1. Annotated protein coding genes: Group of genes Name of genes Subunits of ATP synthase atpA, atpB, atpE, atpF, atpF_copy2, atpH, atpI Subunits of NADH-dehydrogenase ndhA, ndhA_copy2, ndhB, ndhB_copy2, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK Subunits of cytochrome b/f complex petA, petB, petD, petG, petL, petN Subunits of photosystem I psaA, psaB, psaC, psaI, psaJ Subunits of photosystem II psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ, ycf3, ycf3_copy2, ycf3_copy3 Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, rpl22, rpl2_copy2, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps12_copy2, rps14, rps15, rps18, rps19, rps2, rps3, rps4, rps7, rps8 DNA dependent RNA polymerase rpoA, rpoB, rpoC1, rpoC1_copy2, rpoC2 Subunit of rubisco rbcL c-type cytochrom synthesis gene ccsA Envelop membrane protein cemA Maturase matK Protease None Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor infA Conserved open reading frames ycf4, ycf68 Other genes chlB, chlL, chlN, orf188, orf42, psaM 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 rpl23, rpl32 Small subunit of ribosome rps16 DNA dependent RNA polymerase None Subunit of rubisco None c-type cytochrom synthesis gene None Envelop membrane protein None Maturase None Protease clpP Subunit of Acetyl-CoA-carboxylase None Translational initiation factor None Conserved open reading frames ycf1, ycf15, ycf2 Other genes None 2. Multicopy genes with different lengths: Genes Length Location ycf3 135 [9972:10107](+) ycf3_copy2 249 [10803:11052](+) ycf3_copy3 141 [11764:11905](+) rpoC1 447 [30715:31162](+) rpoC1_copy2 1659 [31856:33515](+) atpF 165 [40363:40528](+) atpF_copy2 429 [41212:41641](+) rps12 120 [62034:62154](+) rps12_copy2 252 [99648:99900](-) rpl2 426 [85098:85524](-) rpl2_copy2 402 [86172:86574](-) ndhB 732 [96096:96828](-) ndhB_copy2 780 [97530:98310](-) ndhA 528 [121668:122196](-) ndhA_copy2 600 [122935:123535](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (1/2) [40364:40528](+) atpF_copy2 (1/2) [41213:41641](+) ndhA (1/2) [121669:122196](-) ndhA_copy2 (1/2) [122936:123535](-) ndhB (1/2) [96097:96828](-) ndhB_copy2 (1/2) [97531:98310](-) petB (1/2) [76155:76811](+) petD (1/2) [77635:78150](+) rpl16 (1/2) [82111:82533](-) rpl2 (1/2) [85099:85524](-) rpl2_copy2 (1/2) [86173:86574](-) rpoC1 (1/2) [30716:31162](+) rpoC1_copy2 (1/2) [31857:33515](+) rps12 (1/3) [62035:62154](+) rps12_copy2 (1/3) [99649:99900](-) ycf3 (1/3) [9973:10107](+) ycf3_copy2 (1/3) [10804:11052](+) ycf3_copy3 (1/3) [11765:11905](+) ### The exon column shows the number of (actual exons/expected exons). ### 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon ycf3_copy3 ATT rps2 ATA atpF_copy2 ATT psaM ATA ndhJ ATA ndhK ATA accD ATA rps12 GTG rps18 ATT petB TTG petD ATT rps11 GTG rpl16 ATC rpl2 ATA ndhB ATT ndhB_copy2 ATT rps12_copy2 ATC orf42 ATC ndhE ATT ndhA ATT ndhA_copy2 GTG ndhH ATT 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 88 genes (80 unique genes). Including: 88 protein-coding genes (80 are unique) 0 tRNA genes (0 are unique) 0 rRNA genes (0 are unique) Details are as follows: 88 protein-coding genes (80 are unique) Genes Length Location accD 591 [59425:60015](+) atpA 1524 [41748:43271](+) atpB 1476 [52734:54209](+) atpE 408 [54218:54625](+) atpF 165 [40364:40528](+) atpF_copy2 429 [41213:41641](+) atpH 246 [39782:40027](+) atpI 747 [38367:39113](+) ccsA 957 [116212:117168](+) cemA 786 [69863:70648](-) chlB 1542 [5898:7439](-) chlL 873 [135041:135913](-) chlN 1395 [133618:135012](-) infA 252 [80747:80998](-) matK 1488 [1706:3193](-) ndhA 528 [121669:122196](-) ndhA_copy2 600 [122936:123535](-) ndhB 732 [96097:96828](-) ndhB_copy2 780 [97531:98310](-) ndhC 363 [49915:50277](-) ndhD 1503 [117413:118915](-) ndhE 306 [119673:119978](-) ndhF 2199 [111363:113561](-) ndhG 543 [120135:120677](-) ndhH 1179 [123540:124718](-) ndhI 492 [121055:121546](-) ndhJ 492 [48568:49059](-) ndhK 861 [49145:50005](-) orf188 591 [122936:123526](-) orf42 153 [105251:105403](-) petA 966 [68682:69647](-) petB 657 [76155:76811](+) petD 516 [77635:78150](+) petG 114 [65390:65503](-) petL 96 [65641:65736](-) petN 90 [26349:26438](-) psaA 2253 [12520:14772](+) psaB 2205 [14798:17002](+) psaC 246 [119058:119303](-) psaI 111 [72463:72573](-) psaJ 135 [64540:64674](-) psaM 87 [44908:44994](+) psbA 1062 [1:1062](-) psbB 1527 [72930:74456](+) psbC 1422 [18827:20248](-) psbD 1062 [20196:21257](-) psbE 258 [66938:67195](+) psbF 120 [67205:67324](+) psbH 228 [75005:75232](+) psbI 108 [45303:45410](-) psbJ 123 [67591:67713](+) psbK 180 [46113:46292](-) psbL 117 [67356:67472](+) psbM 105 [25367:25471](+) psbN 132 [74792:74923](-) psbT 108 [74611:74718](+) psbZ 189 [18093:18281](-) rbcL 1452 [54888:56339](+) rpl14 369 [81650:82018](-) rpl16 423 [82111:82533](-) rpl2 426 [85099:85524](-) rpl20 351 [62870:63220](+) rpl22 354 [84306:84659](-) rpl2_copy2 402 [86173:86574](-) rpl33 201 [64019:64219](-) rpl36 114 [80046:80159](-) rpoA 1011 [78358:79368](-) rpoB 3276 [27414:30689](+) rpoC1 447 [30716:31162](+) rpoC1_copy2 1659 [31857:33515](+) rpoC2 3597 [33646:37242](+) rps11 399 [79426:79824](-) rps12 120 [62035:62154](+) rps12_copy2 252 [99649:99900](-) rps14 303 [17152:17454](+) rps15 261 [124825:125085](-) rps18 288 [63391:63678](-) rps19 297 [84731:85027](-) rps2 711 [37428:38138](+) rps3 684 [83532:84215](-) rps4 630 [8249:8878](+) rps7 468 [98588:99055](-) rps8 399 [81121:81519](-) ycf3 135 [9973:10107](+) ycf3_copy2 249 [10804:11052](+) ycf3_copy3 141 [11765:11905](+) ycf4 555 [71311:71865](-) ycf68 60 [104289:104348](+) 0 tRNA genes (0 are unique) Genes Location 0 rRNA genes (0 are unique) Genes Location This genome has 0 genes with intron(s). Details are as follows: