Fig. 2: Plastid relationships among major photosynthetic eukaryotes.

The maximum-likelihood tree was constructed using a concatenated alignment of PLASTID54 marker under the LG + F + I + G4 substitution model, following the nsgtree pipeline and IQ-TREE analysis. A similar topology was recovered under site-heterogeneous models LG + C60 + F + G/R6 (see Supplementary Figs. 6-10). In the tree, the NCBI reference plastome names are colored according to the “Taxonomy” color key, ptMAGs are labeled in black font, and three Gloeomargaritales species were used as the outgroup. Two long-branch taxa (NC_056103, Pteridomonas danica, and a ptMAG) were excluded here but are shown in Supplementary Figs. 6–10. The bar plot insert illustrates the number of novel ptMAGs identified per major photosynthetic group. The inner ring indicates the assigned taxonomy for each clade, as described in the color key. Different background shades of gray are used to distinguish separate clades; clades representing secondary/complex green-algal plastids in Euglenophyceae, Chlorarachinophyceae, and the dinoflagellate Lepidodinium chlorophorum, and complex red-algal plastids in dinoflagellates and Centroplasthelida are excluded from the shaded areas. The outer ring indicates the ecosystem of origin for the ptMAGs. A single ptMAG, which diverges before the diversification of Haptophyta and Cryptophyta, is highlighted with blue background shading and marked with a black star. Ultrafast bootstrap values are displayed only for branches with support below 95%. Some examples of clades represented exclusively by two or more ptMAGs are highlighted with magenta branches.