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Figure S1. Alignment of putative NDH subunits among plants. Putative nuclear-encoded subunits of subcomplex A, NdhL (a), NdhM (b), NdhN (c) and NdhO (d) are aligned among Arabidopsis (At), Marchantia (Mp) and Synechocystis sp. PCC6803 (Sc). Similarly, NdhS is aligned (e). Because NdhT and NdhU are not conserved in cyanobacteria, the sequences of maize (Zm) are used for NdhT (f) and NdhU (g). Putative nuclear-encoded subunits of subcomplex B, PnsB1 (h), PnsB2 (i), PnsB3 (j), PnsB4 (k), and PnsB5 (l) are aligned among Arabidopsis (At), rice (Os), and Marchantia (Mp).

Figure S2. Survey of EST clones encoding the homologous proteins of lumen subunits. (a) The Marchantia EST contig (MpPPL1) that encodes the protein most similar to AtPPL2 (PnsL1) is more similar to AtPPL1. (b) The Marchantia EST contig (MpPsbQ) that encodes the protein most similar to AtPnsL2 or AtPnsL3 is more similar to AtPsbQ1 or AtPsbQ2. (c) The Marchantia EST contig (MpFKBP13) that encodes the protein most similar to AtPnsL4/FKBP16-2 is more similar to AtFKBP13. (d) Alignment of putative PnsL5 among Arabidopsis, rice, and Marchantia.

Figure S3. Comparison of LhcI genes of Arabidopsis and Marchantia. Marchantia EST clones that were similar to AtLhca5 and Lhca6 were summarized into four EST contigs, which probably corresponded to Lhca1-4. EST clones with lesser similarity are likely to encode LHCII rather than LHCI.

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