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, petN_copy2 Subunits of photosystem I psaA, psaB, psaC, psaI, psaJ Subunits of photosystem II psbA, psbB, psbC, psbC_copy2, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbM, psbM_copy2, psbN, psbT, psbZ, psbZ_copy2, ycf3 Large subunit of ribosome rpl14, rpl14_copy2, rpl14_copy3, rpl16, rpl2, rpl20, rpl22, rpl23, rpl23_copy2, rpl32, rpl33, rpl33_copy2 Small subunit of ribosome rps11, rps11_copy2, rps12, rps14, rps15, rps18, rps19, rps2, rps3, rps4, rps7, rps8 DNA dependent RNA polymerase rpoA, rpoB, rpoB_copy2, 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 None Conserved open reading frames 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 psbL Large subunit of ribosome rpl36 Small subunit of ribosome rps16 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 infA Conserved open reading frames ycf1, ycf15, ycf2 Other genes None 2. Multicopy genes with different lengths: Genes Length Location rps11 432 [15752:16184](+) rps11_copy2 957 [114576:115533](-) rpl23 303 [24453:24756](+) rpl23_copy2 312 join{[69431:69528](-), [64757:64972](-)} rpl33 231 [54961:55192](-) rpl33_copy2 216 [133716:133932](+) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [11314:11458](-) [10161:10570](-) clpP (1/3) [136451:137410](-) ndhA (2/2) [42630:43182](-) [40963:41501](-) ndhB (2/2) [27221:27941](+) [28632:29389](+) petB (2/2) [19998:20003](-) [18902:19543](-) petD (2/2) [18682:18689](-) [17466:17940](-) rpl16 (1/2) [13582:14010](+) rpl2 (2/2) [64363:64753](-) [63230:63663](-) rpoC1 (2/2) [79029:79460](-) [76649:78262](-) rps12 (3/3) [136156:136269](-) [25505:25736](+) [26279:26304](+) ycf3 (3/3) [105300:105423](-) [104291:104520](-) [103254:103406](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: rpl23_copy2 2 [69432:69528](-) [64758:64972](-)] accD 2 [121591:121786](+) [121904:124905](+)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon rpl16 ATC rps19 TTG rpl23_copy2 TTG rps14 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 125 genes (102 unique genes). Including: 83 protein-coding genes (73 are unique) 37 tRNA genes (25 are unique) 5 rRNA genes (4 are unique) Details are as follows: 83 protein-coding genes (73 are unique) Genes Length Location accD 3198 [121591:121786](+) [121904:124905](+) atpA 1533 [8569:10101](-) atpB 1497 [116858:118354](-) atpE 399 [116463:116861](-) atpF 555 [11314:11458](-) [10161:10570](-) atpH 246 [12001:12246](-) atpI 747 [70262:71008](-) ccsA 960 [35448:36407](+) cemA 708 [126941:127648](+) clpP 960 [136451:137410](-) matK 1329 [2152:3480](-) ndhA 1092 [42630:43182](-) [40963:41501](-) ndhB 1479 [27221:27941](+) [28632:29389](+) ndhC 438 [111883:112320](-) ndhD 1557 [36689:38245](-) ndhE 306 [38863:39168](-) ndhF 2244 [46530:48773](+) ndhG 531 [39486:40016](-) ndhH 1182 [43184:44365](-) ndhI 522 [40345:40866](-) ndhJ 477 [110539:111015](-) ndhK 690 [111134:111823](-) petA 963 [127851:128813](+) petB 648 [19998:20003](-) [18902:19543](-) petD 483 [18682:18689](-) [17466:17940](-) petG 114 [131987:132100](+) petL 96 [131713:131808](+) petN 90 [84393:84482](+) petN_copy2 90 [147899:147988](-) psaA 2253 [100168:102420](-) psaB 2205 [97938:100142](-) psaC 246 [38350:38595](-) psaI 114 [125467:125580](+) psaJ 183 [133022:133204](+) psbA 1062 [422:1483](-) psbB 1527 [21452:22978](-) psbC 1422 [92524:93945](-) psbC_copy2 1422 [138436:139857](+) psbD 1062 [93893:94954](-) psbE 252 [130595:130846](-) psbF 120 [130462:130581](-) psbH 222 [20570:20791](-) psbI 111 [5964:6074](+) psbJ 144 [130034:130177](-) psbK 186 [5341:5526](+) psbM 105 [85189:85293](-) psbM_copy2 105 [147088:147192](+) psbN 132 [20893:21024](+) psbT 102 [21093:21194](-) psbZ 189 [91613:91801](-) psbZ_copy2 189 [140580:140768](+) rbcL 1428 [119177:120604](+) rpl14 369 [14149:14517](+) rpl14_copy2 369 [88028:88396](+) rpl14_copy3 369 [143985:144353](-) rpl16 429 [13582:14010](+) rpl2 825 [64363:64753](-) [63230:63663](-) rpl20 432 [134930:135361](-) rpl22 417 [62325:62741](-) rpl23 303 [24454:24756](+) rpl23_copy2 312 [69432:69528](-) [64758:64972](-) rpl32 216 [45405:45620](-) rpl33 231 [54962:55192](-) rpl33_copy2 216 [133717:133932](+) rpoA 1014 [16225:17238](+) rpoB 3342 [79498:82839](-) rpoB_copy2 3342 [149542:152883](+) rpoC1 2046 [79029:79460](-) [76649:78262](-) rpoC2 4263 [72210:76472](-) rps11 432 [15753:16184](+) rps11_copy2 957 [114577:115533](-) rps12 372 [136156:136269](-) [25505:25736](+) [26279:26304](+) rps14 303 [97501:97803](-) rps15 300 [44522:44821](-) rps18 459 [134187:134645](+) rps19 288 [62802:63089](-) rps2 738 [71252:71989](-) rps3 699 [61543:62241](-) rps4 618 [106671:107288](-) rps7 471 [26358:26828](+) rps8 399 [14603:15001](+) ycf3 507 [105300:105423](-) [104291:104520](-) [103254:103406](-) ycf4 555 [125857:126411](+) 37 tRNA genes (25 are unique) Genes Location trnH-GUG [37:110](-) trnQ-UUG [4518:4591](-) trnS-GGA [6201:6287](-) trnG-UCC [7154:7176](+) [7871:7918](+) trnR-UCU [8111:8182](+) trnI-CAU [12786:12859](-) trnL-CAA [29967:30047](+) trnL-UAG [35126:35205](+) trnN-GUU [49128:49199](+) trnR-ACG [49439:49512](-) trnI-GAU [53464:53498](-) [53379:53413](-) trnI-GAU_copy2 [55461:55495](-) [53763:53799](-) trnV-GAC [59168:59239](-) trnQ-UUG_copy2 [65804:65877](-) trnC-GCA [84062:84132](+) trnD-GUC [86536:86609](-) trnY-GUA [86993:87075](-) trnE-UUC [87135:87207](-) trnG-GCC [90776:90846](+) trnS-UGA [92189:92281](+) trnfM-CAU [96169:96242](-) trnfM-CAU_copy2 [96725:96798](-) trnfM-CAU_copy3 [97251:97322](-) trnS-GGA_copy2 [106316:106402](+) trnT-UGU [107623:107695](-) trnL-UAA [109036:109070](+) [109556:109605](+) trnF-GAA [109994:110066](+) trnM-CAU [116110:116182](+) trnW-CCA [132209:132282](-) trnP-UGG [132457:132530](-) trnI-CAU_copy2 [137781:137854](+) trnS-UGA_copy2 [140100:140192](-) trnG-GCC_copy2 [141535:141605](-) trnE-UUC_copy2 [145174:145246](+) trnY-GUA_copy2 [145306:145388](+) trnD-GUC_copy2 [145772:145845](+) trnC-GCA_copy2 [148249:148319](-) 5 rRNA genes (4 are unique) Genes Location rrn5S [49781:49901](-) rrn4.5S [50148:50250](-) rrn23S [50351:53275](-) rrn16S [56712:58293](-) rrn16S_copy2 [58713:58820](-) This genome has 15 genes with intron(s). Details are as follows: 13 gene(s) have 1 intron(s) Genes Exons atpF [11314:11458](-) [10161:10570](-) petD [18682:18689](-) [17466:17940](-) petB [19998:20003](-) [18902:19543](-) ndhB [27221:27941](+) [28632:29389](+) ndhA [42630:43182](-) [40963:41501](-) rpl2 [64363:64753](-) [63230:63663](-) rpl23_copy2 [69432:69528](-) [64758:64972](-) rpoC1 [79029:79460](-) [76649:78262](-) accD [121591:121786](+) [121904:124905](+) trnG-UCC [7154:7176](+) [7871:7918](+) trnI-GAU [53464:53498](-) [53379:53413](-) trnI-GAU_copy2 [55461:55495](-) [53763:53799](-) trnL-UAA [109036:109070](+) [109556:109605](+) 2 gene(s) have 2 intron(s) Genes Exons rps12 [136156:136269](-) [25505:25736](+) [26279:26304](+) ycf3 [105300:105423](-) [104291:104520](-) [103254:103406](-)