Polydnaviruses (PDVs) are double-stranded DNA viruses with segmented genomes that replicate only in the oviducts of some species of parasitic wasps and are required for the successful parasitization of lepidopteran insects. PDV DNA segments are integrated in the genomes of their associated wasp hosts, and some are nested; i.e., smaller segments are produced from and largely colinear with larger segments. To determine the internal structure of nested viral segments, the first complete nucleotide sequence of a PDV genome segment and its integration locus was determined. By restriction mapping, Southern blot, and sequence analyses, we demonstrated that the Campoletis sonorensis PDV segment W is integrated into wasp genomic DNA. DNA sequence analysis revealed that proviral segment W terminates in two 1,185-bp direct long terminal repeats (LTRs) in the wasp chromosome, while only one LTR copy is present in the extrachromosomal (viral) W. The results suggest that terminal direct repeats are a general feature of PDV DNA segment integration but that the homology and size of the repeats can vary extensively. Segment W contains 12 imperfect direct repeats of six different types between 89 bp and 1.9 kbp with 65 to 90% homology. The orientation and structure of the repeats suggest that W itself may have arisen through sequence duplication and subsequent divergence. Mapping, hybridization, and sequence analyses of cloned R and M demonstrated that these segments are nested within segment W and that internal imperfect direct repeats of one type are implicated in the homologous intramolecular recombination events that generate segments R and M. Interestingly, segment nesting differentially increases the copy number of genes encoded by segment W, suggesting that the unusual genomic organization of PDVs may be directly linked to the unique functions of this virus in its obligate mutualistic association with parasitic wasps.Insects and viruses. The wasp C. sonorensis was maintained on its host Heliothis virescens larvae, and virus and viral DNA were isolated from the female wasp ovaries as described previously (30).Cloning and mapping of viral segments. Viral DNA was separated on 0.7% agarose gel in TAE buffer, and bands of superhelical viral DNA segments R and M were isolated (2, 5). DNA segments were purified by using Geneclean (Bio 101), digested with a restriction enzyme (BamHI, PstI, or XbaI), and cloned into compatibly digested plasmid pZero-1 (Invitrogen). Since some DNA bands contain comigrating but different viral DNA segments, the resulting clones were screened for hybridization to labeled W. Hybridizing clones were mapped with restriction enzymes (27), and subclones were generated in pZero-1 for detailed mapping and sequencing.Wasp genomic DNA isolation and genomic library. Wasp genomic DNA was extracted from pooled male wasps by using a modified procedure (46). A C. sonorensis genomic library was constructed by ligating BamHI-digested GEM-11 (Promega) arms to size-selected, Sau3AI-digested wasp genomic DNA (27). Genomi...