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, 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, psbT, psbZ 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 cemA Maturase matK Protease None Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor infA Conserved open reading frames ycf1, ycf1_copy2, ycf2, ycf2_copy2 Other genes clpP1, ndh5, pafI, pafII, pbf1 Possible missing protein coding genes: Group of genes Name of genes Subunits of ATP synthase None Subunits of NADH-dehydrogenase ndhF Subunits of cytochrome b/f complex None Subunits of photosystem I None Subunits of photosystem II psbN, ycf3 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 clpP Subunit of Acetyl-CoA-carboxylase None Translational initiation factor None Conserved open reading frames ycf15, ycf4 Other genes None 2. Multicopy genes with different lengths: Genes Length Location ycf1 5742 [115827:121569](+) ycf1_copy2 756 [136172:136928](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [13506:13650](-) [12285:12694](-) ndhA (2/2) [123517:124068](+) [125228:125767](+) ndhB (2/2) [102516:103292](-) [101077:101832](-) ndhB_copy2 (2/2) [149464:150240](+) [150924:151679](+) petB (2/2) [80653:80658](+) [81472:82113](+) petD (2/2) [82329:82336](+) [83080:83554](+) rpl16 (2/2) [88605:88613](-) [87065:87463](-) rpl2 (2/2) [91515:91905](-) [90383:90816](-) rpl2_copy2 (2/2) [160851:161241](+) [161940:162373](+) rpoC1 (2/2) [24523:24954](-) [22127:23737](-) rps12 (3/3) [75287:75400](-) [104700:104930](-) [104137:104163](-) rps12_copy2 (3/3) [75287:75400](-) [147826:148057](+) [148594:148619](+) rps16 (2/2) [6463:6502](-) [5366:5592](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: pafI 3 [47667:47792](-) [46617:46842](-) [45667:45821](-)] clpP1 3 [77694:77760](-) [76469:76763](-) [75579:75807](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon ndhD ACG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 131 genes (114 unique genes). Including: 86 protein-coding genes (79 are unique) 37 tRNA genes (31 are unique) 8 rRNA genes (4 are unique) Details are as follows: 86 protein-coding genes (79 are unique) Genes Length Location accD 1488 [62312:63799](+) atpA 1524 [10698:12221](-) atpB 1476 [57523:58998](-) atpE 402 [57099:57500](-) atpF 555 [13506:13650](-) [12285:12694](-) atpH 246 [14324:14569](-) atpI 744 [15817:16560](-) ccsA 984 [130333:131316](-) cemA 690 [66333:67022](+) clpP1 591 [77694:77760](-) [76469:76763](-) [75579:75807](-) infA 126 [85662:85787](-) matK 1515 [2205:3719](-) ndh5 2211 [133976:136186](+) ndhA 1092 [123517:124068](+) [125228:125767](+) ndhB 1533 [102516:103292](-) [101077:101832](-) ndhB_copy2 1533 [149464:150240](+) [150924:151679](+) ndhC 363 [54068:54430](-) ndhD 1503 [128479:129981](+) ndhE 306 [127538:127843](+) ndhG 531 [126778:127308](+) ndhH 1182 [122334:123515](+) ndhI 504 [125850:126353](+) ndhJ 477 [52717:53193](-) ndhK 678 [53330:54007](-) pafI 507 [47667:47792](-) [46617:46842](-) [45667:45821](-) pafII 555 [65091:65645](+) pbf1 132 [80078:80209](-) petA 963 [67249:68211](+) petB 648 [80653:80658](+) [81472:82113](+) petD 483 [82329:82336](+) [83080:83554](+) petG 114 [71310:71423](+) petL 96 [71027:71122](+) petN 90 [30093:30182](+) psaA 2253 [42503:44755](-) psaB 2205 [40273:42477](-) psaC 246 [128100:128345](+) psaI 114 [64583:64696](+) psaJ 129 [72317:72445](+) psbA 1062 [489:1550](-) psbB 1527 [78191:79717](+) psbC 1422 [36236:37657](+) psbD 1062 [35227:36288](+) psbE 252 [69893:70144](-) psbF 120 [69764:69883](-) psbH 222 [80314:80535](+) psbI 111 [8121:8231](+) psbJ 123 [69344:69466](-) psbK 186 [7499:7684](+) psbL 117 [69621:69737](-) psbM 105 [31361:31465](-) psbT 102 [79911:80012](+) psbZ 189 [38386:38574](+) rbcL 1434 [60112:61545](+) rpl14 369 [86569:86937](-) rpl16 408 [88605:88613](-) [87065:87463](-) rpl2 825 [91515:91905](-) [90383:90816](-) rpl20 354 [74173:74526](-) rpl22 456 [89505:89960](-) rpl23 282 [91924:92205](-) rpl23_copy2 282 [160551:160832](+) rpl2_copy2 825 [160851:161241](+) [161940:162373](+) rpl32 165 [132649:132813](-) rpl33 207 [72934:73140](+) rpl36 114 [85425:85538](-) rpoA 984 [83817:84800](-) rpoB 3225 [24981:28205](-) rpoC1 2043 [24523:24954](-) [22127:23737](-) rpoC2 4188 [17757:21944](-) rps11 417 [84865:85281](-) rps12 372 [75287:75400](-) [104700:104930](-) [104137:104163](-) rps12_copy2 372 [75287:75400](-) [147826:148057](+) [148594:148619](+) rps14 303 [39842:40144](-) rps15 273 [121963:122235](+) rps16 267 [6463:6502](-) [5366:5592](-) rps18 306 [73572:73877](+) rps19 279 [90052:90330](-) rps2 711 [16785:17495](-) rps3 657 [88795:89451](-) rps4 606 [48480:49085](-) rps7 468 [103616:104083](-) rps7_copy2 468 [148673:149140](+) rps8 405 [86005:86409](-) ycf1 5742 [115828:121569](+) ycf1_copy2 756 [136173:136928](-) ycf2 6900 [92533:99432](+) ycf2_copy2 6900 [153324:160223](-) 37 tRNA genes (31 are unique) Genes Location trnH-GUG [1:75](-) trnK-UUU [4460:4496](-) [1838:1872](-) trnQ-UUG [7062:7133](-) trnS-GCU [8318:8405](-) trnS-UCC [9350:9372](+) [10190:10237](+) trnR-UCU [10430:10501](+) trnC-GCA [29426:29497](+) trnD-GUC [31970:32043](-) trnY-GUA [32572:32655](-) trnE-UUC [32715:32787](-) trnI-GGU [33581:33652](+) trnS-UGA [37913:38005](-) trnG-UCC [39363:39433](+) trnfM-CAU [39611:39684](-) trnS-GGA [48081:48167](+) trnT-UGU [49739:49811](-) trnL-UAA [50775:50811](+) [51406:51455](+) trnF-GAA [51865:51937](+) trnV-UAC [56524:56561](-) [55880:55914](-) trnM-CAU [56764:56836](+) trnW-CCA [71620:71693](-) trnP-UGG [71877:71950](-) trnM-CAU_copy2 [92371:92444](-) trnL-CAA [100372:100452](-) trnV-GAC [106870:106941](+) trnI-GAU [108953:108989](+) [109947:109981](+) trnA-UGC [110045:110082](+) [110877:110911](+) trnR-ACG [114720:114793](+) trnN-GUU [115439:115510](-) trnL-UAG [131420:131499](-) trnN-GUU_copy2 [137246:137317](+) trnR-ACG_copy2 [137963:138036](-) trnA-UGC_copy2 [142674:142711](-) [141845:141879](-) trnL-GAU [143768:143803](-) [143716:143751](-) trnV-GAC_copy2 [145815:145886](-) trnL-CAA_copy2 [152304:152384](+) trnl-CAU [160312:160385](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [107169:108659](+) rrn23 [111079:113888](+) rrn4.5 [113987:114089](+) rrn5 [114352:114472](+) rrn5_copy2 [138284:138404](-) rrn4.5_copy2 [138667:138769](-) rrn23_copy2 [138868:141677](-) rrn16_copy2 [144097:145587](-) This genome has 23 genes with intron(s). Details are as follows: 19 gene(s) have 1 intron(s) Genes Exons rps16 [6463:6502](-) [5366:5592](-) atpF [13506:13650](-) [12285:12694](-) rpoC1 [24523:24954](-) [22127:23737](-) petB [80653:80658](+) [81472:82113](+) petD [82329:82336](+) [83080:83554](+) rpl16 [88605:88613](-) [87065:87463](-) rpl2 [91515:91905](-) [90383:90816](-) ndhB [102516:103292](-) [101077:101832](-) ndhA [123517:124068](+) [125228:125767](+) ndhB_copy2 [149464:150240](+) [150924:151679](+) rpl2_copy2 [160851:161241](+) [161940:162373](+) trnK-UUU [4460:4496](-) [1838:1872](-) trnS-UCC [9350:9372](+) [10190:10237](+) trnL-UAA [50775:50811](+) [51406:51455](+) trnV-UAC [56524:56561](-) [55880:55914](-) trnI-GAU [108953:108989](+) [109947:109981](+) trnA-UGC [110045:110082](+) [110877:110911](+) trnA-UGC_copy2 [142674:142711](-) [141845:141879](-) trnL-GAU [143768:143803](-) [143716:143751](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [75287:75400](-) [104700:104930](-) [104137:104163](-) pafI [47667:47792](-) [46617:46842](-) [45667:45821](-) rps12_copy2 [75287:75400](-) [147826:148057](+) [148594:148619](+) clpP1 [77694:77760](-) [76469:76763](-) [75579:75807](-)