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, psbN, psbT, psbZ, ycf3 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, 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, ycf1_copy2, ycf2, ycf2_copy2, ycf4 Other genes None 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 ycf1 1956 [113350:115306](+) ycf1_copy2 5721 [128438:134159](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [13897:14040](-) [12759:13169](-) clpP (3/3) [75539:75608](-) [74414:74703](-) [73506:73736](-) ndhA (2/2) [125947:126499](-) [124326:124864](-) ndhB (2/2) [100213:100989](-) [98778:99533](-) ndhB_copy2 (2/2) [146521:147297](+) [147977:148732](+) petB (2/2) [78540:78545](+) [79355:79996](+) petD (2/2) [80190:80197](+) [80946:81420](+) rpl16 (2/2) [86457:86465](-) [84968:85366](-) rpl2 (2/2) [89480:89870](-) [88370:88803](-) rpl2_copy2 (2/2) [157640:158030](+) [158707:159140](+) rpoC1 (2/2) [24482:24937](-) [22087:23697](-) rps12 (3/3) [73135:73248](-) [102396:102627](-) [101834:101859](-) rps12_copy2 (3/3) [73135:73248](-) [144883:145114](+) [145651:145676](+) rps16 (2/2) [5892:5931](-) [4805:5040](-) ycf3 (3/3) [46012:46137](-) [45049:45276](-) [44145:44297](-) ### 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 psbL ACG rps19 GTG ndhD ACG rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 132 genes (112 unique genes). Including: 88 protein-coding genes (79 are unique) 36 tRNA genes (29 are unique) 8 rRNA genes (4 are unique) Details are as follows: 88 protein-coding genes (79 are unique) Genes Length Location accD 1644 [59807:61450](+) atpA 1524 [11165:12688](-) atpB 1494 [54686:56179](-) atpE 402 [54288:54689](-) atpF 555 [13897:14040](-) [12759:13169](-) atpH 246 [14432:14677](-) atpI 744 [15861:16604](-) ccsA 966 [118948:119913](+) cemA 690 [64196:64885](+) clpP 591 [75539:75608](-) [74414:74703](-) [73506:73736](-) infA 240 [83470:83709](-) matK 1515 [1899:3413](-) ndhA 1092 [125947:126499](-) [124326:124864](-) ndhB 1533 [100213:100989](-) [98778:99533](-) ndhB_copy2 1533 [146521:147297](+) [147977:148732](+) ndhC 363 [51806:52168](-) ndhD 1515 [120163:121677](-) ndhE 306 [122315:122620](-) ndhF 2268 [115441:117708](+) ndhG 531 [122845:123375](-) ndhH 1182 [126501:127682](-) ndhI 498 [123742:124239](-) ndhJ 477 [50500:50976](-) ndhK 678 [51072:51749](-) petA 963 [65112:66074](+) petB 648 [78540:78545](+) [79355:79996](+) petD 483 [80190:80197](+) [80946:81420](+) petG 114 [69175:69288](+) petL 96 [68897:68992](+) petN 90 [30123:30212](+) psaA 2253 [41061:43313](-) psaB 2205 [38831:41035](-) psaC 246 [121810:122055](-) psaI 111 [62163:62273](+) psaJ 135 [70210:70344](+) psbA 1062 [286:1347](-) psbB 1527 [76060:77586](+) psbC 1422 [35313:36734](+) psbD 1062 [34304:35365](+) psbE 252 [67611:67862](-) psbF 120 [67482:67601](-) psbH 222 [78194:78415](+) psbI 111 [8845:8955](+) psbJ 120 [67073:67192](-) psbK 186 [8141:8326](+) psbL 117 [67343:67459](-) psbM 105 [31402:31506](-) psbN 132 [77951:78082](-) psbT 108 [77784:77891](+) psbZ 189 [37407:37595](+) rbcL 1428 [57045:58472](+) rpl14 369 [84423:84791](-) rpl16 408 [86457:86465](-) [84968:85366](-) rpl2 825 [89480:89870](-) [88370:88803](-) rpl20 402 [71935:72336](-) rpl22 669 [87262:87930](-) rpl22_copy2 669 [159580:160248](+) rpl23 285 [89889:90173](-) rpl23_copy2 285 [157337:157621](+) rpl2_copy2 825 [157640:158030](+) [158707:159140](+) rpl32 171 [117830:118000](+) rpl33 201 [70813:71013](+) rpl36 114 [83236:83349](-) rpoA 1008 [81627:82634](-) rpoB 3240 [24949:28188](-) rpoC1 2067 [24482:24937](-) [22087:23697](-) rpoC2 4203 [17711:21913](-) rps11 417 [82709:83125](-) rps12 372 [73135:73248](-) [102396:102627](-) [101834:101859](-) rps12_copy2 372 [73135:73248](-) [144883:145114](+) [145651:145676](+) rps14 354 [38347:38700](-) rps15 192 [127848:128039](-) rps16 276 [5892:5931](-) [4805:5040](-) rps18 507 [71187:71693](+) rps19 279 [88032:88310](-) rps19_copy2 279 [159200:159478](+) rps2 711 [16814:17524](-) rps3 654 [86624:87277](-) rps4 612 [46945:47556](-) rps7 468 [101313:101780](-) rps7_copy2 468 [145730:146197](+) rps8 420 [83825:84244](-) ycf1 1956 [113351:115306](+) ycf1_copy2 5721 [128439:134159](-) ycf2 6999 [90884:97882](+) ycf2_copy2 6999 [149628:156626](-) ycf3 507 [46012:46137](-) [45049:45276](-) [44145:44297](-) ycf4 555 [62697:63251](+) 36 tRNA genes (29 are unique) Genes Location trnH-GUG [10:84](-) trnK-UUU [4186:4222](-) [1588:1622](-) trnQ-UUG [7718:7789](-) trnS-GCU [9069:9156](-) trnG-UCC [9945:9970](+) [10686:10732](+) trnR-UCU [10926:10997](+) trnC-GCA [29491:29571](+) trnD-GUC [32442:32515](-) trnY-GUA [32627:32710](-) trnE-UUC [32991:33063](-) trnS-UGA [36960:37051](-) trnG-GCC [37877:37947](+) trnfM-CAU [38132:38204](-) trnS-GGA [46572:46658](+) trnT-UGU [47948:48020](-) trnL-UAA [48774:48810](+) [49322:49371](+) trnF-GAA [49732:49804](+) trnV-UAC [53756:53794](-) [53144:53180](-) trnM-CAU [53970:54041](+) trnW-CCA [69412:69485](-) trnP-UGG [69667:69740](-) trnI-CAU [90339:90412](-) trnL-CAA [98129:98209](-) trnV-GAC [104370:104440](+) trnI-GAU [106453:106494](+) [107436:107470](+) trnA-UGC [107535:107572](+) [108379:108413](+) trnR-ACG [112219:112292](+) trnN-GUU [112455:112526](-) trnL-UAG [118780:118859](+) trnN-GUU_copy2 [134984:135055](+) trnR-ACG_copy2 [135218:135291](-) trnA-UGC_copy2 [139938:139975](-) [139097:139131](-) trnI-GAU_copy2 [141016:141057](-) [140040:140074](-) trnV-GAC_copy2 [143070:143140](-) trnL-CAA_copy2 [149301:149381](+) trnI-CAU_copy2 [157098:157171](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [104668:106160](+) rrn23 [108565:111412](+) rrn4.5 [111511:111613](+) rrn5 [111839:111958](+) rrn5_copy2 [135552:135671](-) rrn4.5_copy2 [135897:135999](-) rrn23_copy2 [136098:138945](-) rrn16_copy2 [141350:142842](-) This genome has 23 genes with intron(s). Details are as follows: 19 gene(s) have 1 intron(s) Genes Exons rps16 [5892:5931](-) [4805:5040](-) atpF [13897:14040](-) [12759:13169](-) rpoC1 [24482:24937](-) [22087:23697](-) petB [78540:78545](+) [79355:79996](+) petD [80190:80197](+) [80946:81420](+) rpl16 [86457:86465](-) [84968:85366](-) rpl2 [89480:89870](-) [88370:88803](-) ndhB [100213:100989](-) [98778:99533](-) ndhA [125947:126499](-) [124326:124864](-) ndhB_copy2 [146521:147297](+) [147977:148732](+) rpl2_copy2 [157640:158030](+) [158707:159140](+) trnK-UUU [4186:4222](-) [1588:1622](-) trnG-UCC [9945:9970](+) [10686:10732](+) trnL-UAA [48774:48810](+) [49322:49371](+) trnV-UAC [53756:53794](-) [53144:53180](-) trnI-GAU [106453:106494](+) [107436:107470](+) trnA-UGC [107535:107572](+) [108379:108413](+) trnA-UGC_copy2 [139938:139975](-) [139097:139131](-) trnI-GAU_copy2 [141016:141057](-) [140040:140074](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [73135:73248](-) [102396:102627](-) [101834:101859](-) ycf3 [46012:46137](-) [45049:45276](-) [44145:44297](-) rps12_copy2 [73135:73248](-) [144883:145114](+) [145651:145676](+) clpP [75539:75608](-) [74414:74703](-) [73506:73736](-)