Genome-wide models of bracovirus chromosomal integration in multiple host tissues during parasitism

Regardless of whether the chromosomal integration of wasp circles involves a single mechanism or multiple mechanisms, it appears that the vast majority of AEs, if not all, occur at the double-stranded breaks generated within HIMs. Our study thus confirms the central role played by HIMs in integration. Although these motifs have been found in all studies of Microgastrinae wasps so far, they could not be identified in Chelonus inanitus, a microgastoid wasp containing bracoviruses belonging to another subfamily (Cheloninae) (30). It has thus been proposed that HIMs could have been acquired by the ancestor of Microgastrinae around 54 million years ago, independently and well after the domestication of the nudivirus shared by all microgastroid wasps (30). The recent discovery that the ichnovirus surrounds the ichneumonid wasp Diadegma semiclausum undergo chromosomal integration in their host via HIM-type motifs raises the question of the evolutionary link between these motifs in bracoviruses and ichnoviruses. Structurally, the ichnovirus and bracovirus HIMs also consist of J1 and J2 motifs separated by a stretch of sequence which is deleted upon integration of the circle. The size of the sequence between J1 and J2 is relatively homogeneous in most bracovirus and ichnovirus segments (33 to 78 bp), although some ichnovirus segments have longer intermediate sequences (eg, DsIV-38 and Rostral tranosema ichnovirus F1, which respectively have intermediate sequences of 311 bp and 1781 bp). Like bracovirus HIMs, which do not appear to be ubiquitous in microgastoids (i.e., they were not found in Chelonus inanitus bracovirus segments), ichnovirus HIMs have not been found in all Campoleginae wasps known to harbor ichnovirus that have been investigated (31). Indeed, in addition to DsIV, Wang et al. found HIMs in Rostral tranosema and Hyposoter fugitivus ichnovirus but not in Campoletis sonorensis ichnovirus (31). We believe that three evolutionary scenarios could explain the presence of HIM in the bracovirus and ichnovirus segments. The first scenario postulates that HIMs and other integrating factors were present in ancestor viruses (bracovirus and ichnovirus) and were lost in several wasp lineages. In support of this scenario, the HzNV1 nudivirus is known to integrate into the DNA of cultured cells and to persist for a latent phase in both integrated and episomal form (56). The integrative properties of nudiviruses may have favored the recurrent domestication of nudiviruses by parasitic wasps (9, 11). However, the mechanism of integration of HzNV1 has not yet been characterized. Regarding ichnoviruses, the ancestor belonging to a possibly extinct family of viruses, nothing is known about the potential properties of ancient integration. The second scenario assumes that the integration of DNA circles evolved after viral domestication. This implies that HIMs would have been acquired in Braconidae and Ichneumonidae after viral domestication. This acquisition may have occurred through the independent recruitment of recombinase and protein sites from related viral elements or ETs present in the genomes of braconid and ichneumonid wasps. Consistent with this scenario, HIM-like motifs that contain inverted terminal repeats and are involved in site-specific recombination are common in prokaryotes, yeasts, viral genomes, and TEs (57). The recombination sites of site-specific recombinases involved in insertions, inversions or circularizations of DNA are generally between 30 and 200 nucleotides in length and consist of two motifs with partial reverse repeat symmetry, to which the recombinase binds. and which flank a central crossover sequence at which recombination takes place (58). HIM sites fit this description quite well. In eukaryotes, several examples of recombinases from TEs have been reported, such as the RAG1 protein, responsible for the shuffling of immunoglobulin genes in vertebrates (19), and the transposases involved in the maturation of the nuclei of paramecium (59). Finally, a third scenario would imply that the HIMs were acquired only once, by wasps Ichneumonidae or Braconidae, then transferred between the two polydnaviruses. Such a transfer could have been favored by the integrative properties of polydnavirus circles and by the fact that some wasps of both families are known to parasitize the same host species (60, 61). This seems rather unlikely, however, since it is not enough to transfer the HIM sequence to provide a functional mechanism, and the recombinase gene must be transferred at the same time; however, the latter is not present on a bracovirus circle (it is packaged as a protein in polydnavirus particles). The characterization of the different proteins involved in the integration of the circle and the integrases / recombinases encoded in the genomes of parasitoid wasps will probably be useful to further shed light on the evolutionary history of HIM and polydnaviruses in general.

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