Adaptive selection on bracovirus genomes drives the specialization of Cotesia parasitoid wasps

Abstract

The geographic mosaic of coevolution predicts parasite virulence should be locally adapted to the host community. Cotesia parasitoid wasps adapt to local lepidopteran species possibly through their symbiotic bracovirus. The virus, essential for the parasitism success, is at the heart of the complex coevolutionary relationship linking the wasps and their hosts. The large segmented genome contained in the virus particles encodes virulence genes involved in host immune and developmental suppression. Coevolutionary arms race should result in the positive selection of particular beneficial alleles. To understand the global role of bracoviruses in the local adaptation or specialization of parasitoid wasps to their hosts, we studied the molecular evolution of four bracoviruses associated with wasps of the genus Cotesia, including C congregata, C vestalis and new data and annotation on two ecologically differentiated populations of C sesamie, Kitale and Mombasa. Paired orthologs analyses revealed more genes under positive selection when comparing the two C sesamiae bracoviruses belonging to the same species, and more genes under strong evolutionary constraint between species. Furthermore branch-site evolutionary models showed that 17 genes, out of the 54 currently available shared by the four bracoviruses, harboured sites under positive selection including: the histone H4-like, a C-type lectin, two ep1-like, ep2, a viral ankyrin, CrV1, a ben-domain, a Serine-rich, and eight unknown genes. Lastly the phylogenetic analyses of the histone, ep2 and CrV1 genes in different African C sesamiae populations showed that each gene described differently the individual relationships. In particular we found recombination had happened between the ep2 and CrV1 genes, which are localized 37.5 kb apart on the wasp chromosomes. Involved in multidirectional coevolutionary interactions, C sesamiae wasps rely on different bracovirus mediated molecular pathways to overcome local host resistance.

Figure 1. Functional analysis of 139 CskBV genes.

(A) Bracovirus gene homologies identified by BLAST; (B) PSORT protein sub-localization analysis; within the pie charts values indicate the number (>1) of genes identified in each class; nd: not determined.

Figure 2. Gene content similarities between 4 Cotesia bracovirus genomes.

Values within the Venn diagram indicate the number of genes identified in each class; orthologs were identified by reciprocal best hits.

Figure 3. Pairwise dN/dS ratio distribution in Cotesia bracovirus orthologous genes.

(A) interspecific comparisons CcBV vs CvBV; (B) Intraspecific comparison CskBV vs CsmBV; due to weak polymorphism of several orthologs identified between CskBV and CsmBV, only 66 dN/dS ratios could be correctly estimated with codeml (PAML) among the 79 orthologous pairs; (C) CcBV vs CskBV, CcBV vs CsmBV, CvBV vs. CskBV and CvBV vs CsmBV. The x axis represents dN/dS ratio and the y axis the number of orthologs found 0.05 dN/dS intervals.

Figure 4. Evolution of Bracovirus histone, ep2 and CrV1 genes in different Cotesia sesamiae populations.

(A) Evolution of the histone gene: on the left, CsBV histone tree; on the right, genetic map showing the alignment of different isoforms, lines indicated the presence of deletions between boxed regions; (B) ep2 (left) and CrV1 (right) trees; lines between trees indicate the genotypes for which the 2 genes have different histories. Each genotype was assigned a color based on its main phylogenetic affiliation: purple = histone isoform b, orange = histone isoform c, pink = histone isoform d, green = ep2 CskBV clade, light blue = CrV1 CsmBV clade, and black = unassigned (refer to Table S1 for sampling details). Phylogenetic clustering is based on HKY genetic distance; ** and * indicate bootstrap support above 75 and 50 respectively; colored branches indicate results from Branch site REL analyses (HYPHY): in red with dN/dS >5 and in blue dN/dS = 0.