LysR transcriptional regulator Identities = 57/164 (35%), Positives = 82/164 (50%), Gaps = 13/164 (8%) 70530- SNQAIKTYLMPK*LRLLRQK*SPVEFQLQVHLIKKIRLNIVIRDINLTIIEN-TPVKLKI -70354 ++Q TYLMP+ + L RQK V QLQVH ++I ++ INL II P++LK 86251- ASQTTGTYLMPRLIGLFRQKYPQVAVQLQVHSTRRIAWSVANGHINLAIIGGEVPIELKN -86072 70353- FYTLLRMKERI*H*YCLGFL------FQFLIAYKKKNLYGLRLIKVDIPFPIRGIMNNP* -70192 + E L + F L + +K++LY LR I +D IR +++ 86071- MLQVTSYAED-----ELALILPKSHPFSMLRSIQKEDLYRLRFIALDRQSTIRKVIDKVL -85907 70191- IKTELIPRNLN-EMELSLFKPIKNAV*PGLNVTLIFVSAIAKEL -70063 + + EMEL+ + IKNAV GL + VSAIAKEL 85906- NQNGIDSTRFKIEMELNSVEAIKNAVQSGLGAAFVSVSAIAKEL -85775 ycf3 Photosystem I assembly protein Identities = 25/59 (42%), Positives = 39/59 (66%), Gaps = 3/59 (5%) 19162- NRSYML-SIQCM-PNNSDYVNTLKHCR*ALDLSSKL-LAIRNVTISYYCQDIIFSEKKD -19329 +RSY+L +I + +N +YV L++ ALDL+S+L AI N+ + Y+ Q + SEKKD 19583- DRSYILYNIGLIYASNGEYVKALEYYHQALDLNSRLPPAINNIAVIYHYQGVKASEKKD -19759 Fig.S1. The pairwise aligments of high scoring pairs of recognizable pseudogenes. The upper amino acid sequences indicates Cryptomonas sp. SAG977-2f. The lower sequences are corresponding amino acid sequences of homologs in C. curvata CCAP979/52. Table S1. Presence/absence of protein genes in the plastid genomes of Cryptomonas and representative species of Cryptomonadales. Note; y indicates pseudogenes. Photosynthetic Non-Photosynthetic Guillardia Rhodomonas Cryptomonas C. C. curvata C. curvata parameciu Guillardia Rhodomonas FBCC300 CCAP979/ SAG977 CCAC1634 m theta salina -2f B 012D 52 CCAP977/2 a rps2 + + + + + + + rps3 + + + + + + + rps4 + + + + + + + rps5 + + + + + + + rps6 + + + + + + - rps7 + + + + + + + rps8 + + + + + + + rps9 + + + + + + + rps10 + + + + + + + rps11 + + + + + + + rps12 + + + + + + + rps13 + + + + + + + rps14 + + + + + + + rps16 + + + + + + + rps17 + + + + + + + rps18 + + + + + + + rps19 + + + + + + + rps20 + + + + + + + rpl1 + + + + + + + rpl2 + + + + + + + rpl3 + + + + + + + rpl4 + + + + + + + rpl5 + + + + + + + rpl6 + + + + + + + rpl11 + + + + + + + rpl12 + + + + + + + rpl13 + + + + + + + rpl14 + + + + + + + rpl16 + + + + + + + rpl18 + + + + + + + rpl19 + + + + + + + rpl20 + + + + + + + rpl21 + + + + + + + rpl22 + + + + + + + rpl23 + + + + + + + rpl24 + + + + + + + rpl27 + + + + + + + rpl29 + + + + + + + rpl31 + + + + + + + rpl32 + + + + + + - rpl33 + + + + + + + rpl34 + + + + + - + rpl35 + + + + + + + rpl36 + + + + + + + infB + + + + + + + tufA + + + + + + + tsf + + + + + + + rpoA + + + + + + + rpoB + + + + + + + rpoC1 + + + + + + + rpoC2 + + + + + + + atpA + + + + + + + atpB + + + + + + + atpD + + + + + + + atpE + + + + + + + atpF + + + + + + y atpG + + + + + + + atpH + + + + + + + atpI + + + + + + + sufB + + + + + + + sufC + + + + + + + petF + + + + + + + tatC + + + + + + + secA + + + + + + + secG + + + + + - - secY + + + + + + + clpC + + + + + + + dnaK + + + + + + + groEL + + + + + + + ftsH + + + + + + - dnaX - + y - - - - dnaB + + y - - - - rbcL + + + + y - + rbcR(lysR) + + + + y - - rbcS + + + + - - + cbbX + + + + y - + chlB - y + + + + - chlI + + + + + + + chlL - y + + + + - chlN - y + + + + - pbsA + + + + + - + hlpA + + + + - - - hlip + + + + - - - ccsA + + + + - - - cemA + + + + + + + rne + + + + + - - ftrB + + + + y - - cpeB + + + + + - - ccs1 + + + + - - - ilvB + + + + + + + ilvH + + + + + + + acpP + + + + + + + minD + + + + + + - minE + + + + + + - RT - + + + - - - psaA + + + + - - - psaB + + + + - - - psaC + + + + - - - psaD + + + + - - - psaE + + + + - - - psaF + + + + y - - psaI + + + + - - - psaJ + + + + - - - psaK + + + + - - - psaL + + + + - - - psaM + + + + - - - psbA + + + + - - - psbB + + + + y - - psbC + + + + - - - psbD + + + + - - - psbE + + + + - - - psbF + + + + - - - psbH + + + + - - - psbI + + + + - - - psbJ + + + + - - - psbK + + + + - - - psbL + + + + - - - psbN + + + + - - - psbT + + + + - - - psbV + + + + y - - psbW + + + + - - - psbX + + + + - - - psbY + + + + - - - psbZ + + + + - - - petA + + + + - - - petB + + + + - - - petD + + + + - - - petG + + + + - - - petL + + + + - - - petM + + + + - - - petN + + + + - - - ycf3 + + + + y - - ycf4 + + + + - - - ycf12 + + + + - - - ycf19 + + + + + + + ycf20 + - - + + - + ycf26 - + - - - - - ycf27(omp + + + + y - - R) ycf29/tctD + + + + + + + ycf33 + + + + - - - ycf35 + + + + - - - ycf36 + + + + - - - ycf37 + + + + - - - ycf39 + + + + y - - ycf46 + + + + - - - ycf61 + + + + + + + ycf65 + + + + + + - Table S2 Synonymous (dS) and nonsynonymous (dN) substitution rates between Cryptomonas curvata CCAC979/52 and FBCC300012D plastid genome genes. dS dN dNdS 146 genes (Average) 7.4467 0.0716 0.0096 Concatenate 2.6798 0.0609 0.0227 Table S3 Averages of synonymous (dS) and nonsynonymous (dN) substitution rates of available rbcL gene sequences of Cryptomonadales genera. dS dN dNdS Cryptomonas (n=12) 1.5286 0.0134 0.0116 Rhodomonas (n=6) 0.3006 0.0052 0.0142 Hemiselmis (n=6) 0.1724 0.0095 0.0587 .