1. Annotated protein coding genes: Group of genes Name of genes Subunits of ATP synthase atpA, atpB, atpE, atpF, atpH, atpI Subunits of NADH-dehydrogenase ndhA, ndhB, ndhB_copy2, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK Subunits of cytochrome b/f complex petA, petB, petB_copy2, petD, petD_copy2, petG, petL, petN Subunits of photosystem I psaA, psaB, psaC, psaI, psaJ Subunits of photosystem II psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbI_copy2, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ, ycf3 Large subunit of ribosome rpl14, rpl16, rpl16_copy2, rpl2, rpl20, rpl22, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps12_copy2, rps12_copy3, rps14, rps15, rps16, rps16_copy2, rps18, rps19, rps19_copy2, rps2, rps3, rps4, rps7, rps7_copy2, rps8 DNA dependent RNA polymerase rpoA, rpoB, rpoC1, rpoC2 Subunit of rubisco rbcL c-type cytochrom synthesis gene ccsA Envelop membrane protein cemA Maturase matK Protease clpP Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor infA Conserved open reading frames ycf1, ycf1_copy2, ycf2, ycf2_copy2, ycf4, ycf68, ycf68_copy2 Other genes None Possible missing protein coding genes: Group of genes Name of genes Subunits of ATP synthase None Subunits of NADH-dehydrogenase None Subunits of cytochrome b/f complex None Subunits of photosystem I None Subunits of photosystem II None Large subunit of ribosome None Small subunit of ribosome None DNA dependent RNA polymerase None Subunit of rubisco None c-type cytochrom synthesis gene None Envelop membrane protein None Maturase None Protease None Subunit of Acetyl-CoA-carboxylase None Translational initiation factor None Conserved open reading frames ycf15 Other genes None 2. Multicopy genes with different lengths: Genes Length Location rps12 369 join{[71716:71830](-), [101156:101385](-), [100589:100615](-)} rps12_copy2 357 join{[71716:71830](-), [101145:101388](-)} rps12_copy3 369 join{[71716:71830](-), [143275:143504](+), [144045:144071](+)} rps16 261 join{[5949:5989](-), [4869:5090](-)} rps16_copy2 216 [4869:5085](-) psbI 156 [8047:8203](+) psbI_copy2 111 [8092:8203](+) petB 654 join{[76962:76968](+), [77748:78396](+)} petB_copy2 657 [77739:78396](+) petD 522 join{[78609:78617](+), [79354:79868](+)} petD_copy2 564 [79304:79868](+) rpl16 408 join{[84856:84865](-), [83338:83737](-)} rpl16_copy2 411 [83338:83749](-) rpl2 822 join{[87938:>88329](-), [86845:87276](-)} rpl2_copy2 816 join{[156337:156722](+), [157384:157815](+)} ycf1 1347 [112128:113475](+) ycf1_copy2 5634 [126898:132532](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [13619:13763](-) [12426:12835](-) clpP (3/3) [73975:74045](-) [72866:73157](-) [71967:72218](-) ndhA (2/2) [124402:124954](-) [122822:123360](-) ndhB (2/2) [98976:99752](-) [97511:98266](-) ndhB_copy2 (2/2) [144909:145685](+) [146395:147150](+) petB (2/2) [76963:76968](+) [77749:78396](+) petB_copy2 (1/2) [77740:78396](+) petD (2/2) [78610:78617](+) [79355:79868](+) petD_copy2 (1/2) [79305:79868](+) rpl16 (2/2) [84857:84865](-) [83339:83737](-) rpl16_copy2 (1/2) [83339:83749](-) rpl2 (2/2) [87939:>88329](-) [86846:87276](-) rpl2_copy2 (2/2) [156338:156722](+) [157385:157815](+) rpoC1 (2/2) [23988:24419](-) [21632:23248](-) rps12 (3/3) [71717:71830](-) [101157:101385](-) [100590:100615](-) rps12_copy2 (2/3) [71717:71830](-) [101146:101388](-) rps12_copy3 (3/3) [71717:71830](-) [143276:143504](+) [144046:144071](+) rps16 (2/2) [5950:5989](-) [4870:5090](-) rps16_copy2 (1/2) [4870:5085](-) ycf3 (3/3) [44849:44972](-) [43899:44128](-) [43008:43166](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: ycf68 2 [105499:105540](+) [105572:105874](+)] ycf68_copy2 2 [139121:139162](-) [138787:139089](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon rps16_copy2 ATC psbI ATC cemA AAA petB_copy2 ATT rpl16_copy2 ATC rps19 GTG rpl2 ACG ndhD ATC rpl2_copy2 ATA rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 147 genes (117 unique genes). Including: 95 protein-coding genes (80 are unique) 44 tRNA genes (33 are unique) 8 rRNA genes (4 are unique) Details are as follows: 95 protein-coding genes (80 are unique) Genes Length Location accD 1476 [59154:60629](+) atpA 1545 [10799:12343](-) atpB 1497 [54644:56140](-) atpE 405 [54243:54647](-) atpF 555 [13619:13763](-) [12426:12835](-) atpH 246 [14303:14548](-) atpI 744 [15387:16130](-) ccsA 969 [117036:118004](+)