Fig. 3: Closest relatives of green-alga-derived plastids in the dinoflagellate Lepidodinium chlorophorum.

a Phylogenetic position of the L. chlorophorum plastid compared to Pedinomonas spp. plastids and novel ptMAGs. Additional Pedinophyceae plastomes available in GenBank are included. Microrhizoidea and Chloropicon spp. were used as an outgroup. Ultrafast bootstrap values < 95% are shown. The reference species are color-coded, green for chlorophytes and purple for L. chlorophorum. Asterisks denote plastomes/ptMAGs used for whole genome alignment analysis. The number in the parentheses indicates the number of inverted syntenic blocks compared against P. minor (Fig. 3c). b A Venn diagram showing gene contents among P. minor, ptMAGs (IMGM3300042988_BIN337 and IMGM3300027621_BIN154), and L. chlorophorum, along with their respective plastome sizes. Two genes, petL and rpoA, missing only in IMGM3300027621_BIN154, are highlighted with a red dotted box. c Whole plastome alignment of ptMAGs and L. chlorophorum relative to P. minor generated using progressiveMauve alignment. Each locally collinear block representing synteny is color-coded; the blocks below the horizontal center indicate inversions. For simplicity, the ptMAGs labels have been abbreviated to associated bins. A copy of inverted repeats and single copy regions were removed from the plastome of Pedinomonas for the alignment.