Exploring the determinants of polydnavirus chromosomal integration across host-parasitoid wasp systems

Fig. 1.. Bracovirus genomic structure in the wasp and after injection in the host. The ovaries of the parasitoid wasp contain proviral segments within the wasp genome. Nudiviral genes encode viral structural components, including capsid proteins. Proviral segments are amplified, circularized through direct repeat junction motifs (DRJ), and subsequently encapsidated into viral particles in the calyx cells. During oviposition, the wasp injects encapsidated bracovirus particles into the host. In host cells, bracovirus circles can integrate into the host genome through host integration motifs (HIMs). DRJ: direct repeat junction; HIM, host integration motif; J1, junction 1; J2, junction 2. Created with BioRender.com.

Fig. 2.. Integration numbers and sequencing depth of HIM-bearing bracovirus circles in 8 wasp–host systems. The maximum likelihood phylogeny of the 4 species of Cotesia parasitoid wasps was reconstructed based on an alignment of BUSCO gene sequences. Microplitis demolitor was used as outgroup. Node support values (ALRT/Bootstrap) are shown at the internal nodes. Wasp–host systems are indicated at the tip of the branches. The number of bracovirus circle integrations and the sequencing depth over each circle are shown for all the circles that carry an HIM. The number of integrations is shown in black, and the sequencing depth in gray. Both variables were normalized to 1× on the host BUSCO genes (corresponding to a haploid host genome).

Fig. 3.. The number of bracovirus circle integrations is positively correlated with the abundance of circles injected by the wasps in their hosts. a) Integration number by circle per haploid host genome (hhg) as a function of the sequencing depth on circles per hhg. Each point represents a circle from one sample. Spearman's rank correlation coefficient: rho = 0.83, F = 790,405, P-value < 2.2 * 10−16. b) Model predictions for the number of integrations for circle 1 and circle 14, at different quantities of injected BV circles. The estimate for the circle quantity has been corrected by subtracting the amount of wasp genomic DNA detected and then normalized for library size (see Supplementary Methods for details). The other predictors have been fixed at the default values specified in the Supplementary Methods. The thick lines represent the posterior median, while the semi-transparent lines represent 1,000 randomly selected posterior draws. DPM: Depth Per Million.

Fig. 4.. Estimated wasp–host system effects on the number of integrations and BV quantity. a) Marginal posterior distribution for the difference in integration number between B. fusca–C. sesamiae Kitale (the baseline) and every other pair are shown b) Marginal posterior distributions for the difference in corrected Depth Per Million relative to the same baseline.

Fig. 5.. The effect of host suitability on the number of integrations. Number of integrations for C. sesamiae mombasa and C. flavipes when paired with a suitable host (S. calamistis and C. partellus, respectively) versus a nonsuitable host (B. fusca and S. frugiperda, respectively). a) Mean numbers of integrations as predicted by the regression model, controlling for circle and for corrected Depth Per Million. The violin plots represent the estimation uncertainty, as evaluated through 1,000 randomly sample Markov Chain Monte Carlo draws. Each line corresponds to one of these draws, with red used for posterior samples that returned a higher value in the suitable host and blue for the samples that gave the opposite result. b) The observed number of integrations in suitable and non-suitable hosts, for Cotesia sesamiae Mombasa and C. flavipes. Each point corresponds to the median number of integrations observed for a given circle.

Fig. 6.. Estimated differences in the number of integrations between circles. Marginal posterior distributions for the difference in the estimated efficiency of integration between circle 35 (baseline) and every other circle are shown. The integration numbers have undergone a natural logarithmic transformation. The effects of corrected Depth Per Million and wasp–host system are controlled for.

Fig. 7.. Estimated differences in BV quantity between circles. Marginal posterior distributions for the difference in corrected Depth Per Million (DPM) values between circle 35 (the baseline) and every other circle are shown. A cube root transformation has been applied to the corrected DPM. HIM-bearing circles have been coded in dark pink and HIM-lacking circles in light blue. The effects of wasp species, host species, and host suitability are controlled for. See the Supplementary Methods for a detailed explanation of the corrected depth metric.