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, psbK, psbL, psbM, psbN, psbT, psbZ, ycf3 Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps12_copy2, rps14, rps15, 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 cemA Maturase matK Protease clpP Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor None Conserved open reading frames ycf1, ycf2, ycf2_copy2, ycf4, ycf68, ycf68_copy2 Other genes orf42, orf42_copy2 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 psbJ Large subunit of ribosome rpl22 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 ycf15 Other genes None 2. Multicopy genes with different lengths: Genes Length Location None None None 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [50513:50671](+) [51425:51832](+) clpP (3/3) [75142:75210](-) [74036:74326](-) [73218:73445](-) ndhA (2/2) [125354:125905](-) [123579:124121](-) ndhB (2/2) [100295:101017](-) [98854:99609](-) ndhB_copy2 (2/2) [145734:146456](+) [147142:147897](+) petB (2/2) [78178:78183](+) [78991:79632](+) petD (2/2) [79846:79853](+) [80563:81037](+) rpl16 (2/2) [86639:86647](-) [85048:85449](-) rpl2 (2/2) [89455:89847](-) [88358:88792](-) rpl2_copy2 (2/2) [156904:157296](+) [157959:158393](+) rpoC1 (2/2) [39427:39859](+) [40672:42227](+) rps12 (2/3) [72890:73003](-) [102461:102703](-) rps12_copy2 (2/3) [72890:73003](-) [144048:144290](+) ycf3 (3/3) [17108:17233](+) [17952:18179](+) [18962:19114](+) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: ycf68 2 [106787:106828](+) [106857:107276](+)] ndhI 2 [123023:123499](-) [122739:122795](-)] ycf1 2 [130017:133203](-) [127861:129977](-)] ycf68_copy2 2 [139923:139964](-) [139475:139894](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon psbL ACG rps19 GTG orf42 ATC ndhD ATC orf42_copy2 ATC 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 129 genes (110 unique genes). Including: 85 protein-coding genes (77 are unique) 36 tRNA genes (29 are unique) 8 rRNA genes (4 are unique) Details are as follows: 85 protein-coding genes (77 are unique) Genes Length Location accD 1506 [59953:61458](+) atpA 1533 [51908:53440](+) atpB 1497 [7366:8862](+) atpE 402 [8859:9260](+) atpF 567 [50513:50671](+) [51425:51832](+) atpH 246 [49849:50094](+) atpI 744 [47784:48527](+) ccsA 972 [118237:119208](+) cemA 690 [63284:63973](+) clpP 588 [75142:75210](-) [74036:74326](-) [73218:73445](-) matK 1326 [2309:3634](-) ndhA 1095 [125354:125905](-) [123579:124121](-) ndhB 1479 [100295:101017](-) [98854:99609](-) ndhB_copy2 1479 [145734:146456](+) [147142:147897](+) ndhC 363 [10830:11192](+) ndhD 1500 [119522:121021](-) ndhE 306 [121664:121969](-) ndhF 2259 [114008:116266](-) ndhG 531 [122209:122739](-) ndhH 1182 [125907:127088](-) ndhI 534 [123023:123499](-) [122739:122795](-) ndhJ 477 [12062:12538](+) ndhK 672 [11234:11905](+) orf42 129 [107896:108024](-) orf42_copy2 129 [138727:138855](+) petA 963 [64193:65155](+) petB 648 [78178:78183](+) [78991:79632](+) petD 483 [79846:79853](+) [80563:81037](+) petG 114 [68839:68952](+) petL 96 [68578:68673](+) petN 90 [33728:33817](-) psaA 2253 [19948:22200](+) psaB 2205 [22226:24430](+) psaC 246 [121150:121395](-) psaI 105 [61976:62080](+) psaJ 135 [70029:70163](+) psbA 1062 [385:1446](-) psbB 1527 [75673:77199](+) psbC 1422 [26703:28124](-) psbD 1062 [28072:29133](-) psbE 252 [66927:67178](-) psbF 120 [66798:66917](-) psbH 222 [77811:78032](+) psbI 111 [55866:55976](-) psbK 186 [56485:56670](-) psbL 117 [66659:66775](-) psbM 105 [32355:32459](+) psbN 132 [77568:77699](-) psbT 117 [77386:77502](+) psbZ 189 [25819:26007](-) rbcL 1428 [5148:6575](-) rpl14 369 [84546:84914](-) rpl16 411 [86639:86647](-) [85048:85449](-) rpl2 828 [89455:89847](-) [88358:88792](-) rpl20 360 [71684:72043](-) rpl23 276 [89872:90147](-) rpl23_copy2 276 [156604:156879](+) rpl2_copy2 828 [156904:157296](+) [157959:158393](+) rpl32 147 [117051:117197](+) rpl33 201 [70667:70867](+) rpl36 114 [83238:83351](-) rpoA 996 [81272:82267](-) rpoB 3213 [36188:39400](+) rpoC1 1989 [39427:39859](+) [40672:42227](+) rpoC2 4122 [42399:46520](+) rps11 393 [82347:82739](-) rps12 357 [72890:73003](-) [102461:102703](-) rps12_copy2 357 [72890:73003](-) [144048:144290](+) rps14 303 [24554:24856](+) rps15 273 [127204:127476](-) rps18 339 [71125:71463](+) rps19 279 [88019:88297](-) rps2 711 [46832:47542](+) rps3 657 [86821:87477](-) rps4 606 [15957:16562](+) rps7 468 [101390:101857](-) rps7_copy2 468 [144894:145361](+) rps8 405 [83775:84179](-) ycf1 5304 [130017:133203](-) [127861:129977](-) ycf2 6861 [90754:97614](+) ycf2_copy2 6861 [149137:155997](-) ycf3 507 [17108:17233](+) [17952:18179](+) [18962:19114](+) ycf4 555 [62264:62818](+) ycf68 462 [106787:106828](+) [106857:107276](+) ycf68_copy2 462 [139923:139964](-) [139475:139894](-) 36 tRNA genes (29 are unique) Genes Location trnH-GUG [42:116](-) trnK-UUU [4353:4389](-) [1763:1791](-) trnM-CAU [9422:9493](-) trnV-UAC [9677:9715](+) [10313:10349](+) trnF-GAA [13337:13409](-) trnL-UAA [14402:14438](-) [13814:13863](-) trnT-UGU [15608:15680](+) trnS-GGA [16760:16847](-) trnfM-CAU [25024:25097](+) trnG-UCC [25145:25215](-) trnS-UGA [26367:26459](+) trnT-GGU [30208:30279](-) trnE-UUC [31092:31164](+) trnY-GUA [31225:31308](+) trnD-GUC [31853:31926](+) trnC-GCA [34960:35030](-) trnR-UCU [53677:53748](-) trnS-GCU [55605:55691](+) trnQ-UUG [57315:57386](+) trnW-CCA [69085:69158](-) trnP-UGG [69333:69406](-) trnI-CAU [90592:90665](-) trnL-CAA [98196:98276](-) trnV-GAC [104576:104647](+) trnI-GAU [106646:106687](+) [107635:107669](+) trnA-UGC [107729:107766](+) [108567:108601](+) trnR-ACG [112388:112461](+) trnN-GUU [113095:113166](-) trnL-UAG [118055:118134](+) trnN-GUU_copy2 [133585:133656](+) trnR-ACG_copy2 [134290:134363](-) trnA-UGC_copy2 [138985:139022](-) [138150:138184](-) trnI-GAU_copy2 [140064:140105](-) [139082:139116](-) trnV-GAC_copy2 [142104:142175](-) trnL-CAA_copy2 [148475:148555](+) trnI-CAU_copy2 [156086:156159](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [104869:106359](+) rrn23 [108759:111573](+) rrn4.5 [111673:111776](+) rrn5 [112001:112121](+) rrn5_copy2 [134630:134750](-) rrn4.5_copy2 [134975:135078](-) rrn23_copy2 [135177:137991](-) rrn16_copy2 [140392:141882](-) This genome has 25 genes with intron(s). Details are as follows: 23 gene(s) have 1 intron(s) Genes Exons rps12 [72890:73003](-) [102461:102703](-) rpoC1 [39427:39859](+) [40672:42227](+) atpF [50513:50671](+) [51425:51832](+) rps12_copy2 [72890:73003](-) [144048:144290](+) petB [78178:78183](+) [78991:79632](+) petD [79846:79853](+) [80563:81037](+) rpl16 [86639:86647](-) [85048:85449](-) rpl2 [89455:89847](-) [88358:88792](-) ndhB [100295:101017](-) [98854:99609](-) ycf68 [106787:106828](+) [106857:107276](+) ndhI [123023:123499](-) [122739:122795](-) ndhA [125354:125905](-) [123579:124121](-) ycf1 [130017:133203](-) [127861:129977](-) ycf68_copy2 [139923:139964](-) [139475:139894](-) ndhB_copy2 [145734:146456](+) [147142:147897](+) rpl2_copy2 [156904:157296](+) [157959:158393](+) trnK-UUU [4353:4389](-) [1763:1791](-) trnV-UAC [9677:9715](+) [10313:10349](+) trnL-UAA [14402:14438](-) [13814:13863](-) trnI-GAU [106646:106687](+) [107635:107669](+) trnA-UGC [107729:107766](+) [108567:108601](+) trnA-UGC_copy2 [138985:139022](-) [138150:138184](-) trnI-GAU_copy2 [140064:140105](-) [139082:139116](-) 2 gene(s) have 2 intron(s) Genes Exons ycf3 [17108:17233](+) [17952:18179](+) [18962:19114](+) clpP [75142:75210](-) [74036:74326](-) [73218:73445](-)