1. Annotated protein coding genes: Group of genes Name of genes Subunits of ATP synthase ORF192, ORF227, ORF298, atpA, atpB, atpE, atpF, atpH, atpI Subunits of NADH-dehydrogenase ORF192, ORF227, ORF298, 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 ORF192, ORF227, ORF298, petA, petB, petD, petG, petL, petN Subunits of photosystem I ORF192, ORF227, ORF298, psaA, psaB, psaC, psaI, psaJ Subunits of photosystem II ORF192, ORF227, ORF298, psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ Large subunit of ribosome ORF192, ORF227, ORF298, rpl14, rpl16, rpl2, rpl20, rpl22, rpl2_copy2, rpl32, rpl33, rpl36 Small subunit of ribosome ORF192, ORF227, ORF298, rps11, rps12, rps12_copy2, rps14, rps15, rps15_copy2, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps7_copy2, rps8 DNA dependent RNA polymerase ORF192, ORF227, ORF298, rpoA, rpoB, rpoC1, rpoC2 Subunit of rubisco ORF192, ORF227, ORF298, rbcL c-type cytochrom synthesis gene ORF192, ORF227, ORF298, ccsA Envelop membrane protein ORF192, ORF227, ORF298, cemA Maturase ORF192, ORF227, ORF298, matK Protease ORF192, ORF227, ORF298, clpP Subunit of Acetyl-CoA-carboxylase ORF192, ORF227, ORF298 Translational initiation factor ORF192, ORF227, ORF298 Conserved open reading frames ORF192, ORF227, ORF298, ycf1, ycf1_copy2, ycf2, ycf2_copy2 Other genes ORF192, ORF227, ORF298, pafI, pafII 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 ycf3 Large subunit of ribosome rpl23 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 None Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor infA Conserved open reading frames ycf15, ycf4 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) [18443:18587](-) [17292:17701](-) clpP (3/3) [70072:70148](-) [69001:69292](-) [68088:68360](-) ndhA (2/2) [115417:115969](+) [116992:117530](+) ndhA_copy2 (2/2) [130888:131440](-) [129327:129865](-) ndhB (2/2) [93845:94621](-) [92417:93172](-) ndhB_copy2 (2/2) [152236:153012](+) [153685:154440](+) petB (2/2) [73043:73048](+) [73807:74448](+) petD (2/2) [74634:74641](+) [75341:75815](+) rpl16 (2/2) [80811:80819](-) [79328:79726](-) rpl2 (2/2) [83612:84002](-) [82514:82947](-) rpl2_copy2 (2/2) [162855:163245](+) [163910:164343](+) rpoC1 (2/2) [28668:29099](-) [26301:27917](-) rps12 (3/3) [67858:67971](-) [96016:96247](-) [95459:95484](-) rps12_copy2 (3/3) [67858:67971](-) [150610:150841](+) [151373:151398](+) rps16 (1/2) [11324:11590](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: pafI 3 [49983:50106](-) [49056:49285](-) [48163:48315](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon ndhD ACG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 134 genes (112 unique genes). Including: 90 protein-coding genes (79 are unique) 36 tRNA genes (29 are unique) 8 rRNA genes (4 are unique) Details are as follows: 90 protein-coding genes (79 are unique) Genes Length Location ORF192 579 [11749:12327](-) ORF227 684 [56803:57486](+) ORF298 897 [32742:33638](-) atpA 1506 [15720:17225](-) atpB 1497 [4759:6255](+) atpE 402 [6252:6653](+) atpF 555 [18443:18587](-) [17292:17701](-) atpH 246 [19012:19257](-) atpI 744 [20071:20814](-) ccsA 942 [121942:122883](-) cemA 693 [59302:59994](+) clpP 642 [70072:70148](-) [69001:69292](-) [68088:68360](-) matK 1530 [8449:9978](-) ndhA 1092 [115417:115969](+) [116992:117530](+) ndhA_copy2 1092 [130888:131440](-) [129327:129865](-) ndhB 1533 [93845:94621](-) [92417:93172](-) ndhB_copy2 1533 [152236:153012](+) [153685:154440](+) ndhC 363 [55986:56348](-) ndhD 1497 [120215:121711](+) ndhE 306 [119287:119592](+) ndhF 2232 [125047:127278](+) ndhG 531 [118527:119057](+) ndhG_copy2 531 [127800:128330](-) ndhH 1182 [114234:115415](+) ndhH_copy2 1182 [131442:132623](-) ndhI 504 [117613:118116](+) ndhI_copy2 504 [128741:129244](-) ndhJ 477 [54662:55138](-) ndhK 684 [55253:55936](-) pafI 507 [49983:50106](-) [49056:49285](-) [48163:48315](-) pafII 555 [58042:58596](+) petA 963 [60223:61185](+) petB 648 [73043:73048](+) [73807:74448](+) petD 483 [74634:74641](+) [75341:75815](+) petG 114 [64181:64294](+) petL 96 [63907:64002](+) petN 90 [34748:34837](+) psaA 2253 [45248:47500](-) psaB 2205 [43018:45222](-) psaC 246 [119857:120102](+) psaI 111 [57588:57698](+) psaJ 135 [65131:65265](+) psbA 1062 [425:1486](-) psbB 1527 [70566:72092](+) psbC 1422 [39629:41050](+) psbD 1062 [38620:39681](+) psbE 252 [62754:63005](-) psbF 120 [62625:62744](-) psbH 222 [72704:72925](+) psbI 111 [13673:13783](+) psbJ 123 [62220:62342](-) psbK 186 [13051:13236](+) psbL 117 [62486:62602](-) psbM 105 [35318:35422](-) psbN 132 [72470:72601](-) psbT 102 [72298:72399](+) psbZ 189 [41617:41805](+) rbcL 1428 [2520:3947](-) rpl14 369 [78816:79184](-) rpl16 408 [80811:80819](-) [79328:79726](-) rpl2 825 [83612:84002](-) [82514:82947](-) rpl20 372 [66729:67100](-) rpl22 510 [81618:82127](-) rpl2_copy2 825 [162855:163245](+) [163910:164343](+) rpl32 165 [123758:123922](-) rpl33 201 [65712:65912](+) rpl36 114 [77597:77710](-) rpoA 1008 [76029:77036](-) rpoB 3213 [29143:32355](-) rpoC1 2049 [28668:29099](-) [26301:27917](-) rpoC2 4161 [21975:26135](-) rps11 402 [77117:77518](-) rps12 372 [67858:67971](-) [96016:96247](-) [95459:95484](-) rps12_copy2 372 [67858:67971](-) [150610:150841](+) [151373:151398](+) rps14 303 [42592:42894](-) rps15 330 [113810:114139](+) rps15_copy2 330 [132718:133047](-) rps16 267 [11324:11590](-) rps18 363 [66082:66444](+) rps19 282 [82180:82461](-) rps2 711 [21030:21740](-) rps3 657 [80977:81633](-) rps4 606 [51312:51917](-) rps7 468 [94938:95405](-) rps7_copy2 468 [151452:151919](+) rps8 411 [78193:78603](-) ycf1 6591 [106860:113450](+) ycf1_copy2 6591 [133407:139997](-) ycf2 6426 [84799:91224](+) ycf2_copy2 6426 [155633:162058](-) 36 tRNA genes (29 are unique) Genes Location trnH (GUG) [5:79](-) trnM (CAU) [6882:6954](-) trnV (UAC) [7153:7190](+) [7764:7798](+) trnK (UUU) [10712:10748](-) [8156:8190](-) trnQ (UUG) [12589:12660](-) trnS (GCU) [13854:13941](-) trnG (UCC) [14669:14691](+) [15380:15427](+) trnR (UCU) [15556:15627](+) trnC (GCA) [34415:34485](+) trnD (GUC) [36209:36282](-) trnY (GUA) [36391:36474](-) trnE (UUC) [36534:36606](-) trnS (UGA) [41271:41359](-) trnG (GCC) [42110:42180](+) trnfM (CAU) [42350:42423](-) trnS (GGA) [50913:50999](+) trnT (UGU) [52351:52423](-) trnL (UAA) [53093:53127](+) [53630:53679](+) trnF (GAA) [54045:54117](+) trnW (CCA) [64402:64475](-) trnP (UGG) [64647:64720](-) trnI (CAU) [84604:84677](-) trnL (CAA) [91751:91831](-) trnV (GAC) [98052:98123](+) trnI (GAU) [100131:100168](+) [101113:101147](+) trnA (UGC) [101212:101249](+) [102064:102098](+) trnR (ACG) [105833:105906](+) trnN (GUU) [106183:106254](-) trnL (UAG) [122987:123066](-) trnN (GUU)_copy2 [140603:140674](+) trnR (ACG)_copy2 [140951:141024](-) trnA (UGC)_copy2 [145608:145645](-) [144759:144793](-) trnI (GAU)_copy2 [146689:146726](-) [145710:145744](-) trnV (GAC)_copy2 [148734:148805](-) trnL (CAA)_copy2 [155026:155106](+) trnI (CAU)_copy2 [162180:162253](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [98351:99843](+) rrn23 [102247:105061](+) rrn4.5 [105160:105262](+) rrn5 [105463:105583](+) rrn5_copy2 [141274:141394](-) rrn4.5_copy2 [141595:141697](-) rrn23_copy2 [141796:144610](-) rrn16_copy2 [147014:148506](-) This genome has 23 genes with intron(s). Details are as follows: 19 gene(s) have 1 intron(s) Genes Exons atpF [18443:18587](-) [17292:17701](-) rpoC1 [28668:29099](-) [26301:27917](-) petB [73043:73048](+) [73807:74448](+) petD [74634:74641](+) [75341:75815](+) rpl16 [80811:80819](-) [79328:79726](-) rpl2 [83612:84002](-) [82514:82947](-) ndhB [93845:94621](-) [92417:93172](-) ndhA [115417:115969](+) [116992:117530](+) ndhA_copy2 [130888:131440](-) [129327:129865](-) ndhB_copy2 [152236:153012](+) [153685:154440](+) rpl2_copy2 [162855:163245](+) [163910:164343](+) trnV (UAC) [7153:7190](+) [7764:7798](+) trnK (UUU) [10712:10748](-) [8156:8190](-) trnG (UCC) [14669:14691](+) [15380:15427](+) trnL (UAA) [53093:53127](+) [53630:53679](+) trnI (GAU) [100131:100168](+) [101113:101147](+) trnA (UGC) [101212:101249](+) [102064:102098](+) trnA (UGC)_copy2 [145608:145645](-) [144759:144793](-) trnI (GAU)_copy2 [146689:146726](-) [145710:145744](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [67858:67971](-) [96016:96247](-) [95459:95484](-) pafI [49983:50106](-) [49056:49285](-) [48163:48315](-) rps12_copy2 [67858:67971](-) [150610:150841](+) [151373:151398](+) clpP [70072:70148](-) [69001:69292](-) [68088:68360](-)