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, 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 Large subunit of ribosome rpl14, rpl14_copy2, rpl16, rpl16_copy2, rpl2, rpl20, rpl22, rpl22_copy2, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36, rpl36_copy2 Small subunit of ribosome rps11, rps12, rps12_copy2, rps14, rps15, rps16, rps18, rps19, rps19_copy2, rps2, rps3, rps3_copy2, rps4, rps7, rps7_copy2, rps8, rps8_copy2 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, infA_copy2 Conserved open reading frames ycf1, ycf15, ycf15_copy2, ycf1_copy2, ycf2, ycf2_copy2, ycf4 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 None Other genes None 2. Multicopy genes with different lengths: Genes Length Location ycf1 1971 [108303:110274](+) ycf1_copy2 5496 [124036:129532](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [12584:12728](-) [11453:11853](-) clpP (3/3) [71678:71748](-) [70542:70833](-) [69670:69900](-) ndhA (2/2) [121581:122132](-) [119981:120520](-) ndhB (2/2) [95147:95923](-) [93709:94464](-) ndhB_copy2 (2/2) [141913:142689](+) [143372:144127](+) petB (2/2) [74692:74697](+) [75449:76090](+) petD (2/2) [76275:76282](+) [77032:77506](+) rpl16 (2/2) [82345:82353](-) [80992:81390](-) rpl16_copy2 (2/2) [155483:155491](+) [156446:156844](+) rpl2 (2/2) [85137:85527](-) [84052:84485](-) rpl2_copy2 (2/2) [152309:152699](+) [153351:153784](+) rpoC1 (2/2) [23080:23514](-) [20731:22335](-) rps12 (3/3) [69430:69543](-) [97308:97539](-) [96746:96771](-) rps12_copy2 (3/3) [69430:69543](-) [140297:140528](+) [141065:141090](+) rps16 (2/2) [5920:5959](-) [4940:5136](-) ycf3 (3/3) [44492:44617](-) [43574:43799](-) [42632:42786](-) ### 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 rps19 GTG ndhD CTG rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 141 genes (114 unique genes). Including: 96 protein-coding genes (80 are unique) 37 tRNA genes (30 are unique) 8 rRNA genes (4 are unique) Details are as follows: 96 protein-coding genes (80 are unique) Genes Length Location accD 1458 [57288:58745](+) atpA 1524 [9875:11398](-) atpB 1494 [52955:54448](-) atpE 423 [52536:52958](-) atpF 546 [12584:12728](-) [11453:11853](-) atpH 246 [13021:13266](-) atpI 744 [14402:15145](-) ccsA 975 [114653:115627](+) cemA 690 [60994:61683](+) clpP 594 [71678:71748](-) [70542:70833](-) [69670:69900](-) infA 234 [79522:79755](-) infA_copy2 234 [158081:158314](+) matK 1566 [1882:3447](-) ndhA 1092 [121581:122132](-) [119981:120520](-) ndhB 1533 [95147:95923](-) [93709:94464](-) ndhB_copy2 1533 [141913:142689](+) [143372:144127](+) ndhC 363 [50420:50782](-) ndhD 1530 [115850:117379](-) ndhE 306 [117968:118273](-) ndhF 2238 [110263:112500](-) ndhG 531 [118489:119019](-) ndhH 1182 [122134:123315](-) ndhI 504 [119384:119887](-) ndhJ 477 [49104:49580](-) ndhK 678 [49697:50374](-) petA 963 [61936:62898](+) petB 648 [74692:74697](+) [75449:76090](+) petD 483 [76275:76282](+) [77032:77506](+) petG 114 [65849:65962](+) petL 96 [65601:65696](+) petN 90 [28317:28406](+) psaA 2253 [39694:41946](-) psaB 2205 [37464:39668](-) psaC 246 [117468:117713](-) psaI 111 [59245:59355](+) psaJ 129 [66754:66882](+) psbA 1062 [340:1401](-) psbB 1527 [72207:73733](+) psbC 1422 [33938:35359](+) psbD 1062 [32929:33990](+) psbE 252 [64361:64612](-) psbF 120 [64232:64351](-) psbH 222 [74337:74558](+) psbI 111 [7952:8062](+) psbJ 123 [63838:63960](-) psbK 186 [7450:7635](+) psbL 117 [64093:64209](-) psbM 108 [29506:29613](-) psbN 132 [74103:74234](-) psbT 108 [73934:74041](+) psbZ 189 [36070:36258](+) rbcL 1428 [55246:56673](+) rpl14 369 [80485:80853](-) rpl14_copy2 369 [156983:157351](+) rpl16 408 [82345:82353](-) [80992:81390](-) rpl16_copy2 408 [155483:155491](+) [156446:156844](+) rpl2 825 [85137:85527](-) [84052:84485](-) rpl20 387 [68276:68662](-) rpl22 495 [83148:83642](-) rpl22_copy2 495 [154194:154688](+) rpl23 282 [85546:85827](-) rpl23_copy2 282 [152009:152290](+) rpl2_copy2 825 [152309:152699](+) [153351:153784](+) rpl32 159 [113432:113590](+) rpl33 201 [67330:67530](+) rpl36 114 [79291:79404](-) rpl36_copy2 114 [158432:158545](+) rpoA 1062 [77635:78696](-) rpoB 3213 [23541:26753](-) rpoC1 2040 [23080:23514](-) [20731:22335](-) rpoC2 4161 [16346:20506](-) rps11 417 [78764:79180](-) rps12 372 [69430:69543](-) [97308:97539](-) [96746:96771](-) rps12_copy2 372 [69430:69543](-) [140297:140528](+) [141065:141090](+) rps14 303 [37038:37340](-) rps15 270 [123411:123680](-) rps16 237 [5920:5959](-) [4940:5136](-) rps18 306 [67739:68044](+) rps19 279 [83713:83991](-) rps19_copy2 279 [153845:154123](+) rps2 711 [15429:16139](-) rps3 657 [82507:83163](-) rps3_copy2 657 [154673:155329](+) rps4 606 [45843:46448](-) rps7 468 [96223:96690](-) rps7_copy2 468 [141146:141613](+) rps8 405 [79877:80281](-) rps8_copy2 405 [157555:157959](+) ycf1 1971 [108304:110274](+) ycf15 192 [98526:98717](-) ycf15_copy2 192 [139119:139310](+) ycf1_copy2 5496 [124037:129532](-) ycf2 6267 [86155:92421](+) ycf2_copy2 6267 [145415:151681](-) ycf3 507 [44492:44617](-) [43574:43799](-) [42632:42786](-) ycf4 555 [59760:60314](+) 37 tRNA genes (30 are unique) Genes Location trnH-GUG [54:128](-) trnK-UUU [4168:4204](-) [1617:1651](-) trnQ-UUG [7020:7091](-) trnS-GCU [8203:8290](-) trnG-UCC [8806:8828](+) [9527:9574](+) trnR-UCU [9696:9767](+) trnC-GCA [27981:28051](+) trnD-GUC [30297:30354](-) trnY-GUA [30447:30518](-) trnE-UUC [30611:30681](-) trnT-GGU [31409:31480](+) trnS-UGA [35593:35685](-) trnG-GCC [36549:36619](+) trnfM-CAU [36800:36873](-) trnS-GGA [45447:45533](+) trnT-UGU [46813:46885](-) trnL-UAA [47686:47720](+) [48223:48271](+) trnF-GAA [48627:48699](+) trnV-UAC [52056:52094](-) [51455:51489](-) trnM-CAU [52271:52343](+) trnW-CCA [66092:66165](-) trnP-UGG [66302:66375](-) trnI-CAU [85993:86066](-) trnL-CAA [93048:93128](-) trnV-GAC [99400:99471](+) trnI-GAU [101484:101520](+) [102468:102502](+) trnA-UGC [102567:102604](+) [103418:103452](+) trnR-ACG [107246:107319](+) trnN-GUU [107905:107976](-) trnL-UAG [114479:114558](+) trnN-GUU_copy2 [129860:129931](+) trnR-ACG_copy2 [130517:130590](-) trnA-UGC_copy2 [135232:135269](-) [134384:134418](-) trnI-GAU_copy2 [136316:136352](-) [135334:135368](-) trnV-GAC_copy2 [138365:138436](-) trnL-CAA_copy2 [144708:144788](+) trnI-CAU_copy2 [151770:151843](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [99699:101188](+) rrn23 [103605:106409](+) rrn4.5 [106508:106610](+) rrn5 [106868:106988](+) rrn5_copy2 [130848:130968](-) rrn4.5_copy2 [131226:131328](-) rrn23_copy2 [131427:134231](-) rrn16_copy2 [136647:138136](-) This genome has 24 genes with intron(s). Details are as follows: 20 gene(s) have 1 intron(s) Genes Exons rps16 [5920:5959](-) [4940:5136](-) atpF [12584:12728](-) [11453:11853](-) rpoC1 [23080:23514](-) [20731:22335](-) petB [74692:74697](+) [75449:76090](+) petD [76275:76282](+) [77032:77506](+) rpl16 [82345:82353](-) [80992:81390](-) rpl2 [85137:85527](-) [84052:84485](-) ndhB [95147:95923](-) [93709:94464](-) ndhA [121581:122132](-) [119981:120520](-) ndhB_copy2 [141913:142689](+) [143372:144127](+) rpl2_copy2 [152309:152699](+) [153351:153784](+) rpl16_copy2 [155483:155491](+) [156446:156844](+) trnK-UUU [4168:4204](-) [1617:1651](-) trnG-UCC [8806:8828](+) [9527:9574](+) trnL-UAA [47686:47720](+) [48223:48271](+) trnV-UAC [52056:52094](-) [51455:51489](-) trnI-GAU [101484:101520](+) [102468:102502](+) trnA-UGC [102567:102604](+) [103418:103452](+) trnA-UGC_copy2 [135232:135269](-) [134384:134418](-) trnI-GAU_copy2 [136316:136352](-) [135334:135368](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [69430:69543](-) [97308:97539](-) [96746:96771](-) ycf3 [44492:44617](-) [43574:43799](-) [42632:42786](-) rps12_copy2 [69430:69543](-) [140297:140528](+) [141065:141090](+) clpP [71678:71748](-) [70542:70833](-) [69670:69900](-)