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Fig. 4 | Genome Biology

Fig. 4

From: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species

Fig. 4

Cathepsin B genes that are differentially expressed upon M. persicae host change belong predominantly to a single aphid-expanded clade and form gene clusters in the M. persicae genome. a Maximum likelihood phylogenic tree of arthropod cathepsin B protein sequences. The sequences were aligned with Muscle [76] and the phylogeny estimated using FastTree [92] (JTT + CAT rate variation). Circles on branches indicate SH-like local support values >80%, scale bar below indicates 0.1 substitutions per site. Rings from outside to inside: ring 1, M. persicae cathepsin B (MpCathB) gene identities (IDs) with numbers in red indicating upregulation of these genes in M. persicae reared for one year on B. rapa relative to those reared for one year on N. benthamiana and bold font indicating location on the cathepsin B multigene clusters shown in (b); ring 2, red squares indicating MpCathB genes that are differentially expressed upon M. persicae host change; ring 3, cathB genes from different arthropods following the colour scheme of the legend in the upper left corner and matching the colours of the branches of the phylogenetic tree; ring 4, aphid-expanded (AE) clades with AE_Clade I labelled light green and AE_Clade II light blue. b MpCathB multigene clusters of the M. persicae genome. Lines indicate the genomic scaffolds on which the MpCathB genes are indicated with block arrows. Gene IDs above the genes match those of the phylogenetic tree in A, with block arrows and fonts highlighted in red being differentially expressed upon host change. Scale bar on right shows 1 kb. c Relative expression levels of MpCathB genes of M. persicae at seven weeks being reared on N. benthamiana (Nb), B. rapa (Br) and A. thaliana (At). Numbers under the graphs indicate MpCathB gene IDs with those in red font DE as in (a). Batches of five adult females were harvested for RNA extraction and quantitative real-time polymerase chain reaction assays. Bars represent expression values (mean ± standard deviation (SD)) of three independent biological replicates. *p < 0.05 (ANOVA with Fishers LSD to control for multiple tests). d As in (c), except that individual aphids reared on At were transferred to At (At to At) or Nb (At to Nb) and harvested at two days upon transfer. e As in (d), except that individual aphids reared on Nb were transferred to Nb (Nb to Nb) or At (Nb to At) and harvested at two days upon transfer

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