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, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, ycf3 Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, rpl22, rpl23, rpl23_copy2, rpl2_copy2, 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 None Maturase matK Protease clpP Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor infA Conserved open reading frames ycf1, ycf10, ycf15, ycf15_copy2, ycf1_copy2, ycf2, ycf2_copy2, ycf4 Other genes lhbA 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 psbB, psbZ 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 cemA Maturase None Protease None Subunit of Acetyl-CoA-carboxylase None Translational initiation factor None Conserved open reading frames None Other genes None 2. Multicopy genes with different lengths: Genes Length Location ycf1 867 [109751:110618](+) ycf1_copy2 5460 [123729:129189](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [13263:13409](-) [12155:12625](-) clpP (3/3) [73089:73157](-) [71986:72281](-) [71119:71344](-) ndhA (2/2) [121240:121794](-) [119647:120186](-) ndhB (2/2) [96888:97667](-) [95456:96211](-) ndhB_copy2 (2/2) [141277:142056](+) [142733:143488](+) petB (1/2) [76969:77457](+) petD (1/2) [78376:78900](+) rpl16 (1/2) [82262:82621](-) rpl2 (2/2) [86280:86675](-) [85178:85612](-) rpl2_copy2 (2/2) [152269:152664](+) [153332:153766](+) rpoC1 (2/2) [23669:24124](-) [21252:22871](-) rps12 (3/3) [70872:70985](-) [99024:99255](-) [98467:98492](-) rps12_copy2 (3/3) [70872:70985](-) [139689:139920](+) [140452:140477](+) rps16 (2/2) [6146:6193](-) [4994:5203](-) ycf3 (3/3) [45194:45325](-) [44267:44497](-) [43409:43561](-) ### 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 petN ATT rbcL TTG accD ATC psbT ATC rpl22 ATA rps19 GTG ycf15 GTG ycf1 GTG ycf15_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 133 genes (112 unique genes). Including: 88 protein-coding genes (80 are unique) 37 tRNA genes (28 are unique) 8 rRNA genes (4 are unique) Details are as follows: 88 protein-coding genes (80 are unique) Genes Length Location accD 1527 [58566:60092](+) atpA 1524 [10570:12093](-) atpB 1497 [54120:55616](-) atpE 402 [53722:54123](-) atpF 618 [13263:13409](-) [12155:12625](-) atpH 246 [13867:14112](-) atpI 744 [15068:15811](-) ccsA 963 [114345:115307](+) clpP 591 [73089:73157](-) [71986:72281](-) [71119:71344](-) infA 234 [80850:81083](-) lhbA 189 [36835:37023](+) matK 1527 [1926:3452](-) ndhA 1095 [121240:121794](-) [119647:120186](-) ndhB 1536 [96888:97667](-) [95456:96211](-) ndhB_copy2 1536 [141277:142056](+) [142733:143488](+) ndhC 363 [51286:51648](-) ndhD 1152 [115571:116722](-) ndhE 306 [117686:117991](-) ndhF 2262 [110482:112743](-) ndhG 531 [118198:118728](-) ndhH 1182 [121796:122977](-) ndhI 507 [119067:119573](-) ndhJ 477 [49978:50454](-) ndhK 852 [50555:51406](-) petA 963 [63657:64619](+) petB 489 [76969:77457](+) petD 525 [78376:78900](+) petG 114 [67598:67711](+) petL 96 [67337:67432](+) petN 96 [29376:29471](+) psaA 2253 [40376:42628](-) psaB 2205 [38146:40350](-) psaC 246 [117192:117437](-) psaI 111 [60807:60917](+) psaJ 135 [68401:68535](+) psbA 1059 [316:1374](-) psbC 1422 [34723:36144](+) psbD 1062 [33714:34775](+) psbE 252 [66179:66430](-) psbF 120 [66045:66164](-) psbH 240 [75706:75945](+) psbI 111 [8328:8438](+) psbJ 123 [65649:65771](-) psbK 186 [7742:7927](+) psbL 117 [65905:66021](-) psbM 105 [30469:30573](-) psbN 132 [75487:75618](-) psbT 111 [75311:75421](+) psi_psbT 1527 [73618:75144](+) rbcL 1452 [56360:57811](+) rpl14 369 [81764:82132](-) rpl16 360 [82262:82621](-) rpl2 831 [86280:86675](-) [85178:85612](-) rpl20 390 [69656:70045](-) rpl22 393 [84402:84794](-) rpl23 282 [86700:86981](-) rpl23_copy2 282 [151963:152244](+) rpl2_copy2 831 [152269:152664](+) [153332:153766](+) rpl32 183 [113427:113609](+) rpl33 201 [68742:68942](+) rpl36 114 [80641:80754](-) rpoA 1062 [78983:80044](-) rpoB 3213 [24130:27342](-) rpoC1 2076 [23669:24124](-) [21252:22871](-) rpoC2 4146 [16952:21097](-) rps11 417 [80123:80539](-) rps12 372 [70872:70985](-) [99024:99255](-) [98467:98492](-) rps12_copy2 372 [70872:70985](-) [139689:139920](+) [140452:140477](+) rps14 303 [37721:38023](-) rps15 273 [123076:123348](-) rps16 258 [6146:6193](-) [4994:5203](-) rps18 306 [69090:69395](+) rps19 279 [84844:85122](-) rps2 711 [16042:16752](-) rps3 663 [83709:84371](-) rps4 606 [46620:47225](-) rps7 468 [97946:98413](-) rps7_copy2 468 [140531:140998](+) rps8 405 [81190:81594](-) ycf1 867 [109752:110618](+) ycf10 693 [62765:63457](+) ycf15 249 [94227:94475](+) ycf15_copy2 249 [144469:144717](-) ycf1_copy2 5460 [123730:129189](-) ycf2 6822 [87315:94136](+) ycf2_copy2 6822 [144808:151629](-) ycf3 516 [45194:45325](-) [44267:44497](-) [43409:43561](-) ycf4 555 [61349:61903](+) 37 tRNA genes (28 are unique) Genes Location trnH-GUG [13:86](-) trnK-UUU [4145:4181](-) [1613:1638](-) trnQ-UUG [7326:7397](-) trnS-GCU [8555:8642](-) trnG-UCC [9437:9459](+) [10165:10212](+) trnR-UCU [10421:10492](+) trnC-GCA [28480:28563](+) trnD-GUC [31099:31172](-) trnY-GUA [31281:31364](-) trnE-UUC [31424:31496](-) trnT-GGU [32304:32375](+) trnS-UGA [36387:36478](-) trnG-GCC [37249:37319](+) trnM-CAU [37495:37568](-) trnS-GCU_copy2 [46229:46315](+) trnT-GGU_copy2 [47618:47689](-) trnL-UAA [48348:48384](+) [48859:48908](+) trnF-GAA [49245:49317](+) trnV-UAC [53245:53282](-) [52622:52658](-) trnM-CAU_copy2 [53451:53522](+) trnW-CCA [67834:67907](-) trnP-UGG [68049:68122](-) trnI-CAU [87153:87226](-) trnL-CAA [94822:94902](-) trnV-GAC [100871:100942](+) trnI-GAU [102960:103001](+) [103938:103972](+) trnA-UGC [104043:104080](+) [104892:104926](+) trnR-ACG [108714:108787](+) trnN-GUU [109354:109426](-) trnL-UAG [114179:114258](+) trnN-GUU_copy2 [129518:129590](+) trnR-ACG_copy2 [130157:130230](-) trnA-UGC_copy2 [134864:134901](-) [134018:134052](-) trnI-GAU_copy2 [135943:135984](-) [134972:135006](-) trnV-GAC_copy2 [138002:138073](-) trnL-GAG [144042:144122](+) trnM-CAU_copy3 [151718:151791](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [101170:102659](+) rrn23 [105075:107884](+) rrn4.5 [107986:108088](+) rrn5 [108346:108466](+) rrn5_copy2 [130478:130598](-) rrn4.5_copy2 [130856:130958](-) rrn23_copy2 [131057:133866](-) rrn16_copy2 [136284:137773](-) This genome has 20 genes with intron(s). Details are as follows: 16 gene(s) have 1 intron(s) Genes Exons rps16 [6146:6193](-) [4994:5203](-) atpF [13263:13409](-) [12155:12625](-) rpoC1 [23669:24124](-) [21252:22871](-) rpl2 [86280:86675](-) [85178:85612](-) ndhB [96888:97667](-) [95456:96211](-) ndhA [121240:121794](-) [119647:120186](-) ndhB_copy2 [141277:142056](+) [142733:143488](+) rpl2_copy2 [152269:152664](+) [153332:153766](+) trnK-UUU [4145:4181](-) [1613:1638](-) trnG-UCC [9437:9459](+) [10165:10212](+) trnL-UAA [48348:48384](+) [48859:48908](+) trnV-UAC [53245:53282](-) [52622:52658](-) trnI-GAU [102960:103001](+) [103938:103972](+) trnA-UGC [104043:104080](+) [104892:104926](+) trnA-UGC_copy2 [134864:134901](-) [134018:134052](-) trnI-GAU_copy2 [135943:135984](-) [134972:135006](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [70872:70985](-) [99024:99255](-) [98467:98492](-) ycf3 [45194:45325](-) [44267:44497](-) [43409:43561](-) rps12_copy2 [70872:70985](-) [139689:139920](+) [140452:140477](+) clpP [73089:73157](-) [71986:72281](-) [71119:71344](-)