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. 2022 Feb 28;189(2):644–665. doi: 10.1093/plphys/kiac089

Figure 2.

Figure 2

Phylogenetic analysis of DCL family members encoded in the Solanaceae highlights a Solanum/Capsicum-specific expansion of DCL2. Phylogenetic tree of protein sequences indicating DCL subfamily members in the Solanaceae (A). Subclades of the DCL family are drawn with distinct colors and a box highlights a group of DCL2 paralogs that expanded in Capsicum and Solanum genera. Circles indicate tomato paralogs for DCL2. Heatmaps show the relative abundance of these tomato DCL2 paralogs in diverse samples (B). Protein orthologous groups were identified using OrthoFinder and SonicParanoid. Protein alignments and phylogeny analysis were done using MUSCLE and IQ-TREE. Phylogenetic tree was visualized using iTOL. The scale bar and branch lengths in (A) correspond to the expected number of substitutions per site. The scale bars in (B and C) show expression of DCL2 paralogs across samples normalized as reads per million (RPM).