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, ndhA_copy2, ndhB, ndhB_copy2, ndhC, ndhD, ndhD_copy2, ndhE, ndhE_copy2, ndhF, ndhG, ndhG_copy2, ndhH, ndhH_copy2, ndhI, ndhI_copy2, ndhJ, ndhK Subunits of cytochrome b/f complex petA, petB, petD, petG, petL, petN Subunits of photosystem I psaA, psaB, psaC, psaC_copy2, 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, rpl32, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps14, rps15, rps15_copy2, rps16, rps16_copy2, 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, ccsA_copy2 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 rps16 267 join{[5918:5958](-), [4827:5054](-)} rps16_copy2 51 [106704:106755](+) ccsA 432 [121340:121772](-) ccsA_copy2 954 [125665:126619](+) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [12311:12455](-) [11164:11579](-) ndhA (2/2) [114863:115415](+) [116488:117017](+) ndhA_copy2 (2/2) [132545:133097](-) [130943:131472](-) ndhB (2/2) [103757:104479](+) [105155:105910](+) ndhB_copy2 (2/2) [143481:144203](-) [142050:142805](-) petB (2/2) [73785:73790](+) [74519:75160](+) petD (2/2) [75399:75406](+) [76117:76591](+) rpl16 (2/2) [81310:81318](-) [80064:80462](-) rpl2 (2/2) [84157:84547](-) [83048:83481](-) rpl2_copy2 (2/2) [163412:163802](+) [164478:164911](+) rpoC1 (2/2) [22835:23285](-) [20476:22088](-) rps12 (3/3) [67895:68008](-) [145614:145842](-) [145053:145078](-) rps16 (2/2) [5919:5958](-) [4828:5054](-) rps16_copy2 (1/2) [106705:106755](+) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: pafI 3 [43415:43538](-) [42481:42708](-) [41599:41753](-)] clpP1 3 [70164:70232](-) [69143:69433](-) [68268:68504](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon rpoC2 GTG rps19 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 141 genes (112 unique genes). Including: 95 protein-coding genes (79 are unique) 38 tRNA genes (29 are unique) 8 rRNA genes (4 are unique) Details are as follows: 95 protein-coding genes (79 are unique) Genes Length Location accD 1392 [56394:57785](+) atpA 1524 [9586:11109](-) atpB 1497 [51436:52932](-) atpE 402 [51038:51439](-) atpF 561 [12311:12455](-) [11164:11579](-) atpH 246 [12811:13056](-) atpI 744 [14054:14797](-) ccsA 432 [121341:121772](-) ccsA_copy2 954 [125666:126619](+) cemA 690 [59558:60247](+) clpP1 597 [70164:70232](-) [69143:69433](-) [68268:68504](-) infA 234 [78607:78840](-) matK 1509 [1910:3418](-) ndhA 1083 [114863:115415](+) [116488:117017](+) ndhA_copy2 1083 [132545:133097](-) [130943:131472](-) ndhB 1479 [103757:104479](+) [105155:105910](+) ndhB_copy2 1479 [143481:144203](-) [142050:142805](-) ndhC 363 [48744:49106](-) ndhD 1539 [119588:121126](+) ndhD_copy2 1539 [126834:128372](-) ndhE 306 [118679:118984](+) ndhE_copy2 306 [128976:129281](-) ndhF 2247 [121613:123859](-) ndhG 537 [117919:118455](+) ndhG_copy2 537 [129505:130041](-) ndhH 1182 [113680:114861](+) ndhH_copy2 1182 [133099:134280](-) ndhI 507 [117100:117606](+) ndhI_copy2 507 [130354:130860](-) ndhJ 477 [47419:47895](-) ndhK 678 [48012:48689](-) pafI 507 [43415:43538](-) [42481:42708](-) [41599:41753](-) pafII 555 [58637:59191](+) pbf1 132 [73203:73334](-) petA 963 [60417:61379](+) petB 648 [73785:73790](+) [74519:75160](+) petD 483 [75399:75406](+) [76117:76591](+) petG 114 [64274:64387](+) petL 96 [63978:64073](+) petN 90 [28226:28315](+) psaA 2253 [38752:41004](-) psaB 2205 [36522:38726](-) psaC 246 [119246:119491](+) psaC_copy2 246 [128469:128714](-) psaI 111 [58074:58184](+) psaJ 135 [65147:65281](+) psbA 1059 [336:1394](-) psbB 1527 [70626:72152](+) psbC 1422 [33051:34472](+) psbD 1062 [32042:33103](+) psbE 252 [62857:63108](-) psbF 120 [62723:62842](-) psbH 225 [73441:73665](+) psbI 111 [7516:7626](+) psbJ 123 [62322:62444](-) psbK 183 [6987:7169](+) psbL 117 [62583:62699](-) psbM 105 [28831:28935](-) psbT 102 [72347:72448](+) psbZ 189 [35121:35309](+) rbcL 1434 [53561:54994](+) rpl14 369 [79568:79936](-) rpl16 408 [81310:81318](-) [80064:80462](-) rpl2 825 [84157:84547](-) [83048:83481](-) rpl20 381 [66743:67123](-) rpl22 519 [82103:82621](-) rpl23 282 [84566:84847](-) rpl23_copy2 282 [163112:163393](+) rpl2_copy2 825 [163412:163802](+) [164478:164911](+) rpl32 165 [124641:124805](+) rpl33 201 [65778:65978](+) rpl36 114 [78397:78510](-) rpoA 1008 [76804:77811](-) rpoB 3213 [23291:26503](-) rpoC1 2064 [22835:23285](-) [20476:22088](-) rpoC2 4134 [15961:20094](-) rps11 417 [77885:78301](-) rps12 369 [67895:68008](-) [145614:145842](-) [145053:145078](-) rps14 303 [36101:36403](-) rps15 273 [113303:113575](+) rps15_copy2 273 [134385:134657](-) rps16 267 [5919:5958](-) [4828:5054](-) rps16_copy2 51 [106705:106755](+) rps18 381 [66131:66511](+) rps19 279 [82690:82968](-) rps2 717 [15024:15740](-) rps3 678 [81441:82118](-) rps4 612 [44180:44791](-) rps7 468 [102961:103428](+) rps7_copy2 468 [144532:144999](-) rps8 405 [78959:79363](-) ycf1 5862 [107012:112873](+) ycf1_copy2 5862 [135087:140948](-) ycf2 5592 [86079:91670](+) ycf2_copy2 5592 [156289:161880](-) 38 tRNA genes (29 are unique) Genes Location trnH-GUG [1:75](-) trnK-UUU [4106:4142](-) [1629:1663](-) trnQ-UUG [6538:6609](-) trnS-GCU [7752:7839](-) trnG-UCC [8460:8482](+) [9181:9228](+) trnR-UCU [9410:9481](+) trnC-GCA [27683:27753](+) trnD-GUC [29506:29579](-) trnY-GUA [29681:29764](-) trnE-UUC [29824:29896](-) trnT-GGU [30650:30721](+) trnS-UGA [34677:34769](-) trnG-GCC [35578:35648](+) trnfM-CAU [35863:35936](-) trnS-GGA [43794:43880](+) trnT-UGU [45082:45154](-) trnL-UAA [45863:45897](+) [46409:46458](+) trnF-GAA [46803:46875](+) trnV-UAC [50553:50588](-) [49939:49975](-) trnM-CAU [50779:50851](+) trnW-CCA [64510:64583](-) trnP-UGG [64768:64841](-) trnL-CAA [72847:72927](-) trnM-CAU_copy2 [85761:85834](-) trnL-CAA_copy2 [92079:92159](-) trnR-ACG [92949:93022](-) trnA-UGC [97676:97713](-) [96825:96859](-) trnI-GAU [98623:98659](-) [97778:97812](-) trnV-GAC [100677:100748](-) trnN-GUU [106191:106262](-) trnL-UAG [125478:125557](+) trnN-GUU_copy2 [141698:141769](+) trnV-GAC_copy2 [147212:147283](+) trnI-GAU_copy2 [149301:149337](+) [150148:150182](+) trnA-UGC_copy2 [150247:150284](+) [151101:151135](+) trnR-ACG_copy2 [154938:155011](+) trnL-CAA_copy3 [155801:155881](+) trnM-CAU_copy3 [162125:162198](+) 8 rRNA genes (4 are unique) Genes Location rrn5 [93264:93384](-) rrn4.5 [93640:93742](-) rrn23 [93841:96656](-) rrn16 [98959:100449](-) rrn16_copy2 [147511:149001](+) rrn23_copy2 [151304:154119](+) rrn4.5_copy2 [154218:154320](+) rrn5_copy2 [154576:154696](+) This genome has 23 genes with intron(s). Details are as follows: 20 gene(s) have 1 intron(s) Genes Exons rps16 [5919:5958](-) [4828:5054](-) atpF [12311:12455](-) [11164:11579](-) rpoC1 [22835:23285](-) [20476:22088](-) petB [73785:73790](+) [74519:75160](+) petD [75399:75406](+) [76117:76591](+) rpl16 [81310:81318](-) [80064:80462](-) rpl2 [84157:84547](-) [83048:83481](-) ndhB [103757:104479](+) [105155:105910](+) ndhA [114863:115415](+) [116488:117017](+) ndhA_copy2 [132545:133097](-) [130943:131472](-) ndhB_copy2 [143481:144203](-) [142050:142805](-) rpl2_copy2 [163412:163802](+) [164478:164911](+) trnK-UUU [4106:4142](-) [1629:1663](-) trnG-UCC [8460:8482](+) [9181:9228](+) trnL-UAA [45863:45897](+) [46409:46458](+) trnV-UAC [50553:50588](-) [49939:49975](-) trnA-UGC [97676:97713](-) [96825:96859](-) trnI-GAU [98623:98659](-) [97778:97812](-) trnI-GAU_copy2 [149301:149337](+) [150148:150182](+) trnA-UGC_copy2 [150247:150284](+) [151101:151135](+) 3 gene(s) have 2 intron(s) Genes Exons rps12 [67895:68008](-) [145614:145842](-) [145053:145078](-) pafI [43415:43538](-) [42481:42708](-) [41599:41753](-) clpP1 [70164:70232](-) [69143:69433](-) [68268:68504](-)