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.
Table 1.
Cotesia bracovirus genome features.
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.
Table 2.
Detection of amino-acids evolving under positive selection.
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.