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, rpl22_copy2, rpl23, rpl23_copy2, rpl2_copy2, rpl32, 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 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 infA Conserved open reading frames ycf1, 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 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 clpP Subunit of Acetyl-CoA-carboxylase None Translational initiation factor None Conserved open reading frames ycf15, ycf4 Other genes None 2. Multicopy genes with different lengths: Genes Length Location ycf1 5562 [111538:117100](+) ycf1_copy2 1491 [131018:132509](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [13213:13356](-) [12008:12418](-) ndhA (2/2) [119053:119603](+) [120732:121272](+) ndhB (2/2) [98376:99152](-) [96943:97689](-) ndhB_copy2 (2/2) [144896:145672](+) [146359:147105](+) petB (2/2) [76787:76792](+) [77613:78254](+) petD (2/2) [78460:78467](+) [79212:79686](+) rpl16 (2/2) [84614:84622](-) [83130:83528](-) rpl2 (2/2) [87411:87801](-) [86314:86747](-) rpl2_copy2 (2/2) [156247:156637](+) [157301:157734](+) rpoC1 (2/2) [23719:24153](-) [21394:23013](-) rps12 (3/3) [71476:71589](-) [100565:100796](-) [99998:100023](-) rps12_copy2 (3/3) [71476:71589](-) [143252:143483](+) [144025:144050](+) rps16 (2/2) [6159:6198](-) [5094:5314](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: pafI 3 [46208:46333](-) [45246:45471](-) [44328:44482](-)] clpP1 3 [73798:73868](-) [72653:72944](-) [71747:71992](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon rps19 GTG rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 134 genes (113 unique genes). Including: 89 protein-coding genes (79 are unique) 37 tRNA genes (30 are unique) 8 rRNA genes (4 are unique) Details are as follows: 89 protein-coding genes (79 are unique) Genes Length Location accD 1518 [58972:60489](+) atpA 1524 [10425:11948](-) atpB 1497 [54567:56063](-) atpE 402 [54169:54570](-) atpF 555 [13213:13356](-) [12008:12418](-) atpH 246 [13736:13981](-) atpI 744 [15147:15890](-) ccsA 972 [125588:126559](-) cemA 699 [62733:63431](+) clpP1 609 [73798:73868](-) [72653:72944](-) [71747:71992](-) infA 114 [81738:81851](-) matK 1524 [1992:3515](-) ndhA 1092 [119053:119603](+) [120732:121272](+) ndhB 1524 [98376:99152](-) [96943:97689](-) ndhB_copy2 1524 [144896:145672](+) [146359:147105](+) ndhC 363 [51780:52142](-) ndhD 1521 [123792:125312](+) ndhE 303 [122883:123185](+) ndhF 2196 [128834:131029](+) ndhG 537 [122096:122632](+) ndhH 1182 [117870:119051](+) ndhI 504 [121359:121862](+) ndhJ 477 [50428:50904](-) ndhK 690 [51032:51721](-) pafI 507 [46208:46333](-) [45246:45471](-) [44328:44482](-) pafII 564 [61630:62193](+) pbf1 132 [76197:76328](-) petA 963 [63662:64624](+) petB 648 [76787:76792](+) [77613:78254](+) petD 483 [78460:78467](+) [79212:79686](+) petG 114 [67848:67961](+) petL 96 [67579:67674](+) petN 90 [29345:29434](+) psaA 2253 [41268:43520](-) psaB 2205 [39038:41242](-) psaC 246 [123393:123638](+) psaI 114 [61058:61171](+) psaJ 135 [68790:68924](+) psbA 1062 [348:1409](-) psbB 1527 [74320:75846](+) psbC 1428 [35319:36746](+) psbD 1062 [34310:35371](+) psbE 252 [65961:66212](-) psbF 120 [65832:65951](-) psbH 222 [76433:76654](+) psbI 111 [8225:8335](+) psbJ 123 [65420:65542](-) psbK 186 [7647:7832](+) psbL 117 [65693:65809](-) psbM 105 [30720:30824](-) psbT 108 [76029:76136](+) psbZ 189 [37435:37623](+) rbcL 1428 [56912:58339](+) rpl14 369 [82641:83009](-) rpl16 408 [84614:84622](-) [83130:83528](-) rpl2 825 [87411:87801](-) [86314:86747](-) rpl20 387 [70353:70739](-) rpl22 486 [85435:85920](-) rpl22_copy2 486 [158128:158613](+) rpl23 282 [87820:88101](-) rpl23_copy2 282 [155947:156228](+) rpl2_copy2 825 [156247:156637](+) [157301:157734](+) rpl32 171 [127738:127908](-) rpl33 201 [69415:69615](+) rpl36 114 [81463:81576](-) rpoA 990 [79869:80858](-) rpoB 3213 [24180:27392](-) rpoC1 2055 [23719:24153](-) [21394:23013](-) rpoC2 4107 [17103:21209](-) rps11 417 [80924:81340](-) rps12 372 [71476:71589](-) [100565:100796](-) [99998:100023](-) rps12_copy2 372 [71476:71589](-) [143252:143483](+) [144025:144050](+) rps14 303 [38603:38905](-) rps15 273 [117476:117748](+) rps16 261 [6159:6198](-) [5094:5314](-) rps18 336 [69812:70147](+) rps19 279 [85966:86244](-) rps19_copy2 279 [157804:158082](+) rps2 711 [16100:16810](-) rps3 663 [84788:85450](-) rps3_copy2 663 [158598:159260](+) rps4 606 [46995:47600](-) rps7 468 [99477:99944](-) rps7_copy2 468 [144104:144571](+) rps8 405 [82069:82473](-) ycf1 5562 [111539:117100](+) ycf1_copy2 1491 [131019:132509](-) ycf2 6804 [88443:95246](+) ycf2_copy2 6804 [148802:155605](-) 37 tRNA genes (30 are unique) Genes Location trnH-GUG [1:58](-) [159354:159370](-) trnK-UUU [4215:4251](-) [1659:1693](-) trnQ-UUG [7196:7267](-) trnS-GCU [8479:8566](-) trnG-GCC [9134:9156](+) [9882:9930](+) trnR-UCU [10111:10182](+) trnC-GCA [28669:28739](+) trnD-GUC [31274:31347](-) trnY-GUA [31798:31882](-) trnE-UUC [31941:32013](-) trnT-GGU [32825:32896](+) trnS-UGA [36989:37081](-) trnG-UCC [38146:38216](+) trnfM-CAU [38351:38424](-) trnS-GGA [46661:46747](+) trnT-UGU [47960:48032](-) trnL-UAA [49120:49157](+) [49702:49748](+) trnF-GAA [50080:50152](+) trnV-UAC [53615:53653](-) [52982:53018](-) trnM-CAU [53841:53912](+) trnW-CCA [68100:68172](-) trnP-UGG [68373:68446](-) trnI-CAU [88281:88354](-) trnL-CAA [96266:96346](-) trnV-GAC [102623:102694](+) trnI-GAU [104713:104749](+) [105706:105740](+) trnA-UGC [105805:105842](+) [106645:106679](+) trnR-ACG [110446:110519](+) trnN-GUU [111132:111203](-) trnL-UAG [126671:126750](-) trnN-GUU_copy2 [132845:132916](+) trnR-ACG_copy2 [133529:133602](-) trnA-UGC_copy2 [138206:138243](-) [137369:137403](-) trnI-GAU_copy2 [139299:139335](-) [138308:138342](-) trnV-GAC_copy2 [141354:141425](-) trnL-CAA_copy2 [147702:147782](+) trnI-CAU_copy2 [155694:155767](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [102929:104419](+) rrn23 [106849:109658](+) rrn4.5 [109757:109859](+) rrn5 [110071:110191](+) rrn5_copy2 [133857:133977](-) rrn4.5_copy2 [134189:134291](-) rrn23_copy2 [134390:137199](-) rrn16_copy2 [139629:141119](-) This genome has 24 genes with intron(s). Details are as follows: 20 gene(s) have 1 intron(s) Genes Exons rps16 [6159:6198](-) [5094:5314](-) atpF [13213:13356](-) [12008:12418](-) rpoC1 [23719:24153](-) [21394:23013](-) petB [76787:76792](+) [77613:78254](+) petD [78460:78467](+) [79212:79686](+) rpl16 [84614:84622](-) [83130:83528](-) rpl2 [87411:87801](-) [86314:86747](-) ndhB [98376:99152](-) [96943:97689](-) ndhA [119053:119603](+) [120732:121272](+) ndhB_copy2 [144896:145672](+) [146359:147105](+) rpl2_copy2 [156247:156637](+) [157301:157734](+) trnH-GUG [1:58](-) [159354:159370](-) trnK-UUU [4215:4251](-) [1659:1693](-) trnG-GCC [9134:9156](+) [9882:9930](+) trnL-UAA [49120:49157](+) [49702:49748](+) trnV-UAC [53615:53653](-) [52982:53018](-) trnI-GAU [104713:104749](+) [105706:105740](+) trnA-UGC [105805:105842](+) [106645:106679](+) trnA-UGC_copy2 [138206:138243](-) [137369:137403](-) trnI-GAU_copy2 [139299:139335](-) [138308:138342](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [71476:71589](-) [100565:100796](-) [99998:100023](-) pafI [46208:46333](-) [45246:45471](-) [44328:44482](-) rps12_copy2 [71476:71589](-) [143252:143483](+) [144025:144050](+) clpP1 [73798:73868](-) [72653:72944](-) [71747:71992](-)