Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2011:3:209-18.
doi: 10.1093/gbe/evr007. Epub 2011 Feb 2.

Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture

Bethany N Kent  1 , Leonidas Salichos, John G Gibbons, Antonis Rokas, Irene L G Newton, Michael E Clark, Seth R Bordenstein
Affiliations

Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture

Bethany N Kent et al. Genome Biol Evol. 2011.

Abstract

Bacteriophage flux can cause the majority of genetic diversity in free-living bacteria. This tenet of bacterial genome evolution generally does not extend to obligate intracellular bacteria owing to their reduced contact with other microbes and a predominance of gene deletion over gene transfer. However, recent studies suggest intracellular coinfections in the same host can facilitate exchange of mobile elements between obligate intracellular bacteria-a means by which these bacteria can partially mitigate the reductive forces of the intracellular lifestyle. To test whether bacteriophages transfer as single genes or larger regions between coinfections, we sequenced the genome of the obligate intracellular Wolbachia strain wVitB from the parasitic wasp Nasonia vitripennis and compared it against the prophage sequences of the divergent wVitA coinfection. We applied, for the first time, a targeted sequence capture array to specifically trap the symbiont's DNA from a heterogeneous mixture of eukaryotic, bacterial, and viral DNA. The tiled array successfully captured the genome with 98.3% efficiency. Examination of the genome sequence revealed the largest transfer of bacteriophage and flanking genes (52.2 kb) to date between two obligate intracellular coinfections. The mobile element transfer occurred in the recent evolutionary past based on the 99.9% average nucleotide identity of the phage sequences between the two strains. In addition to discovering an evolutionary recent and large-scale horizontal phage transfer between coinfecting obligate intracellular bacteria, we demonstrate that "targeted genome capture" can enrich target DNA to alleviate the problem of isolating symbiotic microbes that are difficult to culture or purify from the conglomerate of organisms inside eukaryotes.

PubMed Disclaimer

Figures

F<sc>IG</sc>. 1.—
FIG. 1.—
Gene presence and synteny between prophages WOVitB and WOVitA1. WO genes are syntenous and homologous between prophages WOVitB and WOVitA1. WOVitB genes contained within a single contig are denoted with an underline. WOVitB reads mapped to repetitive flanking regions of WOVitA1 are denoted with a dashed line. The other genes category includes genes annotated as a holliday junction resolvasome, a leucine-rich repeat protein, DNA polymerase III, an ATPase, and a methyl accepting chemotaxis protein.
F<sc>IG</sc>. 2.—
FIG. 2.—
Percent nucleotide identity between prophage genes encoded on WOVitB, WOVitA1, and other phages. Nucleotide identity between transferred prophage genes is significantly elevated between the genomes of the coinfections. Percent nucleotide identity is compared between phage genes transferred between wVitA with wVitB, other phage genes present in wVitB that are not homologous to genes in WOVitA1, and wVitA and wVitB previously sequenced protein-coding genes. A list of phage gene homologs present in wVitB that are not found in WOVitA1 is provided in supplementary table S2 (Supplementary Material online).
F<sc>IG</sc>. 3.—
FIG. 3.—
Enrichment efficiency of the Wolbachia capture array. Bar graph denotes % of the nucleotides out of the total assembled contigs (≥100 bp) that match to the four taxonomic categories. The no identity category (0.6%) that had no significant homology to any sequence in the NCBI nr database was left in the final assembly because it had a low GC content that is diagnostic of the Wolbachia genome. The Nasonia and other bacteria categories represent 1.04% and 0.67% of the total assembled DNA, respectively.
F<sc>IG</sc>. 4.—
FIG. 4.—
Analysis of genome assembly and coverage with real and simulated data. Top graph: Histogram distributions of assembled contig length in real and simulated sequence reads. The x and y axes correspond to contig length (in bins) and number of occurrences, respectively. Bottom graph: Histogram distributions of assembled contig coverage in real and simulated sequence reads. The x and y axes correspond to contig coverage (in bins) and number of occurrences, respectively.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Akman L, et al. Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia. Nat Genet. 2002;32:402–407. - PubMed
    1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–410. - PubMed
    1. Andersson SG, et al. Comparative genomics of microbial pathogens and symbionts. Bioinformatics. 2002;18(2 Suppl):S17. - PubMed
    1. Baldo L, et al. Multilocus sequence typing system for the endosymbiont Wolbachia pipientis. Appl Environ Microbiol. 2006;72:7098–7110. - PMC - PubMed
    1. Baldridge GD, et al. Wide dispersal and possible multiple origins of low-copy-number plasmids in rickettsia species associated with blood-feeding arthropods. Appl Environ Microbiol. 2010;76:1718–1731. - PMC - PubMed

Publication types

LinkOut - more resources