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, psbD_copy2, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ, ycf3 Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, rpl22, rpl23, rpl23_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 clpP Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor None 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 infA Conserved open reading frames ycf15 Other genes None 2. Multicopy genes with different lengths: Genes Length Location psbD 1062 [33544:34606](+) psbD_copy2 138 [153544:153682](+) ycf1 1407 [109681:111088](+) ycf1_copy2 5592 join{[127469:129788](-), [124166:127439](-)} 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [12540:12684](-) [11421:11830](-) clpP (3/3) [72199:72269](-) [71112:71405](-) [70246:70489](-) ndhA (2/2) [121657:122209](-) [120347:120885](-) ndhB (2/2) [96583:97357](-) [95121:95878](-) ndhB_copy2 (2/2) [142113:142887](+) [143592:144349](+) petB (2/2) [75153:75158](+) [75912:76553](+) petD (2/2) [76752:76759](+) [77481:77976](+) rpl16 (2/2) [82786:82794](-) [81431:81829](-) rpl2 (2/2) [85629:86013](-) [84533:84966](-) rpoC1 (2/2) [23096:23548](-) [20725:22326](-) rps12 (3/3) [69954:70067](-) [98753:98984](-) [98191:98216](-) rps12_copy2 (3/3) [69954:70067](-) [140486:140717](+) [141254:141279](+) rps16 (2/2) [5951:5990](-) [4827:5056](-) ycf3 (3/3) [45066:45189](-) [44112:44341](-) [43214:43366](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: ycf1_copy2 2 [127470:129788](-) [124167:127439](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon rpl2 ATA ndhD AAT 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 130 genes (112 unique genes). Including: 85 protein-coding genes (78 are unique) 37 tRNA genes (30 are unique) 8 rRNA genes (4 are unique) Details are as follows: 85 protein-coding genes (78 are unique) Genes Length Location accD 1446 [58404:59849](+) atpA 1524 [9831:11354](-) atpB 1497 [54127:55623](-) atpE 402 [53729:54130](-) atpF 555 [12540:12684](-) [11421:11830](-) atpH 246 [13087:13332](-) atpI 744 [14513:15256](-) ccsA 972 [114857:115828](+) cemA 690 [62082:62771](+) clpP 609 [72199:72269](-) [71112:71405](-) [70246:70489](-) matK 1527 [1904:3430](-) ndhA 1092 [121657:122209](-) [120347:120885](-) ndhB 1533 [96583:97357](-) [95121:95878](-) ndhB_copy2 1533 [142113:142887](+) [143592:144349](+) ndhC 363 [51098:51460](-) ndhD 1497 [116111:117607](-) ndhE 306 [118229:118534](-) ndhF 2199 [111074:113272](-) ndhG 534 [118795:119328](-) ndhH 1182 [122211:123392](-) ndhI 543 [119726:120268](-) ndhJ 477 [49763:50239](-) ndhK 684 [50349:51032](-) petA 969 [62978:63946](+) petB 648 [75153:75158](+) [75912:76553](+) petD 504 [76752:76759](+) [77481:77976](+) petG 114 [66382:66495](+) petL 96 [66121:66216](+) petN 90 [28904:28993](+) psaA 2253 [40313:42565](-) psaB 2205 [38083:40287](-) psaC 246 [117739:117984](-) psaI 111 [60459:60569](+) psaJ 135 [67290:67424](+) psbA 1062 [338:1399](-) psbB 1527 [72678:74204](+) psbC 1422 [34554:35975](+) psbD 1062 [33545:34606](+) psbD_copy2 138 [153545:153682](+) psbE 252 [64847:65098](-) psbF 120 [64718:64837](-) psbH 222 [74812:75033](+) psbI 132 [7736:7867](+) psbJ 123 [64337:64459](-) psbK 186 [7219:7404](+) psbL 117 [64579:64695](-) psbM 105 [30147:30251](-) psbN 132 [74572:74703](-) psbT 108 [74390:74497](+) psbZ 189 [36594:36782](+) rbcL 1428 [56305:57732](+) rpl14 369 [80941:81309](-) rpl16 408 [82786:82794](-) [81431:81829](-) rpl2 819 [85629:86013](-) [84533:84966](-) rpl20 354 [68829:69182](-) rpl22 546 [83582:84127](-) rpl23 282 [86038:86319](-) rpl23_copy2 282 [153151:153432](+) rpl32 174 [113884:114057](+) rpl33 201 [67849:68049](+) rpl36 114 [79764:79877](-) rpoA 1011 [78178:79188](-) rpoB 3213 [23554:26766](-) rpoC1 2055 [23096:23548](-) [20725:22326](-) rpoC2 4161 [16390:20550](-) rps11 393 [79254:79646](-) rps12 372 [69954:70067](-) [98753:98984](-) [98191:98216](-) rps12_copy2 372 [69954:70067](-) [140486:140717](+) [141254:141279](+) rps14 303 [37648:37950](-) rps15 264 [123509:123772](-) rps16 270 [5951:5990](-) [4827:5056](-) rps18 306 [68233:68538](+) rps19 210 [84189:84398](-) rps2 711 [15477:16187](-) rps3 657 [82941:83597](-) rps4 606 [46455:47060](-) rps7 468 [97670:98137](-) rps7_copy2 468 [141333:141800](+) rps8 399 [80341:80739](-) ycf1 1407 [109682:111088](+) ycf1_copy2 5592 [127470:129788](-) [124167:127439](-) ycf2 6828 [86627:93454](+) ycf2_copy2 6828 [146016:152843](-) ycf3 507 [45066:45189](-) [44112:44341](-) [43214:43366](-) ycf4 555 [61002:61556](+) 37 tRNA genes (30 are unique) Genes Location trnH-GUG [5:79](-) trnK-UUU [4165:4201](-) [1619:1653](-) trnQ-UUG [6822:6893](-) trnS-GCU [8045:8132](-) trnG-GCC [8705:8727](+) [9450:9497](+) trnR-UCU [9650:9721](+) trnC-GCA [28007:28077](+) trnD-GUC [30748:30821](-) trnY-GUA [31215:31298](-) trnE-UUC [31358:31430](-) trnT-GGU [32018:32089](+) trnS-UGA [36170:36261](-) trnG-UCC [37168:37238](+) trnfM-CAU [37412:37485](-) trnS-GGA [46064:46142](+) trnT-UGU [47437:47509](-) trnL-UAA [48223:48259](+) [48760:48815](+) trnF-GAA [49215:49287](+) trnV-UAC [53194:53230](-) [52568:52604](-) trnM-CAU [53421:53493](+) trnW-CCA [66636:66709](-) trnP-UGG [66872:66945](-) trnI-CAU [86485:86558](-) trnL-CAA [94476:94556](-) trnV-GAC [100852:100923](+) trnI-GAU [102936:102972](+) [103919:103953](+) trnA-UGC [104013:104050](+) [104836:104870](+) trnR-ACG [108620:108693](+) trnN-GUU [109287:109358](-) trnL-UAG [114663:114742](+) trnN-GUU_copy2 [130112:130183](+) trnR-ACG_copy2 [130777:130850](-) trnA-UGC_copy2 [135420:135457](-) [134600:134634](-) trnI-GAU_copy2 [136498:136534](-) [135517:135551](-) trnV-GAC_copy2 [138547:138618](-) trnL-CAA_copy2 [144914:144994](+) trnI-CAU_copy2 [152912:152985](+) 8 rRNA genes (4 are unique) Genes Location rrn16S [101151:102640](+) rrn23S [105023:107831](+) rrn4.5S [107931:108033](+) rrn5S [108258:108378](+) rrn5S_copy2 [131092:131212](-) rrn4.5S_copy2 [131437:131539](-) rrn23S_copy2 [131639:134447](-) rrn16S_copy2 [136830:138319](-) This genome has 23 genes with intron(s). Details are as follows: 19 gene(s) have 1 intron(s) Genes Exons rps16 [5951:5990](-) [4827:5056](-) atpF [12540:12684](-) [11421:11830](-) rpoC1 [23096:23548](-) [20725:22326](-) petB [75153:75158](+) [75912:76553](+) petD [76752:76759](+) [77481:77976](+) rpl16 [82786:82794](-) [81431:81829](-) rpl2 [85629:86013](-) [84533:84966](-) ndhB [96583:97357](-) [95121:95878](-) ndhA [121657:122209](-) [120347:120885](-) ycf1_copy2 [127470:129788](-) [124167:127439](-) ndhB_copy2 [142113:142887](+) [143592:144349](+) trnK-UUU [4165:4201](-) [1619:1653](-) trnG-GCC [8705:8727](+) [9450:9497](+) trnL-UAA [48223:48259](+) [48760:48815](+) trnV-UAC [53194:53230](-) [52568:52604](-) trnI-GAU [102936:102972](+) [103919:103953](+) trnA-UGC [104013:104050](+) [104836:104870](+) trnA-UGC_copy2 [135420:135457](-) [134600:134634](-) trnI-GAU_copy2 [136498:136534](-) [135517:135551](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [69954:70067](-) [98753:98984](-) [98191:98216](-) ycf3 [45066:45189](-) [44112:44341](-) [43214:43366](-) rps12_copy2 [69954:70067](-) [140486:140717](+) [141254:141279](+) clpP [72199:72269](-) [71112:71405](-) [70246:70489](-)