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, ndhE, ndhF, 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, psaA_copy2, psaB, psaB_copy2, psaC, psaI, psaJ Subunits of photosystem II psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbT, psbZ, ycf3 Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, rpl22, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps12_copy2, rps14, rps14_copy2, rps15, rps15_copy2, rps16, rps16_copy2, rps19, rps19_copy2, rps2, rps3, rps4, rps7, rps7_copy2, rps8 DNA dependent RNA polymerase rpoB, rpoC1, rpoC2 Subunit of rubisco rbcL c-type cytochrom synthesis gene ccsA Envelop membrane protein cemA Maturase matK Protease None Subunit of Acetyl-CoA-carboxylase None Translational initiation factor None Conserved open reading frames ycf4 Other genes 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 Large subunit of ribosome None Small subunit of ribosome rps18 DNA dependent RNA polymerase rpoA 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 infA Conserved open reading frames ycf1, ycf15, ycf2 Other genes None 2. Multicopy genes with different lengths: Genes Length Location rps16 237 join{[8178:8218](+), [8933:9130](+)} rps16_copy2 159 [138409:138568](-) rps19 210 [80666:80876](-) rps19_copy2 309 [170286:170595](+) ndhB 1545 join{[95315:96104](+), [96795:97551](+)} ndhB_copy2 1554 join{[154637:155435](-), [153199:153955](-)} 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [66396:66540](+) [67399:67793](+) ndhA (2/2) [117245:117794](+) [118832:119370](+) ndhA_copy2 (2/2) [132025:132574](-) [130449:130987](-) ndhB (2/2) [95316:96104](+) [96796:97551](+) ndhB_copy2 (2/2) [154638:155435](-) [153200:153955](-) petB (2/2) [15024:15029](-) [13580:14221](-) petD (2/2) [13378:13385](-) [12135:12609](-) rpl16 (2/2) [1477:1485](+) [2598:2996](+) rpl2 (2/2) [82306:82696](-) [81230:81660](-) rpl2_copy2 (2/2) [168557:168947](+) [169593:170023](+) rpoC1 (2/2) [55177:55608](+) [56316:57953](+) rps12 (3/3) [71158:71271](-) [156859:157090](-) [156274:156308](-) rps12_copy2 (3/3) [71158:71271](-) [93661:93892](+) [94443:94477](+) rps16 (2/2) [8179:8218](+) [8934:9130](+) rps16_copy2 (1/2) [138410:138568](-) ycf3 (3/3) [5674:5797](+) [6521:6750](+) [7570:7728](+) ### 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 psbF ATT psbC GTG rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 130 genes (104 unique genes). Including: 87 protein-coding genes (72 are unique) 35 tRNA genes (28 are unique) 8 rRNA genes (4 are unique) Details are as follows: 87 protein-coding genes (72 are unique) Genes Length Location atpA 1524 [67894:69417](+) atpB 1491 [36533:38023](-) atpE 405 [36132:36536](-) atpF 540 [66396:66540](+) [67399:67793](+) atpH 246 [65750:65995](+) atpI 744 [64514:65257](+) ccsA 933 [124779:125711](+) cemA 690 [26604:27293](+) matK 1542 [77377:78918](+) ndhA 1089 [117245:117794](+) [118832:119370](+) ndhA_copy2 1089 [132025:132574](-) [130449:130987](-) ndhB 1545 [95316:96104](+) [96796:97551](+) ndhB_copy2 1554 [154638:155435](-) [153200:153955](-) ndhC 363 [33891:34253](-) ndhD 1509 [126004:127512](-) ndhE 303 [128308:128610](-) ndhF 2202 [121244:123445](+) ndhG 531 [120374:120904](+) ndhG_copy2 531 [128915:129445](-) ndhH 1182 [116062:117243](+) ndhH_copy2 1182 [132576:133757](-) ndhI 555 [119459:120013](+) ndhI_copy2 555 [129806:130360](-) ndhJ 498 [32585:33082](-) ndhK 756 [33166:33921](-) pbf1 132 [15481:15612](+) petA 969 [27531:28499](+) petB 648 [15024:15029](-) [13580:14221](-) petD 483 [13378:13385](-) [12135:12609](-) petG 114 [22054:22167](-) petL 96 [22327:22422](-) petN 90 [50095:50184](-) psaA 2256 [84060:86315](+) psaA_copy2 2256 [164938:167193](-) psaB 2205 [86341:88545](+) psaB_copy2 2205 [162708:164912](-) psaC 246 [127640:127885](-) psaI 111 [25032:25142](+) psaJ 129 [21169:21297](-) psbA 1062 [79470:80531](+) psbB 1527 [15949:17475](-) psbC 1386 [43393:44778](-) psbD 1062 [44762:45823](-) psbE 249 [29933:30181](-) psbF 120 [29800:29919](-) psbH 222 [15131:15352](-) psbI 117 [73679:73795](-) psbJ 123 [29417:29539](-) psbK 186 [74174:74359](-) psbL 117 [29661:29777](-) psbM 105 [49710:49814](+) psbT 108 [15684:15791](-) psbZ 189 [42565:42753](-) rbcL 1428 [38715:40142](+) rpl14 369 [3123:3491](+) rpl16 408 [1477:1485](+) [2598:2996](+) rpl2 822 [82306:82696](-) [81230:81660](-) rpl20 366 [19297:19662](+) rpl22 456 [53:508](+) rpl23 108 [82715:82822](-) rpl23_copy2 108 [168431:168538](+) rpl2_copy2 822 [168557:168947](+) [169593:170023](+) rpl32 93 [123682:123774](+) rpl33 201 [20472:20672](-) rpl36 114 [4723:4836](+) rpoB 3234 [51918:55151](+) rpoC1 2070 [55177:55608](+) [56316:57953](+) rpoC2 5169 [58126:63294](+) rps11 438 [10068:10505](+) rps12 381 [71158:71271](-) [156859:157090](-) [156274:156308](-) rps12_copy2 381 [71158:71271](-) [93661:93892](+) [94443:94477](+) rps14 306 [88694:88999](+) rps14_copy2 306 [162254:162559](-) rps15 273 [115691:115963](+) rps15_copy2 273 [133856:134128](-) rps16 237 [8179:8218](+) [8934:9130](+) rps16_copy2 159 [138410:138568](-) rps19 210 [80667:80876](-) rps19_copy2 309 [170287:170595](+) rps2 762 [63530:64291](+) rps3 810 [515:1324](+) rps4 642 [24113:24754](+) rps7 474 [94532:95005](+) rps7_copy2 474 [155746:156219](-) rps8 426 [3633:4058](+) ycf3 513 [5674:5797](+) [6521:6750](+) [7570:7728](+) ycf4 558 [25386:25943](+) 35 tRNA genes (28 are unique) Genes Location trnS-GGA [5001:5086](-) trnP-UGG [21660:21733](+) trnW-CCA [21851:21924](+) trnT-UGU [23629:23701](+) trnL-UAA [30942:30976](+) [31547:31596](+) trnF-GAA [31915:31987](+) trnV-UAC [35684:35721](-) [35054:35090](-) trnM-CAU [35897:35970](+) trnV-GAC [40460:40531](+) trnG-GCC [42160:42221](-) trnS-UGA [43153:43241](+) trnT-GGU [46840:46911](-) trnE-UUC [47826:47898](+) trnY-GUA [48154:48237](+) trnD-GUC [48572:48650](+) trnC-GCA [50862:50932](-) trnR-UCU [69534:69605](-) trnG-UCC [70487:70510](-) [69740:69787](-) trnS-GCU [73469:73556](+) trnQ-UUG [75328:75402](+) trnH-GUG [81105:81179](+) trnI-CAU [83027:83100](-) trnI-GAU [103508:103544](+) [104251:104285](+) trnA-UGC [104345:104382](+) [105196:105230](+) trnR-ACG [108992:109066](+) trnN-GUU [109276:109347](+) trnL-CAA [111095:111175](-) trnL-UAG [124614:124694](+) trnL-CAA_copy2 [139818:139898](+) trnN-GUU_copy2 [141646:141717](-) trnR-ACG_copy2 [141927:142001](-) trnA-UGC_copy2 [146611:146648](-) [145763:145797](-) trnI-GAU_copy2 [147449:147485](-) [146708:146742](-) trnI-CAU_copy2 [168153:168226](+) trnH-GUG_copy2 [170074:170148](-) 8 rRNA genes (4 are unique) Genes Location rrn16 [101564:103053](+) rrn23 [105382:108184](+) rrn4.5 [108282:108384](+) rrn5 [108611:108731](+) rrn5_copy2 [142262:142382](-) rrn4.5_copy2 [142609:142711](-) rrn23_copy2 [142809:145611](-) rrn16_copy2 [147940:149429](-) This genome has 22 genes with intron(s). Details are as follows: 19 gene(s) have 1 intron(s) Genes Exons rpl16 [1477:1485](+) [2598:2996](+) rps16 [8179:8218](+) [8934:9130](+) petD [13378:13385](-) [12135:12609](-) petB [15024:15029](-) [13580:14221](-) rpoC1 [55177:55608](+) [56316:57953](+) atpF [66396:66540](+) [67399:67793](+) rpl2 [82306:82696](-) [81230:81660](-) ndhB [95316:96104](+) [96796:97551](+) ndhA [117245:117794](+) [118832:119370](+) ndhA_copy2 [132025:132574](-) [130449:130987](-) ndhB_copy2 [154638:155435](-) [153200:153955](-) rpl2_copy2 [168557:168947](+) [169593:170023](+) trnL-UAA [30942:30976](+) [31547:31596](+) trnV-UAC [35684:35721](-) [35054:35090](-) trnG-UCC [70487:70510](-) [69740:69787](-) trnI-GAU [103508:103544](+) [104251:104285](+) trnA-UGC [104345:104382](+) [105196:105230](+) trnA-UGC_copy2 [146611:146648](-) [145763:145797](-) trnI-GAU_copy2 [147449:147485](-) [146708:146742](-) 3 gene(s) have 2 intron(s) Genes Exons rps12 [71158:71271](-) [156859:157090](-) [156274:156308](-) ycf3 [5674:5797](+) [6521:6750](+) [7570:7728](+) rps12_copy2 [71158:71271](-) [93661:93892](+) [94443:94477](+)