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, rpl33, rpl36 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, 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 None 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 rpl32 Small subunit of ribosome None DNA dependent RNA polymerase rpoC1 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 infA Conserved open reading frames ycf15 Other genes None 2. Multicopy genes with different lengths: Genes Length Location ycf1 5703 [111381:117084](+) ycf1_copy2 1719 [130875:132594](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [43222:43345](+) [44151:44557](+) clpP (3/3) [74075:74145](-) [72995:73283](-) [71994:72239](-) ndhA (2/2) [119095:119647](+) [120520:121058](+) ndhB (2/2) [98155:98931](-) [96693:97448](-) ndhB_copy2 (2/2) [145045:145821](+) [146528:147283](+) petB (2/2) [76955:77038](+) [77915:78556](+) petD (2/2) [78651:78766](+) [79511:80006](+) rpl16 (2/2) [84742:84750](-) [83353:83751](-) rpl16_copy2 (2/2) [159226:159234](+) [160225:160623](+) rpl2 (2/2) [87607:87910](-) [86510:86943](-) rpl2_copy2 (2/2) [156066:156369](+) [157033:157466](+) rps12 (3/3) [71730:71843](-) [100343:100574](-) [99776:99801](-) rps12_copy2 (3/3) [71730:71843](-) [143402:143633](+) [144175:144200](+) rps16 (2/2) [1419:1458](+) [2342:2535](+) ycf3 (3/3) [10133:10256](+) [10982:11221](+) [11974:12128](+) ### 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 rps4 CTG psaB ATT accD TTG petB CTG petD TTG rps19 TTG rpl2 TTG ndhD TTG rpl2_copy2 TTG rps19_copy2 TTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 133 genes (109 unique genes). Including: 89 protein-coding genes (76 are unique) 36 tRNA genes (29 are unique) 8 rRNA genes (4 are unique) Details are as follows: 89 protein-coding genes (76 are unique) Genes Length Location accD 1545 [59426:60970](+) atpA 1524 [44624:46147](+) atpB 1503 [54991:56493](-) atpE 402 [54593:54994](-) atpF 531 [43222:43345](+) [44151:44557](+) atpH 246 [42477:42722](+) atpI 744 [40585:41328](+) ccsA 966 [125249:126214](-) cemA 756 [63400:64155](+) clpP 606 [74075:74145](-) [72995:73283](-) [71994:72239](-) matK 1533 [4193:5725](+) ndhA 1092 [119095:119647](+) [120520:121058](+) ndhB 1533 [98155:98931](-) [96693:97448](-) ndhB_copy2 1533 [145045:145821](+) [146528:147283](+) ndhC 363 [51859:52221](-) ndhD 1467 [123481:124947](+) ndhE 306 [122519:122824](+) ndhF 2223 [128571:130793](+) ndhG 534 [121742:122275](+) ndhH 1182 [117912:119093](+) ndhI 534 [121132:121665](+) ndhJ 477 [50502:50978](-) ndhK 684 [51117:51800](-) petA 969 [64360:65328](+) petB 726 [76955:77038](+) [77915:78556](+) petD 612 [78651:78766](+) [79511:80006](+) petG 114 [68102:68215](+) petL 96 [67801:67896](+) petN 90 [27342:27431](-) psaA 1938 [12856:14793](+) psaB 2040 [15317:17356](+) psaC 246 [123069:123314](+) psaI 111 [61652:61762](+) psaJ 135 [69051:69185](+) psbA 1062 [6350:7411](+) psbB 1527 [74553:76079](+) psbC 1422 [19550:20971](-) psbD 1062 [20919:21980](-) psbE 252 [66280:66531](-) psbF 120 [66151:66270](-) psbH 222 [76712:76933](+) psbI 111 [8976:9086](+) psbJ 123 [65770:65892](-) psbK 186 [8340:8525](+) psbL 117 [66012:66128](-) psbM 105 [25992:26096](+) psbN 132 [76481:76612](-) psbT 108 [76271:76378](+) psbZ 189 [18721:18909](-) rbcL 1428 [57357:58784](+) rpl14 369 [82842:83210](-) rpl14_copy2 369 [160766:161134](+) rpl16 408 [84742:84750](-) [83353:83751](-) rpl16_copy2 408 [159226:159234](+) [160225:160623](+) rpl2 738 [87607:87910](-) [86510:86943](-) rpl20 354 [70591:70944](-) rpl22 546 [85565:86110](-) rpl22_copy2 546 [157866:158411](+) rpl23 282 [88016:88297](-) rpl23_copy2 282 [155679:155960](+) rpl2_copy2 738 [156066:156369](+) [157033:157466](+) rpl33 201 [69627:69827](+) rpl36 114 [81801:81914](-) rpoA 1020 [80197:81216](-) rpoB 3249 [29067:32315](+) rpoC2 4152 [35311:39462](+) rps11 417 [81271:81687](-) rps12 372 [71730:71843](-) [100343:100574](-) [99776:99801](-) rps12_copy2 372 [71730:71843](-) [143402:143633](+) [144175:144200](+) rps14 303 [17486:17788](+) rps15 273 [117493:117765](+) rps16 234 [1419:1458](+) [2342:2535](+) rps18 306 [70040:70345](+) rps19 234 [86170:86403](-) rps19_copy2 234 [157573:157806](+) rps2 708 [39657:40364](+) rps3 657 [84924:85580](-) rps3_copy2 657 [158396:159052](+) rps4 591 [43:633](+) rps7 468 [99255:99722](-) rps7_copy2 468 [144254:144721](+) rps8 399 [82226:82624](-) rps8_copy2 399 [161352:161750](+) ycf1 5703 [111382:117084](+) ycf1_copy2 1719 [130876:132594](-) ycf2 6825 [88605:95429](+) ycf2_copy2 6825 [148547:155371](-) ycf3 519 [10133:10256](+) [10982:11221](+) [11974:12128](+) ycf4 555 [62252:62806](+) 36 tRNA genes (29 are unique) Genes Location trnK-UUU [3373:3409](+) [6004:6038](+) trnH-GUG [7714:7788](+) trnQ-UUG [7915:7986](-) trnS-GGA [9223:9309](-) trnfM-CAU [17951:18024](+) trnG-GCC [18247:18317](-) trnS-UGA [19267:19359](+) trnT-GGU [23420:23491](-) trnE-UUC [24180:24252](+) trnY-GUA [24314:24397](+) trnD-GUC [24801:24874](+) trnC-GCA [27912:27992](-) trnR-UCU [46283:46354](-) trnG-UCC [47280:47302](-) [46529:46576](-) trnS-GCU [48352:48439](-) trnL-UAA [49068:49102](+) [49605:49654](+) trnF-GAA [50082:50154](+) trnV-UAC [53971:54008](-) [53347:53381](-) trnM-CAU [54191:54263](+) trnW-CCA [68366:68439](-) trnP-UGG [68602:68675](-) trnI-CAU [88463:88536](-) trnL-CAA [96052:96132](-) trnV-GAC [102482:102553](+) trnI-GAU [104568:104609](+) [105553:105587](+) trnA-UGC [105652:105689](+) [106505:106539](+) trnR-ACG [110287:110360](+) trnN-GUU [110987:111058](-) trnL-UAG [126322:126401](-) trnN-GUU_copy2 [132918:132989](+) trnR-ACG_copy2 [133616:133689](-) trnA-UGC_copy2 [138287:138324](-) [137437:137471](-) trnI-GAU_copy2 [139367:139408](-) [138389:138423](-) trnV-GAC_copy2 [141423:141494](-) trnL-CAA_copy2 [147844:147924](+) trnI-CAU_copy2 [155440:155513](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [102783:104273](+) rrn23 [106692:109501](+) rrn4.5 [109600:109702](+) rrn5 [109927:110047](+) rrn5_copy2 [133929:134049](-) rrn4.5_copy2 [134274:134376](-) rrn23_copy2 [134475:137284](-) rrn16_copy2 [139703:141193](-) This genome has 23 genes with intron(s). Details are as follows: 19 gene(s) have 1 intron(s) Genes Exons rps16 [1419:1458](+) [2342:2535](+) atpF [43222:43345](+) [44151:44557](+) petB [76955:77038](+) [77915:78556](+) petD [78651:78766](+) [79511:80006](+) rpl16 [84742:84750](-) [83353:83751](-) rpl2 [87607:87910](-) [86510:86943](-) ndhB [98155:98931](-) [96693:97448](-) ndhA [119095:119647](+) [120520:121058](+) ndhB_copy2 [145045:145821](+) [146528:147283](+) rpl2_copy2 [156066:156369](+) [157033:157466](+) rpl16_copy2 [159226:159234](+) [160225:160623](+) trnK-UUU [3373:3409](+) [6004:6038](+) trnG-UCC [47280:47302](-) [46529:46576](-) trnL-UAA [49068:49102](+) [49605:49654](+) trnV-UAC [53971:54008](-) [53347:53381](-) trnI-GAU [104568:104609](+) [105553:105587](+) trnA-UGC [105652:105689](+) [106505:106539](+) trnA-UGC_copy2 [138287:138324](-) [137437:137471](-) trnI-GAU_copy2 [139367:139408](-) [138389:138423](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [71730:71843](-) [100343:100574](-) [99776:99801](-) ycf3 [10133:10256](+) [10982:11221](+) [11974:12128](+) rps12_copy2 [71730:71843](-) [143402:143633](+) [144175:144200](+) clpP [74075:74145](-) [72995:73283](-) [71994:72239](-)