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, psbT, psbZ Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, rpl22, rpl23, rpl23_copy2, rpl2_copy2, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps12_copy2, rps14, rps15, rps18, rps19, rps19_copy2, 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 Envelop membrane protein cemA Maturase matK Protease None Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor None Conserved open reading frames ycf1, ycf15, ycf15_copy2, ycf1_copy2, ycf2, ycf2_copy2 Other genes clpP1, 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 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 infA Conserved open reading frames ycf4 Other genes None 2. Multicopy genes with different lengths: Genes Length Location ycf1 1173 [116320:117493](+) ycf1_copy2 5667 [131451:137118](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (1/2) [12362:12916](-) ndhA (2/2) [128914:129466](-) [127258:127796](-) ndhB (2/2) [103096:103869](-) [101656:102411](-) ndhB_copy2 (2/2) [149570:150343](+) [151028:151783](+) petB (2/2) [81128:81133](+) [81937:82578](+) petD (2/2) [82791:82798](+) [83593:84088](+) rpl16 (2/2) [89049:89057](-) [87397:87795](-) rpl2 (2/2) [92058:92448](-) [90957:91390](-) rpl2_copy2 (2/2) [160991:161381](+) [162049:162482](+) rpoC1 (2/2) [23198:23632](-) [20802:22421](-) rps12 (3/3) [75727:75840](-) [105286:105517](-) [104719:104744](-) rps12_copy2 (3/3) [75727:75840](-) [147922:148153](+) [148695:148720](+) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: pafI 3 [47429:47552](-) [46475:46704](-) [45656:45808](-)] clpP1 3 [78057:78127](-) [76938:77229](-) [76067:76294](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon rps19 GTG ycf15 ATC ndhB ATC ndhD ACG ndhB_copy2 ATC ycf15_copy2 ATC rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 131 genes (111 unique genes). Including: 86 protein-coding genes (77 are unique) 37 tRNA genes (30 are unique) 8 rRNA genes (4 are unique) Details are as follows: 86 protein-coding genes (77 are unique) Genes Length Location accD 1500 [60928:62427](+) atpA 1524 [10780:12303](-) atpB 1488 [56540:58027](-) atpE 402 [56133:56534](-) atpF 555 [12362:12916](-) atpH 246 [13331:13576](-) atpI 744 [14477:15220](-) ccsA 960 [121727:122686](+) cemA 687 [65907:66593](+) clpP1 591 [78057:78127](-) [76938:77229](-) [76067:76294](-) matK 1518 [2451:3968](-) ndhA 1092 [128914:129466](-) [127258:127796](-) ndhB 1530 [103096:103869](-) [101656:102411](-) ndhB_copy2 1530 [149570:150343](+) [151028:151783](+) ndhC 363 [53202:53564](-) ndhD 1503 [122856:124358](-) ndhE 306 [124981:125286](-) ndhF 2235 [117522:119756](-) ndhG 531 [125522:126052](-) ndhH 1182 [129468:130649](-) ndhI 513 [126558:127070](-) ndhJ 477 [51870:52346](-) ndhK 678 [52467:53144](-) pafI 507 [47429:47552](-) [46475:46704](-) [45656:45808](-) pafII 555 [64392:64946](+) pbf1 132 [80543:80674](-) petA 963 [66902:67864](+) petB 648 [81128:81133](+) [81937:82578](+) petD 504 [82791:82798](+) [83593:84088](+) petG 114 [71541:71654](+) petL 96 [71239:71334](+) petN 90 [28440:28529](+) psaA 2253 [42341:44593](-) psaB 2205 [40111:42315](-) psaC 246 [124477:124722](-) psaI 114 [63974:64087](+) psaJ 129 [72507:72635](+) psbA 1062 [779:1840](-) psbB 1527 [78657:80183](+) psbC 1422 [35387:36808](+) psbD 1062 [34378:35439](+) psbE 252 [69230:69481](-) psbF 120 [69102:69221](-) psbH 222 [80783:81004](+) psbI 111 [7717:7827](+) psbJ 123 [68676:68798](-) psbK 186 [7128:7313](+) psbL 117 [68959:69075](-) psbM 105 [29728:29832](-) psbT 108 [80367:80474](+) psbZ 189 [37525:37713](+) rbcL 1428 [58829:60256](+) rpl14 369 [86903:87271](-) rpl16 408 [89049:89057](-) [87397:87795](-) rpl2 825 [92058:92448](-) [90957:91390](-) rpl20 354 [74550:74903](-) rpl22 399 [90162:90560](-) rpl23 282 [92467:92748](-) rpl23_copy2 282 [160691:160972](+) rpl2_copy2 825 [160991:161381](+) [162049:162482](+) rpl33 201 [73076:73276](+) rpl36 114 [85902:86015](-) rpoA 1029 [84273:85301](-) rpoB 3213 [23659:26871](-) rpoC1 2055 [23198:23632](-) [20802:22421](-) rpoC2 4185 [16470:20654](-) rps11 417 [85369:85785](-) rps12 372 [75727:75840](-) [105286:105517](-) [104719:104744](-) rps12_copy2 372 [75727:75840](-) [147922:148153](+) [148695:148720](+) rps14 303 [39685:39987](-) rps15 273 [130764:131036](-) rps18 285 [73945:74229](+) rps19 279 [90626:90904](-) rps19_copy2 279 [162535:162813](+) rps2 711 [15475:16185](-) rps3 657 [89389:90045](-) rps4 606 [48370:48975](-) rps7 468 [104193:104660](-) rps7_copy2 468 [148779:149246](+) rps8 405 [86208:86612](-) ycf1 1173 [116321:117493](+) ycf15 138 [100120:100257](+) ycf15_copy2 138 [153182:153319](-) ycf1_copy2 5667 [131452:137118](-) ycf2 6894 [93076:99969](+) ycf2_copy2 6894 [153470:160363](-) 37 tRNA genes (30 are unique) Genes Location trnH [107:181](-) trnK-UUU [4718:4754](-) [2137:2171](-) trnQ-UUG [6627:6698](-) trnS-GCU [8154:8240](-) trnG-GCC [8778:8798](+) [9526:9576](+) trnR [10484:10555](+) trnC [28022:28094](+) trnD-GUC [31259:31332](-) trnY-GUA [31753:31836](-) trnE [31906:31978](-) trnT-GGU [32401:32472](+) trnS-UGA [37078:37167](-) trnG-UCC [39177:39247](+) trnM [39441:39514](-) trnS-GGA [48002:48088](+) trnT-UGU [49469:49541](-) trnL-UAA [49968:50004](+) [50611:50660](+) trnF-GAA [51099:51171](+) trnV-UAC [55575:55613](-) [54952:54986](-) trnM-CAU [55797:55867](+) trnW [71784:71856](-) trnP-UGG [72046:72120](-) trnI-CAU [92914:92987](-) trnL-CAA [100983:101063](-) trnV-GAC [107432:107503](+) trnI-GAU [109515:109556](+) [110502:110536](+) trnA-UGC [110601:110638](+) [111442:111476](+) trnR-ACG [115227:115300](+) trnN-GUU [115908:115979](-) trnL-UAG [121524:121603](+) trnN-GUU_copy2 [137460:137531](+) trnR-ACG_copy2 [138139:138212](-) trnA-UGC_copy2 [142801:142838](-) [141963:141997](-) trnI-GAU_copy2 [143883:143924](-) [142903:142937](-) trnV-GAC_copy2 [145936:146007](-) trnL-CAA_copy2 [152376:152456](+) trnI-CAU_copy2 [160452:160525](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [107735:109224](+) rrn23 [111629:114438](+) rrn4.5 [114537:114639](+) rrn5 [114864:114984](+) rrn5_copy2 [138455:138575](-) rrn4.5_copy2 [138800:138902](-) rrn23_copy2 [139001:141810](-) rrn16_copy2 [144215:145705](-) This genome has 21 genes with intron(s). Details are as follows: 17 gene(s) have 1 intron(s) Genes Exons rpoC1 [23198:23632](-) [20802:22421](-) petB [81128:81133](+) [81937:82578](+) petD [82791:82798](+) [83593:84088](+) rpl16 [89049:89057](-) [87397:87795](-) rpl2 [92058:92448](-) [90957:91390](-) ndhB [103096:103869](-) [101656:102411](-) ndhA [128914:129466](-) [127258:127796](-) ndhB_copy2 [149570:150343](+) [151028:151783](+) rpl2_copy2 [160991:161381](+) [162049:162482](+) trnK-UUU [4718:4754](-) [2137:2171](-) trnG-GCC [8778:8798](+) [9526:9576](+) trnL-UAA [49968:50004](+) [50611:50660](+) trnV-UAC [55575:55613](-) [54952:54986](-) trnI-GAU [109515:109556](+) [110502:110536](+) trnA-UGC [110601:110638](+) [111442:111476](+) trnA-UGC_copy2 [142801:142838](-) [141963:141997](-) trnI-GAU_copy2 [143883:143924](-) [142903:142937](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [75727:75840](-) [105286:105517](-) [104719:104744](-) pafI [47429:47552](-) [46475:46704](-) [45656:45808](-) rps12_copy2 [75727:75840](-) [147922:148153](+) [148695:148720](+) clpP1 [78057:78127](-) [76938:77229](-) [76067:76294](-)