 were unique to the SujuNPV genome. Seven homologous regions (hrs) were identified in the SujuNPV genome. SujuNPV contained several genes that were duplicated or copied multiple times: two copies of helicase, DNA binding protein gene (dbp), p26 and cg30, three copies of the inhibitor of the apoptosis gene (iap), and four copies of the baculovirus repeated ORF (bro). Phylogenetic analysis suggested that SujuNPV belongs to a subclade of group II alphabaculovirus, which differs from other baculoviruses in that all nine members of this subclade contain a second copy of dbp.

Show MeSH
Related in: MedlinePlus