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, 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, psbA_copy2, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ, ycf3 Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, rpl22, rpl23, rpl32, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps12_copy2, rps14, rps15, rps16, rps18, rps19, 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 clpP Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor infA Conserved open reading frames ycf1, ycf12, ycf2, ycf2_copy2, ycf4, ycf66 Other genes chlB, chlL, chlN, psaM, rpl21 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 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 None Subunit of Acetyl-CoA-carboxylase None Translational initiation factor None Conserved open reading frames ycf15 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) [13451:13577](-) [12361:12770](-) clpP (3/3) [70248:70318](-) [69235:69526](-) [68369:68623](-) ndhA (2/2) [121833:122390](-) [120354:120914](-) ndhB (2/2) [596:1318](-) [156261:157022](-) petB (2/2) [73414:73419](+) [74249:74890](+) petD (2/2) [75108:75115](+) [75829:76303](+) rpl16 (2/2) [81640:81648](-) [80430:80834](-) rpl2 (2/2) [84401:84797](-) [83269:83705](-) rpoC1 (1/2) [21036:23057](-) rps12 (3/3) [67884:68000](-) [143674:143905](-) [143049:143074](-) rps12_copy2 (3/3) [67884:68000](-) [98804:99035](+) [99635:99660](+) rps16 (2/2) [5373:5414](-) [4368:4574](-) ycf3 (3/3) [44775:44900](-) [43844:44071](-) [43018:43182](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: ycf66 2 [28868:28972](-) [27855:28226](-)] 4. Genes with internal stop codon: ['chlB', 'atpA', 'atpI', 'rpoC2', 'rpoC1', 'rpoB', 'ycf3', 'petA', 'rps18', 'rpoA', 'rps3', 'rpl2', 'rpl23', 'ycf2', 'ndhF', 'ndhA', 'ycf2_copy2'] 5. Genes with nonstandard start codon: Genes Start codon rps12 ACG ndhB ACG atpH ACG petN ACG psbM ACG rps4 ACG atpB ACG accD ACG ycf4 ACG psbJ ACG rps12_copy2 ACG psbN ACG petB ACG rps8 ACG rpl22 ACG ycf2 ACG ndhG ACG ndhA ACG ndhH ACG chlL ACG ycf2_copy2 ACG 6. Genes with nonstandard stop codon: Genes Stop codon ndhB CAG petN CAG petA CGA ndhH CGA 7. Conclusion This genome has 130 genes (117 unique genes). Including: 90 protein-coding genes (86 are unique) 32 tRNA genes (27 are unique) 8 rRNA genes (4 are unique) Details are as follows: 90 protein-coding genes (86 are unique) Genes Length Location accD 942 [56275:57216](+) atpA 1524 [10796:12319](-) atpB 1482 [52216:53697](-) atpE 399 [51813:52211](-) atpF 537 [13451:13577](-) [12361:12770](-) atpH 246 [13932:14177](-) atpI 747 [14846:15592](-) ccsA 969 [114850:115818](+) cemA 1491 [59004:60494](+) chlB 1542 [5573:7114](-) chlL 882 [131217:132098](-) chlN 1395 [129761:131155](-) clpP 618 [70248:70318](-) [69235:69526](-) [68369:68623](-) infA 240 [78374:78613](-) matK 1518 [1677:3194](-) ndhA 1119 [121833:122390](-) [120354:120914](-) ndhB 1485 [596:1318](-) [156261:157022](-) ndhC 378 [49729:50106](-) ndhD 1491 [116142:117632](-) ndhE 303 [118391:118693](-) ndhF 2184 [110507:112690](-) ndhG 600 [118762:119361](-) ndhH 1185 [122392:123576](-) ndhI 558 [119694:120251](-) ndhJ 513 [48471:48983](-) ndhK 750 [49004:49753](-) petA 963 [60766:61728](+) petB 648 [73414:73419](+) [74249:74890](+) petD 483 [75108:75115](+) [75829:76303](+) petG 117 [64644:64760](+) petL 96 [64407:64502](+) petN 90 [27718:27807](+) psaA 2253 [40426:42678](-) psaB 2205 [38196:40400](-) psaC 246 [117841:118086](-) psaI 111 [57688:57798](+) psaJ 129 [65621:65749](+) psaM 99 [8833:8931](-) psbA 1062 [101060:102121](+) psbA_copy2 1062 [140588:141649](-) psbB 1527 [70804:72330](+) psbC 1464 [32938:34401](-) psbD 1062 [34307:35368](-) psbE 252 [62843:63094](-) psbF 120 [62714:62833](-) psbH 225 [73074:73298](+) psbI 111 [8272:8382](+) psbJ 123 [62324:62446](-) psbK 177 [7760:7936](+) psbL 117 [62571:62687](-) psbM 105 [29379:29483](-) psbN 132 [72856:72987](-) psbT 105 [72623:72727](+) psbZ 189 [31429:31617](-) rbcL 1428 [54310:55737](+) rpl14 369 [79620:79988](-) rpl16 414 [81640:81648](-) [80430:80834](-) rpl2 834 [84401:84797](-) [83269:83705](-) rpl20 357 [66673:67029](-) rpl21 363 [112937:113299](+) rpl22 414 [82526:82939](-) rpl23 273 [84848:85120](-) rpl32 183 [113509:113691](+) rpl33 201 [65943:66143](+) rpl36 114 [78099:78212](-) rpoA 1011 [76589:77599](-) rpoB 3195 [23100:26294](-) rpoC1 2022 [21036:23057](-) rpoC2 4287 [16633:20919](-) rps11 393 [77637:78029](-) rps12 375 [67884:68000](-) [143674:143905](-) [143049:143074](-) rps12_copy2 375 [67884:68000](-) [98804:99035](+) [99635:99660](+) rps14 303 [37667:37969](-) rps15 270 [123692:123961](-) rps16 249 [5373:5414](-) [4368:4574](-) rps18 228 [66229:66456](+) rps19 279 [82957:83235](-) rps2 732 [15759:16490](-) rps3 657 [81824:82480](-) rps4 624 [45963:46586](-) rps7 474 [99715:100188](+) rps7_copy2 474 [142521:142994](-) rps8 399 [78782:79180](-) ycf1 5016 [124265:129280](-) ycf12 102 [9206:9307](+) ycf2 6123 [102831:108953](+) ycf2_copy2 6123 [133756:139878](-) ycf3 519 [44775:44900](-) [43844:44071](-) [43018:43182](-) ycf4 564 [58162:58725](+) ycf66 477 [28868:28972](-) [27855:28226](-) 32 tRNA genes (27 are unique) Genes Location trnQ-UUG [7349:7420](-) trnS-GCU [8454:8541](-) trnG-UCC [9476:9498](+) [10373:10420](+) trnR-UCU [10613:10684](+) trnC-GCA [27137:27208](+) trnD-GUC [29891:29964](+) trnY-GUA [30062:30143](-) trnE-UUC [30293:30365](-) trnG-GCC [31028:31098](-) trnS-UGA [32025:32113](+) trnT-GGU [36871:36942](-) trnfM-CAU [37431:37504](-) trnS-GGA [45485:45571](+) trnL-CAA [47214:47247](+) [47740:47791](+) trnF-GAA [48203:48275](+) trnV-UAC [51297:51333](-) [50651:50685](-) trnM-CAU [51554:51626](+) trnW-CCA [64967:65040](-) trnP-UGG [65240:65313](-) trnI-CAU [85252:85325](-) trnR-ACG [89241:89314](-) trnA-UGC [93876:93913](-) [93058:93092](-) trnI-GAU [94956:94998](-) [93981:94015](-) trnH-GUG [102511:102585](+) trnN-GUU [110092:110163](-) trnP-GGG [114336:114409](-) trnL-UAG [114578:114657](+) trnN-GUU_copy2 [132546:132617](+) trnH-GUG_copy2 [140124:140198](-) trnI-GAU_copy2 [147711:147753](+) [148694:148728](+) trnA-UGC_copy2 [148796:148833](+) [149617:149651](+) trnR-ACG_copy2 [153395:153468](+) 8 rRNA genes (4 are unique) Genes Location rrn5 [89562:89684](-) rrn4.5 [89969:90071](-) rrn23 [90083:92897](-) rrn16 [95270:96769](-) rrn16_copy2 [145940:147439](+) rrn23_copy2 [149812:152626](+) rrn4.5_copy2 [152638:152740](+) rrn5_copy2 [153025:153147](+) This genome has 20 genes with intron(s). Details are as follows: 16 gene(s) have 1 intron(s) Genes Exons ndhB [596:1318](-) [156261:157022](-) rps16 [5373:5414](-) [4368:4574](-) atpF [13451:13577](-) [12361:12770](-) ycf66 [28868:28972](-) [27855:28226](-) petB [73414:73419](+) [74249:74890](+) petD [75108:75115](+) [75829:76303](+) rpl16 [81640:81648](-) [80430:80834](-) rpl2 [84401:84797](-) [83269:83705](-) ndhA [121833:122390](-) [120354:120914](-) trnG-UCC [9476:9498](+) [10373:10420](+) trnL-CAA [47214:47247](+) [47740:47791](+) trnV-UAC [51297:51333](-) [50651:50685](-) trnA-UGC [93876:93913](-) [93058:93092](-) trnI-GAU [94956:94998](-) [93981:94015](-) trnI-GAU_copy2 [147711:147753](+) [148694:148728](+) trnA-UGC_copy2 [148796:148833](+) [149617:149651](+) 4 gene(s) have 2 intron(s) Genes Exons rps12 [67884:68000](-) [143674:143905](-) [143049:143074](-) ycf3 [44775:44900](-) [43844:44071](-) [43018:43182](-) rps12_copy2 [67884:68000](-) [98804:99035](+) [99635:99660](+) clpP [70248:70318](-) [69235:69526](-) [68369:68623](-)