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Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus.

Desjardins CA, Gundersen-Rindal DE, Hostetler JB, Tallon LJ, Fuester RW, Schatz MC, Pedroni MJ, Fadrosh DW, Haas BJ, Toms BS, Chen D, Nene V - BMC Microbiol. (2007)

Bottom Line: By analyzing sequence polymorphisms in the 8 GiBV viral segment sequences, we found evidence for widespread selection acting on both protein-coding and non-coding DNA.Contrary to current concepts of bracovirus proviral genome organization our results demonstrate that some but not all GiBV proviral segment sequences exist in a tandem array.We hypothesize that selection acting on GiBV proviral sequences maintains the genetic island-like nature of the cluster of proviral genome segments described herein.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Institute for Genomic Research, J. Craig Venter Institute, Rockville, Maryland, USA. cdesjar3@mail.rochester.edu

ABSTRACT

Background: Bracoviruses (BVs), a group of double-stranded DNA viruses with segmented genomes, are mutualistic endosymbionts of parasitoid wasps. Virus particles are replication deficient and are produced only by female wasps from proviral sequences integrated into the wasp genome. Virus particles are injected along with eggs into caterpillar hosts, where viral gene expression facilitates parasitoid survival and therefore perpetuation of proviral DNA. Here we describe a 223 kbp region of Glyptapanteles indiensis genomic DNA which contains a part of the G. indiensis bracovirus (GiBV) proviral genome.

Results: Eighteen of ~24 GiBV viral segment sequences are encoded by 7 non-overlapping sets of BAC clones, revealing that some proviral segment sequences are separated by long stretches of intervening DNA. Two overlapping BACs, which contain a locus of 8 tandemly arrayed proviral segments flanked on either side by ~35 kbp of non-packaged DNA, were sequenced and annotated. Structural and compositional analyses of this cluster revealed it exhibits a G+C and nucleotide composition distinct from the flanking DNA. By analyzing sequence polymorphisms in the 8 GiBV viral segment sequences, we found evidence for widespread selection acting on both protein-coding and non-coding DNA. Comparative analysis of viral and proviral segment sequences revealed a sequence motif involved in the excision of proviral genome segments which is highly conserved in two other bracoviruses.

Conclusion: Contrary to current concepts of bracovirus proviral genome organization our results demonstrate that some but not all GiBV proviral segment sequences exist in a tandem array. Unexpectedly, non-coding DNA in the 8 proviral genome segments which typically occupies ~70% of BV viral genomes is under selection pressure suggesting it serves some function(s). We hypothesize that selection acting on GiBV proviral sequences maintains the genetic island-like nature of the cluster of proviral genome segments described herein. In contrast to large differences in the predicted gene composition of BV genomes, sequences that appear to mediate processes of viral segment formation, such as proviral segment excision and circularization, appear to be highly conserved, supporting the hypothesis of a single origin for BVs.

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Histogram of dN/dS ratios of 39 genes in the viral genome segments.
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Figure 4: Histogram of dN/dS ratios of 39 genes in the viral genome segments.

Mentions: The number of SNPs per gene ranged from 0 to 68, and dN/dS ratios were calculated for the 39 out of 62 genes that contained 5 or more SNPs (Table 3). Most of these genes appear to be under purifying selection and 32 of 39 genes had dN/dS ratio < 0.8 with a majority of the ratios falling in the range of 0.40–0.59 (Figure 4). Three genes appear to be evolving neutrally (dN/dS = 0.8–1.2) and code for 2 hypothetical proteins and 1 member of gene family 3. Four genes had a dN/dS > 1.9, including 1 member each of gene families 1, 10, and 11 (the ribonuclease T2 domain) and an EP1-like protein. No correlation was found between dN/dS ratios and specific genome segments or gene families–most segments and gene families contained genes under different degrees of selection.


Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus.

Desjardins CA, Gundersen-Rindal DE, Hostetler JB, Tallon LJ, Fuester RW, Schatz MC, Pedroni MJ, Fadrosh DW, Haas BJ, Toms BS, Chen D, Nene V - BMC Microbiol. (2007)

Histogram of dN/dS ratios of 39 genes in the viral genome segments.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1919376&req=5

Figure 4: Histogram of dN/dS ratios of 39 genes in the viral genome segments.
Mentions: The number of SNPs per gene ranged from 0 to 68, and dN/dS ratios were calculated for the 39 out of 62 genes that contained 5 or more SNPs (Table 3). Most of these genes appear to be under purifying selection and 32 of 39 genes had dN/dS ratio < 0.8 with a majority of the ratios falling in the range of 0.40–0.59 (Figure 4). Three genes appear to be evolving neutrally (dN/dS = 0.8–1.2) and code for 2 hypothetical proteins and 1 member of gene family 3. Four genes had a dN/dS > 1.9, including 1 member each of gene families 1, 10, and 11 (the ribonuclease T2 domain) and an EP1-like protein. No correlation was found between dN/dS ratios and specific genome segments or gene families–most segments and gene families contained genes under different degrees of selection.

Bottom Line: By analyzing sequence polymorphisms in the 8 GiBV viral segment sequences, we found evidence for widespread selection acting on both protein-coding and non-coding DNA.Contrary to current concepts of bracovirus proviral genome organization our results demonstrate that some but not all GiBV proviral segment sequences exist in a tandem array.We hypothesize that selection acting on GiBV proviral sequences maintains the genetic island-like nature of the cluster of proviral genome segments described herein.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Institute for Genomic Research, J. Craig Venter Institute, Rockville, Maryland, USA. cdesjar3@mail.rochester.edu

ABSTRACT

Background: Bracoviruses (BVs), a group of double-stranded DNA viruses with segmented genomes, are mutualistic endosymbionts of parasitoid wasps. Virus particles are replication deficient and are produced only by female wasps from proviral sequences integrated into the wasp genome. Virus particles are injected along with eggs into caterpillar hosts, where viral gene expression facilitates parasitoid survival and therefore perpetuation of proviral DNA. Here we describe a 223 kbp region of Glyptapanteles indiensis genomic DNA which contains a part of the G. indiensis bracovirus (GiBV) proviral genome.

Results: Eighteen of ~24 GiBV viral segment sequences are encoded by 7 non-overlapping sets of BAC clones, revealing that some proviral segment sequences are separated by long stretches of intervening DNA. Two overlapping BACs, which contain a locus of 8 tandemly arrayed proviral segments flanked on either side by ~35 kbp of non-packaged DNA, were sequenced and annotated. Structural and compositional analyses of this cluster revealed it exhibits a G+C and nucleotide composition distinct from the flanking DNA. By analyzing sequence polymorphisms in the 8 GiBV viral segment sequences, we found evidence for widespread selection acting on both protein-coding and non-coding DNA. Comparative analysis of viral and proviral segment sequences revealed a sequence motif involved in the excision of proviral genome segments which is highly conserved in two other bracoviruses.

Conclusion: Contrary to current concepts of bracovirus proviral genome organization our results demonstrate that some but not all GiBV proviral segment sequences exist in a tandem array. Unexpectedly, non-coding DNA in the 8 proviral genome segments which typically occupies ~70% of BV viral genomes is under selection pressure suggesting it serves some function(s). We hypothesize that selection acting on GiBV proviral sequences maintains the genetic island-like nature of the cluster of proviral genome segments described herein. In contrast to large differences in the predicted gene composition of BV genomes, sequences that appear to mediate processes of viral segment formation, such as proviral segment excision and circularization, appear to be highly conserved, supporting the hypothesis of a single origin for BVs.

Show MeSH
Related in: MedlinePlus