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, 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, ycf2, ycf2_copy2, ycf4, ycf68, ycf68_copy2 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 None None None 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [14994:15138](-) [13747:14147](-) clpP (3/3) [77263:77333](-) [76154:76445](-) [75270:75515](-) ndhA (2/2) [129266:129818](-) [127658:128196](-) ndhB (2/2) [102187:102963](-) [100749:101504](-) ndhB_copy2 (2/2) [150834:151610](+) [152293:153048](+) petB (2/2) [80999:81004](+) [81061:81702](+) petD (2/2) [81905:81912](+) [82653:83127](+) rpl16 (2/2) [88099:88107](-) [86631:87029](-) rpl2 (2/2) [90925:91315](-) [89831:90261](-) rpl2_copy2 (2/2) [162482:162872](+) [163536:163966](+) rpoC1 (2/2) [25369:25821](-) [22992:24611](-) rps12 (3/3) [74971:75096](-) [104439:104670](-) [103881:103906](-) rps12_copy2 (3/3) [74971:75096](-) [149127:149358](+) [149891:149916](+) rps16 (2/2) [6624:6663](-) [5419:5615](-) ycf3 (3/3) [47366:47489](-) [46387:46616](-) [45443:45595](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: ycf68 2 [108788:108829](+) [108861:109163](+)] ycf68_copy2 2 [144968:145009](-) [144634:144936](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon rpl2 ACG ndhD ACG rpl2_copy2 ACG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 131 genes (113 unique genes). Including: 86 protein-coding genes (79 are unique) 37 tRNA genes (30 are unique) 8 rRNA genes (4 are unique) Details are as follows: 86 protein-coding genes (79 are unique) Genes Length Location accD 1479 [61850:63328](+) atpA 1524 [12146:13669](-) atpB 1497 [57393:58889](-) atpE 408 [56989:57396](-) atpF 546 [14994:15138](-) [13747:14147](-) atpH 246 [15638:15883](-) atpI 744 [16756:17499](-) ccsA 972 [121225:122196](+) cemA 477 [66507:66983](+) clpP 609 [77263:77333](-) [76154:76445](-) [75270:75515](-) matK 1539 [2336:3874](-) ndhA 1092 [129266:129818](-) [127658:128196](-) ndhB 1533 [102187:102963](-) [100749:101504](-) ndhB_copy2 1533 [150834:151610](+) [152293:153048](+) ndhC 363 [54236:54598](-) ndhD 1503 [122395:123897](-) ndhE 306 [125184:125489](-) ndhF 2304 [116827:119130](-) ndhG 531 [125852:126382](-) ndhH 1182 [129820:131001](-) ndhI 540 [127021:127560](-) ndhJ 477 [52918:53394](-) ndhK 747 [53499:54245](-) petA 963 [67216:68178](+) petB 648 [80999:81004](+) [81061:81702](+) petD 483 [81905:81912](+) [82653:83127](+) petG 114 [71345:71458](+) petL 96 [71080:71175](+) petN 90 [31453:31542](+) psaA 2253 [42522:44774](-) psaB 2205 [40292:42496](-) psaC 246 [124031:124276](-) psaI 111 [64254:64364](+) psaJ 129 [72256:72384](+) psbA 1062 [713:1774](-) psbB 1527 [77795:79321](+) psbC 1422 [36887:38308](+) psbD 1062 [35878:36939](+) psbE 252 [69601:69852](-) psbF 120 [69471:69590](-) psbH 222 [79919:80140](+) psbI 111 [9093:9203](+) psbJ 123 [69084:69206](-) psbK 189 [8423:8611](+) psbL 117 [69332:69448](-) psbM 105 [32724:32828](-) psbN 132 [79682:79813](-) psbT 102 [79508:79609](+) psbZ 189 [38861:39049](+) rbcL 1443 [59644:61086](+) rpl14 369 [86136:86504](-) rpl16 408 [88099:88107](-) [86631:87029](-) rpl2 822 [90925:91315](-) [89831:90261](-) rpl20 354 [73802:74155](-) rpl22 372 [88997:89368](-) rpl23 282 [91334:91615](-) rpl23_copy2 282 [162182:162463](+) rpl2_copy2 822 [162482:162872](+) [163536:163966](+) rpl32 174 [120234:120407](+) rpl33 201 [72824:73024](+) rpl36 114 [85006:85119](-) rpoA 1020 [83374:84393](-) rpoB 3219 [25827:29045](-) rpoC1 2073 [25369:25821](-) [22992:24611](-) rpoC2 4140 [18685:22824](-) rps11 417 [84467:84883](-) rps12 384 [74971:75096](-) [104439:104670](-) [103881:103906](-) rps12_copy2 384 [74971:75096](-) [149127:149358](+) [149891:149916](+) rps14 303 [39844:40146](-) rps15 279 [131105:131383](-) rps16 237 [6624:6663](-) [5419:5615](-) rps18 312 [73217:73528](+) rps19 279 [89465:89743](-) rps2 723 [17744:18466](-) rps3 657 [88270:88926](-) rps4 606 [48786:49391](-) rps7 483 [103344:103826](-) rps7_copy2 483 [149971:150453](+) rps8 399 [85581:85979](-) ycf1 5823 [132495:138317](-) ycf2 6924 [91950:98873](+) ycf2_copy2 6924 [154924:161847](-) ycf3 507 [47366:47489](-) [46387:46616](-) [45443:45595](-) ycf4 555 [64732:65286](+) ycf68 345 [108788:108829](+) [108861:109163](+) ycf68_copy2 345 [144968:145009](-) [144634:144936](-) 37 tRNA genes (30 are unique) Genes Location trnH [1:68](-) tRNA-Lys(UUU) [4625:4661](-) [2043:2084](-) tRNA-Gln(UUG) [7962:8033](-) tRNA-Ser(GCU) [9343:9430](-) tRNA-Gly(UCC) [10996:11019](+) [11754:11801](+) tRNA-Arg(UCU) [11932:12003](+) tRNA-Cys(GCA) [30520:30600](+) tRNA-Asp(GUC) [33293:33366](-) tRNA-Tyr(GUA) [33685:33768](-) tRNA-Glu(UUC) [33954:34026](-) tRNA-Thr(GGU) [34686:34757](+) tRNA-Ser(UGA) [38436:38528](-) tRNA-Gly(GCC) [39378:39448](+) tRNA-fMet(CAU) [39617:39690](-) tRNA-Ser(GGA) [48379:48482](+) tRNA-Thr(UGU) [49853:49925](-) tRNA-Leu(UAA) [51055:51091](+) [51605:51654](+) tRNA-Phe(GAA) [52027:52099](+) tRNA-Val(UAC) [56529:56566](-) [55897:55933](-) tRNA-Met [56751:56822](+) tRNA-Trp(CCA) [71581:71654](-) tRNA-Pro(UGG) [71819:71891](-) tRNA-Ile(CAU) [91808:91881](-) tRNA-Leu(CAA) [99905:99985](-) tRNA-Val(GAC) [106563:106634](+) tRNA-Ile(GAU) [108647:108688](+) [109631:109665](+) tRNA-Ala(UGC) [109730:109767](+) [110567:110601](+) tRNA-Arg(ACG) [114604:114677](+) tRNA-Asn(GUU) [115267:115338](-) tRNA-Leu(UAG) [121056:121135](+) tRNA-Asn(GUU)_copy2 [138459:138530](+) tRNA-Arg(ACG)_copy2 [139120:139193](-) tRNA-Ala(UGC)_copy2 [144030:144067](-) [143196:143230](-) tRNA-Ile(GAU)_copy2 [145109:145150](-) [144132:144166](-) tRNA-Val(GAC)_copy2 [147163:147234](-) tRNA-Leu(CAA)_copy2 [153812:153892](+) tRNA-Ile(CAU)_copy2 [161916:161989](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [106862:108352](+) rrn23 [110747:113809](+) rrn4.5 [113909:114011](+) rrn5 [114239:114359](+) rrn5_copy2 [139438:139558](-) rrn4.5_copy2 [139786:139888](-) rrn23_copy2 [139988:143050](-) rrn16_copy2 [145445:146935](-) This genome has 25 genes with intron(s). Details are as follows: 21 gene(s) have 1 intron(s) Genes Exons rps16 [6624:6663](-) [5419:5615](-) atpF [14994:15138](-) [13747:14147](-) rpoC1 [25369:25821](-) [22992:24611](-) petB [80999:81004](+) [81061:81702](+) petD [81905:81912](+) [82653:83127](+) rpl16 [88099:88107](-) [86631:87029](-) rpl2 [90925:91315](-) [89831:90261](-) ndhB [102187:102963](-) [100749:101504](-) ycf68 [108788:108829](+) [108861:109163](+) ndhA [129266:129818](-) [127658:128196](-) ycf68_copy2 [144968:145009](-) [144634:144936](-) ndhB_copy2 [150834:151610](+) [152293:153048](+) rpl2_copy2 [162482:162872](+) [163536:163966](+) tRNA-Lys(UUU) [4625:4661](-) [2043:2084](-) tRNA-Gly(UCC) [10996:11019](+) [11754:11801](+) tRNA-Leu(UAA) [51055:51091](+) [51605:51654](+) tRNA-Val(UAC) [56529:56566](-) [55897:55933](-) tRNA-Ile(GAU) [108647:108688](+) [109631:109665](+) tRNA-Ala(UGC) [109730:109767](+) [110567:110601](+) tRNA-Ala(UGC)_copy2 [144030:144067](-) [143196:143230](-) tRNA-Ile(GAU)_copy2 [145109:145150](-) [144132:144166](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [74971:75096](-) [104439:104670](-) [103881:103906](-) ycf3 [47366:47489](-) [46387:46616](-) [45443:45595](-) rps12_copy2 [74971:75096](-) [149127:149358](+) [149891:149916](+) clpP [77263:77333](-) [76154:76445](-) [75270:75515](-)