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, psbN, psbT, psbZ, ycf3 Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, rpl22, rpl22_copy2, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl32_copy2, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps12_copy2, rps14, rps15, rps15_copy2, rps16, rps18, rps19, rps19_copy2, rps2, rps3, rps3_copy2, 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 None 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 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 cemA 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 None None None 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [20257:20401](+) [21153:21562](+) clpP (3/3) [86240:86310](-) [85219:85510](-) [84290:84535](-) ndhA (2/2) [132119:132671](+) [133784:134322](+) ndhA_copy2 (2/2) [157240:157792](-) [155589:156127](-) ndhB (2/2) [111392:112168](-) [109928:110683](-) ndhB_copy2 (2/2) [177743:178519](+) [179228:179983](+) petB (2/2) [89244:89249](+) [89994:90635](+) petD (2/2) [90826:90833](+) [91558:92047](+) rpl16 (2/2) [97528:97536](-) [96119:96517](-) rpl2 (2/2) [100347:100737](-) [99251:99681](-) rpl2_copy2 (2/2) [189174:189564](+) [190230:190660](+) rpoC1 (2/2) [8802:9254](+) [9995:11611](+) rps12 (3/3) [84033:84146](-) [113580:113811](-) [113018:113043](-) rps12_copy2 (3/3) [84033:84146](-) [176100:176331](+) [176868:176893](+) rps16 (2/2) [28352:28391](+) [29233:29429](+) ycf3 (3/3) [53782:53905](-) [51039:51268](-) [50148:50300](-) ### 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 psbI AAA psbL ACG rps19 GTG rpl2 ACG ndhD ACG ndhD_copy2 ACG rpl2_copy2 ACG rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 145 genes (112 unique genes). Including: 99 protein-coding genes (78 are unique) 38 tRNA genes (30 are unique) 8 rRNA genes (4 are unique) Details are as follows: 99 protein-coding genes (78 are unique) Genes Length Location accD 1485 [70904:72388](+) atpA 1524 [21631:23154](+) atpB 1497 [66439:67935](-) atpE 414 [66029:66442](-) atpF 555 [20257:20401](+) [21153:21562](+) atpH 246 [19025:19270](+) atpI 744 [17075:17818](+) ccsA 960 [139025:139984](-) ccsA_copy2 960 [149927:150886](+) clpP 609 [86240:86310](-) [85219:85510](-) [84290:84535](-) infA 234 [94680:94913](-) matK 1527 [31107:32633](+) ndhA 1092 [132119:132671](+) [133784:134322](+) ndhA_copy2 1092 [157240:157792](-) [155589:156127](-) ndhB 1533 [111392:112168](-) [109928:110683](-) ndhB_copy2 1533 [177743:178519](+) [179228:179983](+) ndhC 363 [60415:60777](-) ndhD 1512 [137301:138812](+) ndhD_copy2 1512 [151099:152610](-) ndhE 306 [136277:136582](+) ndhE_copy2 306 [153329:153634](-) ndhF 2205 [142753:144957](+) ndhF_copy2 2205 [144954:147158](-) ndhG 531 [135249:135779](+) ndhG_copy2 531 [154132:154662](-) ndhH 1182 [130936:132117](+) ndhH_copy2 1182 [157794:158975](-) ndhI 516 [134401:134916](+) ndhI_copy2 516 [154995:155510](-) ndhJ 477 [59091:59567](-) ndhK 678 [59678:60355](-) petA 963 [75964:76926](+) petB 648 [89244:89249](+) [89994:90635](+) petD 498 [90826:90833](+) [91558:92047](+) petG 114 [80342:80455](+) petL 96 [80064:80159](+) petN 90 [3590:3679](-) psaA 2253 [47216:49468](-) psaB 2205 [44986:47190](-) psaC 246 [136928:137173](+) psaC_copy2 246 [152738:152983](-) psaI 111 [73012:73122](+) psaJ 135 [81359:81493](+) psbA 1062 [33399:34460](+) psbB 1527 [86769:88295](+) psbC 1422 [41601:43022](+) psbD 1062 [40592:41653](+) psbE 252 [78523:78774](-) psbF 120 [78394:78513](-) psbH 222 [88903:89124](+) psbI 135 [25625:>25759](-) psbJ 123 [77996:78118](-) psbK 186 [26151:26336](-) psbL 117 [78255:78371](-) psbM 105 [2523:2627](+) psbN 132 [88664:88795](-) psbT 108 [88486:88593](+) psbZ 189 [43768:43956](+) rbcL 1428 [68746:70173](+) rpl14 369 [95621:95989](-) rpl16 408 [97528:97536](-) [96119:96517](-) rpl2 822 [100347:100737](-) [99251:99681](-) rpl20 360 [82872:83231](-) rpl22 543 [98293:98835](-) rpl22_copy2 543 [191076:191618](+) rpl23 303 [100756:101058](-) rpl23_copy2 303 [188853:189155](+) rpl2_copy2 822 [189174:189564](+) [190230:190660](+) rpl32 165 [141349:141513](-) rpl32_copy2 165 [148398:148562](+) rpl33 201 [81906:82106](+) rpl36 114 [94451:94564](-) rpoA 1008 [92841:93848](-) rpoB 3213 [5584:8796](+) rpoC1 2070 [8802:9254](+) [9995:11611](+) rpoC2 4134 [11773:15906](+) rps11 417 [93922:94338](-) rps12 372 [84033:84146](-) [113580:113811](-) [113018:113043](-) rps12_copy2 372 [84033:84146](-) [176100:176331](+) [176868:176893](+) rps14 303 [44552:44854](-) rps15 273 [130565:130837](+) rps15_copy2 273 [159074:159346](-) rps16 237 [28352:28391](+) [29233:29429](+) rps18 318 [82282:82599](+) rps19 279 [98884:99162](-) rps19_copy2 279 [190749:191027](+) rps2 711 [16114:16824](+) rps3 657 [97692:98348](-) rps3_copy2 657 [191563:192219](+) rps4 606 [55126:55731](-) rps7 468 [112492:112959](-) rps7_copy2 468 [176952:177419](+) rps8 399 [95035:95433](-) ycf1 5598 [124567:130164](+) ycf1_copy2 5598 [159747:165344](-) ycf2 6921 [101381:108301](+) ycf2_copy2 6921 [181610:188530](-) ycf3 507 [53782:53905](-) [51039:51268](-) [50148:50300](-) ycf4 555 [73498:74052](+) 38 tRNA genes (30 are unique) Genes Location trnE-UUC [724:796](+) trnY-GUA [861:944](+) trnD-GUC [1402:1475](+) trnC-GCA [4130:4200](-) trnR-UCU [23275:23346](-) trnG-UCC [24287:24309](-) [23505:23552](-) trnS-GCU [25369:25456](+) trnQ-UUG [26666:26737](+) trnK-UUU [30325:30361](+) [32904:32938](+) trnH-GUG [36243:36317](+) trnT-GGU [38764:38835](+) trnS-UGA [43305:43397](-) trnG-GCC [44124:44194](+) trnfM-CAU [44317:44390](-) trnS-GGA [54743:54830](+) trnT-UGU [56174:56246](-) trnL-UAA [57337:57371](+) [57895:57944](+) trnF-GAA [58303:58375](+) trnV-UAC [65502:65540](-) [64824:64858](-) trnM-CAU [65723:65795](+) trnW-CCA [80588:80661](-) trnP-UGG [80828:80901](-) trnI-CAU [101224:101297](-) trnL-CAA [109334:109414](-) trnV-GAC [115684:115755](+) trnI-GAU [117764:117800](+) [118743:118777](+) trnA-UGC [118842:118879](+) [119684:119718](+) trnR-ACG [123484:123557](+) trnN-GUU [124178:124249](-) trnL-UAG [140111:140190](-) trnL-UAG_copy2 [149721:149800](+) trnN-GUU_copy2 [165662:165733](+) trnR-ACG_copy2 [166354:166427](-) trnA-UGC_copy2 [171032:171069](-) [170193:170227](-) trnI-GAU_copy2 [172111:172147](-) [171134:171168](-) trnV-GAC_copy2 [174156:174227](-) trnL-CAA_copy2 [180497:180577](+) trnI-CAU_copy2 [188614:188687](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [115983:117473](+) rrn23 [119871:122686](+) rrn4.5 [122785:122887](+) rrn5 [123111:123231](+) rrn5_copy2 [166680:166800](-) rrn4.5_copy2 [167024:167126](-) rrn23_copy2 [167225:170040](-) rrn16_copy2 [172438:173928](-) This genome has 24 genes with intron(s). Details are as follows: 20 gene(s) have 1 intron(s) Genes Exons rpoC1 [8802:9254](+) [9995:11611](+) atpF [20257:20401](+) [21153:21562](+) rps16 [28352:28391](+) [29233:29429](+) petB [89244:89249](+) [89994:90635](+) petD [90826:90833](+) [91558:92047](+) rpl16 [97528:97536](-) [96119:96517](-) rpl2 [100347:100737](-) [99251:99681](-) ndhB [111392:112168](-) [109928:110683](-) ndhA [132119:132671](+) [133784:134322](+) ndhA_copy2 [157240:157792](-) [155589:156127](-) ndhB_copy2 [177743:178519](+) [179228:179983](+) rpl2_copy2 [189174:189564](+) [190230:190660](+) trnG-UCC [24287:24309](-) [23505:23552](-) trnK-UUU [30325:30361](+) [32904:32938](+) trnL-UAA [57337:57371](+) [57895:57944](+) trnV-UAC [65502:65540](-) [64824:64858](-) trnI-GAU [117764:117800](+) [118743:118777](+) trnA-UGC [118842:118879](+) [119684:119718](+) trnA-UGC_copy2 [171032:171069](-) [170193:170227](-) trnI-GAU_copy2 [172111:172147](-) [171134:171168](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [84033:84146](-) [113580:113811](-) [113018:113043](-) ycf3 [53782:53905](-) [51039:51268](-) [50148:50300](-) rps12_copy2 [84033:84146](-) [176100:176331](+) [176868:176893](+) clpP [86240:86310](-) [85219:85510](-) [84290:84535](-)