Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 10 (9), e1004660
eCollection

Widespread Genome Reorganization of an Obligate Virus Mutualist

Affiliations

Widespread Genome Reorganization of an Obligate Virus Mutualist

Gaelen R Burke et al. PLoS Genet.

Abstract

The family Polydnaviridae is of interest because it provides the best example of viruses that have evolved a mutualistic association with their animal hosts. Polydnaviruses in the genus Bracovirus are strictly associated with parasitoid wasps in the family Braconidae, and evolved ∼100 million years ago from a nudivirus. Each wasp species relies on its associated bracovirus to parasitize hosts, while each bracovirus relies on its wasp for vertical transmission. Prior studies establish that bracovirus genomes consist of proviral segments and nudivirus-like replication genes, but how these components are organized in the genomes of wasps is unknown. Here, we sequenced the genome of the wasp Microplitis demolitor to characterize the proviral genome of M. demolitor bracovirus (MdBV). Unlike nudiviruses, bracoviruses produce virions that package multiple circular, double-stranded DNAs. DNA segments packaged into MdBV virions resided in eight dispersed loci in the M. demolitor genome. Each proviral segment was bounded by homologous motifs that guide processing to form mature viral DNAs. Rapid evolution of proviral segments obscured homology between other bracovirus-carrying wasps and MdBV. However, some domains flanking MdBV proviral loci were shared with other species. All MdBV genes previously identified to encode proteins required for replication were identified. Some of these genes resided in a multigene cluster but others, including subunits of the RNA polymerase that transcribes structural genes and integrases that process proviral segments, were widely dispersed in the M. demolitor genome. Overall, our results indicate that genome dispersal is a key feature in the evolution of bracoviruses into mutualists.

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Genomic organization of MdBV proviral segment loci.
The upper part of the figure presents the eight proviral loci identified (L1–L8) and the corresponding M. demolitor genome scaffolds where they are located. Only the portion of the scaffold where the proviral locus resides is shown. For each locus, the upper scale bar in kilobases (k) names the scaffold(s). Below the scale bar, colored bars indicate the segments identified by deep sequencing DNA from MdBV virions (Encapsidated segments) and their corresponding orientation and location in a given locus as a proviral segment in the M. demolitor genome. Average coverage in thousands of reads is indicated above each segment in brackets, while below each segment is shown read coverage per nucleotide relative to the scale indicated to the right of the graph. Gaps in read coverage indicate regions flanking individual proviral segments that are not amplified, excised and packaged into virions. The gap seen in segment S (L6) is due to a region of N's in the reference sequence. Below each MdBV proviral segment is shown predicted genes in forward (black) and reverse (white) orientation. Individual introns, exons and untranslated regions are not shown. The lower part of the figure shows each scaffold containing MdBV proviral loci in their entirety. Scaffolds are drawn to scale and organized from largest (L3) to smallest (L5). Scale bar is in megabases (M).
Figure 2
Figure 2. Wasp Integration Motifs (WIMs) for all MdBV proviral segments.
(A) Alignment of 200 nucleotides (nt) surrounding the 5′ WIM site of each segment with similarity for each site colored in shades of blue. Red box highlights the tetramer AGCT. 31 nt are conserved in each proviral segment following the AGCT motif (red box), while the 5′ flanking region upstream of this motif is AT rich and not well conserved. (B) Alignment of 200 nt surrounding the 3′ WIM site for proviral segments shows that the flanking region preceding the WIM site is AT rich but not conserved, whereas the first 100 nt of each proviral segment downstream of the WIM site shows high conservation. Maximum likelihood analyses indicated that the relationships between segments for the WIM sites (A) and 3′ flanking regions (B) cannot be resolved.
Figure 3
Figure 3. Relatedness of Host Integration Motif (HIM) sequences for all MdBV proviral segments.
Alignment of HIM sequences with similarity for each site colored in shades of blue. Maximum likelihood analysis shows that three segment groups contain HIMs that form monophyletic groups (segments N and J; segments P, K1 and K; segments A and B) but other relationships could not be resolved.
Figure 4
Figure 4. Two genomic regions flanking proviral segments are conserved among BV-carrying wasps.
(A) The area surrounding segments N and J in M. demolitor Locus 3 is homologous to the regions surrounding segment 25 in Locus 5 of G. flavicoxis and G. indiensis and segment 1 in Locus 5 of C. congregata. M. demolitor loci are oriented to match the orientation of sequence scaffolds and similarity between flanking regions reported in prior studies. Although the genes in the proviral segments themselves are usually not recognizably homologous (black background with genes in white), the regions flanking these proviral segments (gray background with genes in white) are conserved as indicated by regions of synteny shaded in light blue. To the right of the figure is shown the phylogenetic relationships between these wasp species and estimated divergence times. (B) The downstream region flanking segment P in M. demolitor Locus 1 is similar to the region between Locus 1 and 2 in G. flavicoxis, G. indiensis, C. congregata and C. sesamiae Kitale. Genes and segments are depicted as in (A) except for odv-e66-like1 homologs are indicated in red in the Glyptapanteles and Cotesia genomes. Although the odv-e66 homologs are located in an area of synteny, no odv-e66 homologs exist in this region for M. demolitor. Accession numbers for sequences are MdL3 (KK043340), GiL5 (EF710656), GfL5 (EF710650), CcL5 (HF586476), MdL1 (KK044729), GfL1 (EF710644), GiL1 (EF710657), GiL2 (AC191960), CcL2 (HF586473), CcL1 (HF586472), CsL2 (EF710635), CsL1 (EF710629).
Figure 5
Figure 5. The nudivirus-like gene cluster in the genome of M. demolitor shares features with the partial nudivirus-like gene cluster from C. congregata.
The M. demolitor nudivirus-like gene cluster is indicated in the lower portion of the figure by the two white boxes, while flanking domains containing predicted M. demolitor genes are indicated by the gray background. Regions of synteny between the M. demolitor nudivirus-like gene cluster and C. congregata nudivirus-like cluster are indicated by light blue. Black regions in gene models represent UTRs, black lines indicate introns, while red and white regions represent exons for nudivirus-like genes and wasp genes respectively. Scale bar indicates the size of these clusters in kilobase pairs (Kbp). Accession numbers are FM212911 for the C. congregata nudivirus-like cluster, and KK043480 for the M. demolitor cluster.
Figure 6
Figure 6. Distribution of nudivirus-like genes in loosely associated clusters in the M. demolitor genome.
Five scaffolds containing nudivirus-like genes arranged from largest (1.6 Mb) to smallest (660 Kb) are shown in in gray. Named nudivirus-like genes (red) are separated by large stretches of DNA containing predicted M. demolitor genes (white). Wasp genes are depicted without indicating introns, exons, and untranslated regions.

Similar articles

See all similar articles

Cited by 21 PubMed Central articles

See all "Cited by" articles

References

    1. Moran NA (2007) Symbiosis as an adaptive process and source of phenotypic complexity. Proc Natl Acad Sci U S A 104 Suppl 1: 8627–8633. - PMC - PubMed
    1. Villarreal LP (2007) Virus-host symbiosis mediated by persistence. Symbiosis 43: 1–9.
    1. Wernegreen JJ (2012) Endosymbiosis. Curr Biol 22: R555–561. - PubMed
    1. Ochman H, Moran NA (2001) Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292: 1096–1099. - PubMed
    1. Raffaele S, Kamoun S (2012) Genome evolution in filamentous plant pathogens: why bigger can be better. Nat Rev Microbiol 10: 417–430. - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources

Feedback