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, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps12_copy2, rps12_copy3, 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, ycf15, ycf15_copy2, ycf15_copy3, ycf15_copy4, 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 None Other genes None 2. Multicopy genes with different lengths: Genes Length Location rps12 129 [69393:69522](-) rps12_copy2 240 [97918:98158](-) rps12_copy3 240 [138960:139200](+) rpl2 867 join{[85136:85530](-), [84047:84520](-)} rpl2_copy2 864 join{[151588:151979](+), [152598:153071](+)} ycf15 195 [93166:93361](+) ycf15_copy2 111 [99190:99301](-) ycf15_copy3 111 [137817:137928](+) ycf15_copy4 195 [143757:143952](-) ndhB 1626 join{[95694:96564](-), [94347:95103](-)} ndhB_copy2 1623 join{[140554:141421](+), [142015:142771](+)} 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [13076:13226](-) [11960:12369](-) clpP (3/3) [71632:71690](-) [70529:70822](-) [69638:69869](-) ndhA (2/2) [120337:120892](-) [118693:119231](-) ndhB (2/2) [95695:96564](-) [94348:95103](-) ndhB_copy2 (2/2) [140555:141421](+) [142016:142771](+) petB (1/2) [75393:76073](+) petD (1/2) [77015:77515](+) rpl16 (1/2) [80964:81374](-) rpl2 (2/2) [85137:85530](-) [84048:84520](-) rpl2_copy2 (2/2) [151589:151979](+) [152599:153071](+) rpoC1 (2/2) [23512:23965](-) [21127:22757](-) rps12 (1/3) [69394:69522](-) rps12_copy2 (1/3) [97919:98158](-) rps12_copy3 (1/3) [138961:139200](+) rps16 (1/2) [5109:5327](-) ycf3 (3/3) [45066:45192](-) [44099:44328](-) [43181:43333](-) ### 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 rps16 ATC psbI ATT rpoC2 ATA petN ATT psbC GTG ndhK CTG ycf4 ATC psbT ATC petB ATC petD ATC infA ATT rpl16 ATC rps19 GTG rps12_copy2 ATC ycf15_copy2 ATT ccsA ATA ndhD TTG ycf15_copy3 ATT rps12_copy3 ATC rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 132 genes (109 unique genes). Including: 91 protein-coding genes (80 are unique) 33 tRNA genes (25 are unique) 8 rRNA genes (4 are unique) Details are as follows: 91 protein-coding genes (80 are unique) Genes Length Location accD 1554 [56993:58546](+) atpA 1524 [10376:11899](-) atpB 1497 [53173:54669](-) atpE 399 [52778:53176](-) atpF 561 [13076:13226](-) [11960:12369](-) atpH 246 [13577:13822](-) atpI 735 [14863:15597](-) ccsA 933 [113492:114424](+) cemA 690 [60965:61654](+) clpP 585 [71632:71690](-) [70529:70822](-) [69638:69869](-) infA 138 [79558:79695](-) matK 1509 [2035:3543](-) ndhA 1095 [120337:120892](-) [118693:119231](-) ndhB 1626 [95695:96564](-) [94348:95103](-) ndhB_copy2 1623 [140555:141421](+) [142016:142771](+) ndhC 363 [50732:51094](-) ndhD 1527 [114690:116216](-) ndhE 306 [116803:117108](-) ndhF 2241 [109779:112019](-) ndhG 531 [117213:117743](-) ndhH 1182 [120894:122075](-) ndhI 504 [118099:118602](-) ndhJ 477 [49395:49871](-) ndhK 738 [49991:50728](-) petA 960 [61898:62857](+) petB 681 [75393:76073](+) petD 501 [77015:77515](+) petG 114 [65910:66023](+) petL 96 [65639:65734](+) petN 96 [29049:29144](+) psaA 2253 [40020:42272](-) psaB 2205 [37790:39994](-) psaC 246 [116310:116555](-) psaI 111 [59275:59385](+) psaJ 135 [66816:66950](+) psbA 1062 [446:1507](-) psbB 1527 [72142:73668](+) psbC 1452 [34268:35719](+) psbD 1062 [33289:34350](+) psbE 252 [64301:64552](-) psbF 120 [64172:64291](-) psbH 240 [74324:74563](+) psbI 153 [8309:8461](+) psbJ 123 [63775:63897](-) psbK 186 [7943:8128](+) psbL 117 [64032:64148](-) psbM 105 [29965:30069](-) psbN 165 [74111:74275](-) psbT 117 [73918:74034](+) psbZ 189 [36401:36589](+) rbcL 1428 [55257:56684](+) rpl14 369 [80476:80844](-) rpl16 411 [80964:81374](-) rpl2 867 [85137:85530](-) [84048:84520](-) rpl20 387 [68264:68650](-) rpl22 405 [83228:83632](-) rpl23 282 [85549:85830](-) rpl23_copy2 282 [151289:151570](+) rpl2_copy2 864 [151589:151979](+) [152599:153071](+) rpl32 162 [112571:112732](+) rpl33 189 [67377:67565](+) rpl36 114 [79297:79410](-) rpoA 1014 [77681:78694](-) rpoB 3213 [23971:27183](-) rpoC1 2085 [23512:23965](-) [21127:22757](-) rpoC2 4200 [16786:20985](-) rps11 417 [78769:79185](-) rps12 129 [69394:69522](-) rps12_copy2 240 [97919:98158](-) rps12_copy3 240 [138961:139200](+) rps14 303 [37352:37654](-) rps15 255 [122194:122448](-) rps16 219 [5109:5327](-) rps18 309 [67713:68021](+) rps19 279 [83718:83996](-) rps19_copy2 279 [153120:153398](+) rps2 711 [15835:16545](-) rps3 657 [82562:83218](-) rps4 606 [45901:46506](-) rps7 468 [96858:97325](-) rps7_copy2 468 [139794:140261](+) rps8 405 [79918:80322](-) ycf1 5616 [122828:128443](-) ycf15 195 [93167:93361](+) ycf15_copy2 111 [99191:99301](-) ycf15_copy3 111 [137818:137928](+) ycf15_copy4 195 [143758:143952](-) ycf2 6852 [86158:93009](+) ycf2_copy2 6852 [144110:150961](-) ycf3 510 [45066:45192](-) [44099:44328](-) [43181:43333](-) ycf4 453 [59892:60344](+) 33 tRNA genes (25 are unique) Genes Location trnH-GTG [83:156](-) trnQ-TTG [7541:7612](-) trnS-GCT [8561:8648](-) trnR-TCT [10184:10255](+) trnC-GCA [28294:28364](+) trnD-GTC [30737:30810](-) trnY-GTA [30932:31015](-) trnE-TTC [31070:31142](-) trnT-GGT [31906:31977](+) trnS-TGA [35984:36076](-) trnG-GCC [36906:36976](+) trnM-CAT [37130:37203](-) trnS-GGA [45501:45587](+) trnT-TGT [46814:46886](-) trnF-GAA [48611:48683](+) trnM-CAT_copy2 [52490:52562](+) trnW-CCA [66142:66215](-) trnP-TGG [66344:66417](-) trnI-CAT [85996:86069](-) trnL-CAA [93721:93801](-) trnV-GAC [99770:99841](+) trnI-GAT [101864:101905](+) [102843:102877](+) trnA-TGC [102941:102978](+) [103797:103831](+) trnR-ACG [107641:107714](+) trnN-GTT [108278:108349](-) trnL-TAG [113303:113382](+) trnN-GTT_copy2 [128770:128841](+) trnR-ACG_copy2 [129405:129478](-) trnA-TGC_copy2 [134141:134178](-) [133288:133322](-) trnI-GAT_copy2 [135214:135255](-) [134242:134276](-) trnV-GAC_copy2 [137278:137349](-) trnL-CAA_copy2 [143318:143398](+) trnI-CAT_copy2 [151050:151123](+) 8 rRNA genes (4 are unique) Genes Location rrn16S [100074:101564](+) rrn23S [103991:106799](+) rrn4.5S [106898:107175](+) rrn5S [107269:107399](+) rrn5S_copy2 [129720:129850](-) rrn4.5S_copy2 [129944:130221](-) rrn23S_copy2 [130320:133128](-) rrn16S_copy2 [135555:137045](-) This genome has 13 genes with intron(s). Details are as follows: 11 gene(s) have 1 intron(s) Genes Exons atpF [13076:13226](-) [11960:12369](-) rpoC1 [23512:23965](-) [21127:22757](-) rpl2 [85137:85530](-) [84048:84520](-) ndhB [95695:96564](-) [94348:95103](-) ndhA [120337:120892](-) [118693:119231](-) ndhB_copy2 [140555:141421](+) [142016:142771](+) rpl2_copy2 [151589:151979](+) [152599:153071](+) trnI-GAT [101864:101905](+) [102843:102877](+) trnA-TGC [102941:102978](+) [103797:103831](+) trnA-TGC_copy2 [134141:134178](-) [133288:133322](-) trnI-GAT_copy2 [135214:135255](-) [134242:134276](-) 2 gene(s) have 2 intron(s) Genes Exons ycf3 [45066:45192](-) [44099:44328](-) [43181:43333](-) clpP [71632:71690](-) [70529:70822](-) [69638:69869](-)