Multiple introductions and recombination in Cryphonectria hypovirus 1: perspective for a sustainable biological control of chestnut blight

Abstract

Cryphonectria hypovirus 1 (CHV1) is a mycovirus which decreases the virulence of its fungal host Cryphonectria parasitica, the causal agent of chestnut blight recently introduced in Europe. The understanding of the evolutionary processes which have shaped CHV1 populations in Europe is required to develop a sustainable biocontrol strategy targeting chestnut blight and effective in European chestnut forests. To retrace the evolutionary history of CHV1, we analyzed sequences from two genomic regions on a collection of 55 CHV1 strains from France and northern Spain, two countries where multiple introductions of C. parasitica occurred. Several recombination events and variable selection pressures contributed to CHV1 evolution, agreeing with a non-clock-like diversification rate. These two mechanisms may be at the origin of CHV1 population diversity observed in western Europe. Considering the actual prevalence of CHV1 and its association with host genotypes, multiple introductions of CHV1 may have occurred in Europe, some of them directly from Asia and some of them through North America. Although some viral strains remained with low frequency in their introduction area, multiple infections might have allowed homologous recombination within parental sequences. Some of these recombinant lineages are associated with the spread of CHV1 in European regions.

Keywords: biological control; disease biology; host parasite interactions; invasive species; microbial biology.

Figure 1

Sampling localities of Cryphonectria hypovirus 1 strains in four regions: southern-eastern France (SEF), Central France (CF), Central Pyrénées (CPyr), and Atlantic Pyrénées (APyr). Pie charts represent the frequency of the main viral lineages (A1B1, A1B2, A2B1, A3B3, A4B1; one color for each, all other lineages are represented in grey) in the four regions.

Figure 2

The phylogenetic network resulting from the split decomposition of concatenated sequences from ORF A and ORF B of Cryphonectria hypovirus 1 using the neighbor-net method implemented in SPLITSTREE v4.11.3.

Figure 3

(A) Firm recombination events detected (E1, E2, E3 and E4) within 55 viral sequences of Cryphonectria hypovirus 1 by using seven methods of the RDP3 software. (B) Putative scenarios of the recombination events with putative parental and resulting recombinant CHV1 lineages identified by split decomposition (cf Fig. 2).

Figure 4

Lineages divergence dates inferred from ORF A_sh and ORF B_sh sequences of Cryphonectria hypovirus 1. The time-scale of evolutionary changes is indicated by the scale bar below the tree. Divergence dates with 95% CI are indicated above nodes; Bayesian posterior probabilities up to 0.5 are indicated below nodes.

Figure 5

Posterior state probabilities of population origin (PSP) inferred from Cryphonectria hypovirus 1 ORF Ash (left panels) and ORF Bsh (right panels) datasets. (A) PSP-values obtained for the original datasets. (B) PSP-values obtained after resampling ORF Ash or ORF Bsh datasets 25 times (see Methods). Letters above columns indicate significant differences among posterior location probabilities means as determined by a Tukey's HSD test after significant one-way anova.