Figure 1.

Bioinfomatic analysis of PPL1 and PPL2 proteins. A, Protein phylogenetic trees of the PsbP and PPL protein family. A rooted tree of 32 protein sequences was produced using the neighbor-joining method with Gloeobacter as an outgroup. The sequences are named for each organism that corresponds to the cyanoP or PsbP protein sequence used (the protein ID no. from UniProt or GenBank is given together with the species-scientific name): GLOVI, Q7NKN7, Gloeobacter violaceus PCC 7421; ANASP, Q8YSK9, Anabaena sp. PCC 7120; SYNPX, Q7U7Q4, Synechococcus sp. WH8102; SYNY3, P73952, Synechocystis sp. PCC 6803; CMN290C and CMT368C, C. merolae annotated coding sequences (http://merolae.biol.s.u-tokyo.ac.jp/blast/blast.html); CHLRE, P11471, C. reinhardtii; CHLIN, ABA01138, C. incerta; ARATH, Q42029, Arabidopsis; LYCES, P29795, Lycopersicon esculentum (Solanum lycoperin); GLYMA, EST reconstructions, Glycine max (http://www.ncbi.nlm.nih.gov/dbEST); ZEAMA, EST reconstructions, Z. mays; SORBI, EST reconstructions, Sorghum bicolor; ORYSA, Q943W1, rice; WHEAT, Q00434, Triticum aestivum; HORVU, EST reconstructions, Hordeum vulgare. The sequences of PPL1 and PPL2 orthologs are as follows: TaPPL1 and TaPPL2, EST reconstructions, T. aestivum; HvPPL1 and HvPPL2, EST reconstructions, H. vulgare; SbPPL1 and SbPPL2, EST reconstructions, S. bicolor; ZmPPL1 and ZmPPL2, EST reconstructions, Z. mays; OsPPL1 and OsPPL2, Q6ZDL1 and EST reconstructions, rice; AtPPL1 and AtPPL2, P82538 and O80634, Arabidopsis; SlPPL1 and SlPPL2, EST reconstructions, S. lycoperin; GmPPL1 and GmPPL2, EST reconstructions, G. max. Bootstrap values from 1,000 replications are shown at the tree nodes. B, Network diagram of the genes that showed a high r value with each other and PPL1. C, Network diagram of the genes that showed a high r value with each other and PPL2. Thick black lines, r ≥ 0.925; thin black lines, 0.925 > r ≥ 0.900; gray lines, 0.900 > r ≥ 0.875; black dotted lines, r < 0.875.