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, ndhA_copy2, ndhB, ndhB_copy2, ndhC, ndhD, ndhD_copy2, ndhE, ndhE_copy2, ndhF, ndhF_copy2, ndhG, ndhG_copy2, ndhH, ndhH_copy2, ndhI, ndhI_copy2, ndhJ, ndhK Subunits of cytochrome b/f complex petA, petB, petD, petG, petL, petN Subunits of photosystem I psaA, psaB, psaC, psaC_copy2, psaI, psaJ Subunits of photosystem II psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbT, psbZ Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, rpl22, rpl23, rpl23_copy2, rpl32, rpl32_copy2, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps12_copy2, rps14, rps15, rps15_copy2, rps16, rps18, rps19, 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, ccsA_copy2 Envelop membrane protein cemA Maturase matK Protease None Subunit of Acetyl-CoA-carboxylase None Translational initiation factor infA Conserved open reading frames ycf1, ycf1_copy2, ycf2, ycf2_copy2 Other genes pafI, pafII, pbf1 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 psbN, ycf3 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 clpP Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor None Conserved open reading frames ycf15, ycf4 Other genes None 2. Multicopy genes with different lengths: Genes Length Location None None None 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [18632:18776](-) [17516:17925](-) ndhA (2/2) [127606:128158](-) [126011:126549](-) ndhA_copy2 (2/2) [157496:158048](+) [159105:159643](+) ndhB (2/2) [110750:111526](+) [112243:112998](+) ndhB_copy2 (2/2) [174128:174904](-) [172656:173411](-) petB (2/2) [79521:79526](+) [80248:80889](+) petD (2/2) [81105:81112](+) [81834:82329](+) rpl16 (2/2) [87229:87237](-) [85823:86221](-) rpl2 (2/2) [90129:90519](-) [89030:89466](-) rpoC1 (2/2) [29277:29708](-) [26913:28514](-) rps12 (3/3) [72716:72829](-) [176302:176533](-) [175739:175764](-) rps12_copy2 (3/3) [72716:72829](-) [109121:109352](+) [109890:109915](+) rps16 (2/2) [12194:12233](-) [11161:11369](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: pafI 3 [52801:52924](-) [51813:52042](-) [50887:51045](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon rps19 GTG rpl2 ACG ndhD ACG ndhD_copy2 ACG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 140 genes (111 unique genes). Including: 94 protein-coding genes (77 are unique) 38 tRNA genes (30 are unique) 8 rRNA genes (4 are unique) Details are as follows: 94 protein-coding genes (77 are unique) Genes Length Location atpA 1524 [15919:17442](-) atpB 1485 [8060:9544](+) atpE 423 [9547:9969](+) atpF 555 [18632:18776](-) [17516:17925](-) atpH 246 [19077:19322](-) atpI 744 [20725:21468](-) ccsA 969 [120640:121608](+) ccsA_copy2 969 [164046:165014](-) cemA 690 [63765:64454](+) infA 234 [84423:84656](-) matK 1500 [2134:3633](-) ndhA 1092 [127606:128158](-) [126011:126549](-) ndhA_copy2 1092 [157496:158048](+) [159105:159643](+) ndhB 1533 [110750:111526](+) [112243:112998](+) ndhB_copy2 1533 [174128:174904](-) [172656:173411](-) ndhC 363 [59108:59470](-) ndhD 1503 [121843:123345](-) ndhD_copy2 1503 [162309:163811](+) ndhE 306 [123968:124273](-) ndhE_copy2 306 [161381:161686](+) ndhF 2253 [115247:117499](-) ndhF_copy2 2253 [168155:170407](+) ndhG 531 [124529:125059](-) ndhG_copy2 531 [160595:161125](+) ndhH 1182 [128160:129341](-) ndhH_copy2 1182 [156313:157494](+) ndhI 498 [125426:125923](-) ndhI_copy2 498 [159731:160228](+) ndhJ 477 [57775:58251](-) ndhK 738 [58380:59117](-) pafI 513 [52801:52924](-) [51813:52042](-) [50887:51045](-) pafII 555 [62308:62862](+) pbf1 132 [78227:78358](-) petA 963 [64682:65644](+) petB 648 [79521:79526](+) [80248:80889](+) petD 504 [81105:81112](+) [81834:82329](+) petG 114 [68999:69112](+) petL 96 [68729:68824](+) petN 90 [35162:35251](+) psaA 2253 [48010:50262](-) psaB 2205 [45780:47984](-) psaC 246 [123466:123711](-) psaC_copy2 246 [161943:162188](+) psaI 111 [61760:61870](+) psaJ 141 [69992:70132](+) psbA 1062 [495:1556](-) psbB 1527 [76353:77879](+) psbC 1416 [42143:43558](+) psbD 1062 [41134:42195](+) psbE 252 [67235:67486](-) psbF 120 [67106:67225](-) psbH 222 [78457:78678](+) psbI 111 [13454:13564](+) psbJ 123 [66716:66838](-) psbK 186 [12844:13029](+) psbL 117 [66963:67079](-) psbM 105 [35657:35761](-) psbT 114 [78053:78166](+) psbZ 189 [44219:44407](+) rbcL 1428 [6114:7541](-) rpl14 369 [85325:85693](-) rpl16 408 [87229:87237](-) [85823:86221](-) rpl2 828 [90129:90519](-) [89030:89466](-) rpl20 420 [71533:71952](-) rpl22 387 [88240:88626](-) rpl23 303 [90525:90827](-) rpl23_copy2 303 [194827:195129](+) rpl32 180 [119506:119685](+) rpl32_copy2 180 [165969:166148](-) rpl33 201 [70559:70759](+) rpl36 114 [84170:84283](-) rpoA 1029 [82506:83534](-) rpoB 3207 [29735:32941](-) rpoC1 2034 [29277:29708](-) [26913:28514](-) rpoC2 4104 [22627:26730](-) rps11 450 [83601:84050](-) rps12 372 [72716:72829](-) [176302:176533](-) [175739:175764](-) rps12_copy2 372 [72716:72829](-) [109121:109352](+) [109890:109915](+) rps14 303 [45328:45630](-) rps15 264 [129470:129733](-) rps15_copy2 264 [155921:156184](+) rps16 249 [12194:12233](-) [11161:11369](-) rps18 459 [70895:71353](+) rps19 279 [88685:88963](-) rps2 711 [21688:22398](-) rps3 714 [87424:88137](-) rps4 609 [54436:55044](-) rps7 468 [109969:110436](+) rps7_copy2 468 [175218:175685](-) rps8 402 [84764:85165](-) ycf1 5865 [135623:141487](-) ycf1_copy2 5865 [144167:150031](+) ycf2 6375 [91288:97662](+) ycf2_copy2 6375 [187992:194366](-) 38 tRNA genes (30 are unique) Genes Location trnH-GUG [168:242](-) trnK-UUU [4354:4390](-) [1866:1900](-) trnM-CAU [10154:10226](-) trnV-UAC [10408:10446](+) [11026:11060](+) trnQ-UUG [12443:12514](-) trnS-GCU [13705:13792](-) trnG-UCC [14781:14803](+) [15498:15545](+) trnR-UCU [15708:15779](+) trnC-GCA [34225:34295](+) trnD-GUC [38906:38979](-) trnY-GUA [39373:39456](-) trnE-UUC [39526:39598](-) trnT-GGU [40155:40226](+) trnS-UGA [43783:43875](-) trnG-GCC [44724:44794](+) trnfM-CAU [45102:45175](-) trnS-GGA [54070:54156](+) trnT-UGU [55399:55471](-) trnL-UAA [56103:56137](+) [56620:56669](+) trnF-GAA [57046:57118](+) trnW-CCA [69241:69314](-) trnP-UGG [69472:69545](-) trnI-CAU [91158:91231](-) trnL-CAA [98725:98805](-) trnR-ACG [99453:99526](-) trnA-UGC [104119:104156](-) [103283:103317](-) trnI-GAU [105206:105242](-) [104221:104255](-) trnV-GAC [107251:107322](-) trnN-GUU [113460:113531](-) trnL-UAG [120450:120529](+) trnL-UAG_copy2 [165125:165204](-) trnN-GUU_copy2 [172123:172194](+) trnV-GAC_copy2 [178332:178403](+) trnI-GAU_copy2 [180412:180448](+) [181399:181433](+) trnA-UGC_copy2 [181498:181535](+) [182337:182371](+) trnR-ACG_copy2 [186128:186201](+) trnL-CAA_copy2 [186849:186929](+) trnI-CAU_copy2 [194423:194496](+) 8 rRNA genes (4 are unique) Genes Location rrn5 [99767:99887](-) rrn4.5 [100126:100228](-) rrn23 [100319:103135](-) rrn16 [105534:107023](-) rrn16_copy2 [178631:180120](+) rrn23_copy2 [182519:185335](+) rrn4.5_copy2 [185426:185528](+) rrn5_copy2 [185767:185887](+) This genome has 22 genes with intron(s). Details are as follows: 19 gene(s) have 1 intron(s) Genes Exons rps16 [12194:12233](-) [11161:11369](-) atpF [18632:18776](-) [17516:17925](-) rpoC1 [29277:29708](-) [26913:28514](-) petB [79521:79526](+) [80248:80889](+) petD [81105:81112](+) [81834:82329](+) rpl16 [87229:87237](-) [85823:86221](-) rpl2 [90129:90519](-) [89030:89466](-) ndhB [110750:111526](+) [112243:112998](+) ndhA [127606:128158](-) [126011:126549](-) ndhA_copy2 [157496:158048](+) [159105:159643](+) ndhB_copy2 [174128:174904](-) [172656:173411](-) trnK-UUU [4354:4390](-) [1866:1900](-) trnV-UAC [10408:10446](+) [11026:11060](+) trnG-UCC [14781:14803](+) [15498:15545](+) trnL-UAA [56103:56137](+) [56620:56669](+) trnA-UGC [104119:104156](-) [103283:103317](-) trnI-GAU [105206:105242](-) [104221:104255](-) trnI-GAU_copy2 [180412:180448](+) [181399:181433](+) trnA-UGC_copy2 [181498:181535](+) [182337:182371](+) 3 gene(s) have 2 intron(s) Genes Exons rps12 [72716:72829](-) [176302:176533](-) [175739:175764](-) pafI [52801:52924](-) [51813:52042](-) [50887:51045](-) rps12_copy2 [72716:72829](-) [109121:109352](+) [109890:109915](+)