1. Annotated protein coding genes: Group of genes Name of genes Subunits of ATP synthase ORF224, atpA, atpB, atpE, atpF, atpH, atpI Subunits of NADH-dehydrogenase ORF224, ndhA, ndhB, ndhB_copy2, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK Subunits of cytochrome b/f complex ORF224, petA, petB, petD, petG, petL, petN Subunits of photosystem I ORF224, psaA, psaB, psaC, psaI, psaJ Subunits of photosystem II ORF224, psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ, ycf3 Large subunit of ribosome ORF224, rpl14, rpl16, rpl2, rpl20, rpl22, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36 Small subunit of ribosome ORF224, rps11, rps12, rps12_copy2, rps14, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps7_copy2, rps8 DNA dependent RNA polymerase ORF224, rpoA, rpoB, rpoC1, rpoC2 Subunit of rubisco ORF224, rbcL c-type cytochrom synthesis gene ORF224, ccsA Envelop membrane protein ORF224, cemA Maturase ORF224, matK Protease ORF224, clpP Subunit of Acetyl-CoA-carboxylase ORF224, accD Translational initiation factor ORF224 Conserved open reading frames ORF224, ycf1, ycf2, ycf2_copy2, ycf4 Other genes ORF224 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) [13956:14100](-) [12769:13178](-) clpP (3/3) [74297:74367](-) [73172:73463](-) [72343:72570](-) ndhA (2/2) [124021:124573](-) [122343:122881](-) ndhB (2/2) [98817:99593](-) [97375:98130](-) ndhB_copy2 (2/2) [144207:144983](+) [145670:146425](+) petB (2/2) [77318:77323](+) [78109:78750](+) petD (2/2) [78943:78950](+) [79677:80151](+) rpl16 (2/2) [85127:85135](-) [83634:84032](-) rpl2 (2/2) [87927:88317](-) [86828:87261](-) rpl2_copy2 (2/2) [155483:155873](+) [156539:156972](+) rpoC1 (2/2) [24132:24562](-) [21833:23444](-) rps12 (3/3) [72056:72169](-) [101014:101245](-) [100448:100473](-) rps12_copy2 (3/3) [72056:72169](-) [142555:142786](+) [143327:143352](+) rps16 (2/2) [6007:6046](-) [4939:5153](-) ycf3 (3/3) [46380:46506](-) [45403:45632](-) [44513:44665](-) ### 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 psbC GTG rps19 GTG ORF224 GTG ndhD ATA ndhE ATC ycf1 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 132 genes (103 unique genes). Including: 85 protein-coding genes (79 are unique) 39 tRNA genes (20 are unique) 8 rRNA genes (4 are unique) Details are as follows: 85 protein-coding genes (79 are unique) Genes Length Location ORF224 1200 [111723:112922](+) accD 1470 [59623:61092](+) atpA 1524 [11186:12709](-) atpB 1497 [55212:56708](-) atpE 411 [54805:55215](-) atpF 555 [13956:14100](-) [12769:13178](-) atpH 246 [14424:14669](-) atpI 744 [15610:16353](-) ccsA 972 [116958:117929](+) cemA 690 [63319:64008](+) clpP 591 [74297:74367](-) [73172:73463](-) [72343:72570](-) matK 1515 [1938:3452](-) ndhA 1092 [124021:124573](-) [122343:122881](-) ndhB 1533 [98817:99593](-) [97375:98130](-) ndhB_copy2 1533 [144207:144983](+) [145670:146425](+) ndhC 363 [52611:52973](-) ndhD 1569 [118199:119767](-) ndhE 306 [120341:120646](-) ndhF 2247 [112891:115137](-) ndhG 531 [120877:121407](-) ndhH 1182 [124575:125756](-) ndhI 501 [121762:122262](-) ndhJ 477 [51295:51771](-) ndhK 681 [51888:52568](-) petA 963 [64201:65163](+) petB 648 [77318:77323](+) [78109:78750](+) petD 483 [78943:78950](+) [79677:80151](+) petG 114 [68477:68590](+) petL 96 [68190:68285](+) petN 90 [29697:29786](+) psaA 2253 [41550:43802](-) psaB 2205 [39320:41524](-) psaC 246 [119850:120095](-) psaI 114 [61811:61924](+) psaJ 135 [69404:69538](+) psbA 1062 [278:1339](-) psbB 1521 [74836:76356](+) psbC 1386 [35674:37059](+) psbD 1062 [34629:35690](+) psbE 252 [66682:66933](-) psbF 120 [66553:66672](-) psbH 222 [76961:77182](+) psbI 111 [8387:8497](+) psbJ 123 [66161:66283](-) psbK 186 [7826:8011](+) psbL 117 [66414:66530](-) psbM 105 [30682:30786](-) psbN 132 [76716:76847](-) psbT 108 [76548:76655](+) psbZ 189 [37722:37910](+) rbcL 1428 [57489:58916](+) rpl14 369 [83121:83489](-) rpl16 408 [85127:85135](-) [83634:84032](-) rpl2 825 [87927:88317](-) [86828:87261](-) rpl20 354 [70911:71264](-) rpl22 504 [85917:86420](-) rpl23 282 [88336:88617](-) rpl23_copy2 282 [155183:155464](+) rpl2_copy2 825 [155483:155873](+) [156539:156972](+) rpl32 162 [115783:115944](+) rpl33 201 [69956:70156](+) rpl36 114 [81969:82082](-) rpoA 1002 [80356:81357](-) rpoB 3213 [24589:27801](-) rpoC1 2043 [24132:24562](-) [21833:23444](-) rpoC2 4173 [17479:21651](-) rps11 417 [81425:81841](-) rps12 372 [72056:72169](-) [101014:101245](-) [100448:100473](-) rps12_copy2 372 [72056:72169](-) [142555:142786](+) [143327:143352](+) rps14 303 [38895:39197](-) rps15 273 [125860:126132](-) rps16 255 [6007:6046](-) [4939:5153](-) rps18 306 [70328:70633](+) rps19 279 [86486:86764](-) rps2 711 [16565:17275](-) rps3 657 [85276:85932](-) rps4 606 [47500:48105](-) rps7 468 [99927:100394](-) rps7_copy2 468 [143406:143873](+) rps8 405 [82568:82972](-) ycf1 5553 [126525:132077](-) ycf2 6849 [88941:95789](+) ycf2_copy2 6849 [148011:154859](-) ycf3 510 [46380:46506](-) [45403:45632](-) [44513:44665](-) ycf4 555 [62348:62902](+) 39 tRNA genes (20 are unique) Genes Location trnH [44:118](-) trnK [4175:4211](-) [1636:1670](-) trnQ [7379:7451](-) trnS [8603:8690](+) trnG [9482:9504](+) [10189:10236](+) trnR [10551:10622](+) trnC [28736:28807](+) trnD [31882:31955](-) trnY [32273:32356](-) trnE [32416:32488](-) trnT [33455:33526](-) trnS_copy2 [37289:37381](-) trnG_copy2 [38411:38481](+) trnM [38672:38745](-) trnS_copy3 [47120:47206](+) trnT_copy2 [48425:48497](-) trnL [49556:49590](+) [50099:50148](+) trnF [50520:50592](+) trnV [54350:54387](-) [53708:53742](-) trnM_copy2 [54558:54630](+) trnW [68706:68779](-) trnP [68943:69016](-) trnI [88779:88852](-) trnL_copy2 [96726:96806](-) trnV_copy2 [102903:102974](+) trnV_copy3 [102904:102975](+) trnI_copy2 [104990:105026](+) [105843:105877](+) trnA [105950:105987](+) [106790:106824](+) trnR_copy2 [110637:110710](+) trnN [111330:111401](-) trnL_copy3 [116776:116855](+) trnN_copy2 [132399:132470](+) trnR_copy3 [133090:133163](-) trnA_copy2 [137813:137850](-) [136976:137010](-) trnI_copy3 [138774:138810](-) [137923:137957](-) trnV_copy4 [140825:140896](-) trnV_copy5 [140826:140897](-) trnL_copy4 [146994:147074](+) trnI_copy4 [154948:155021](+) 8 rRNA genes (4 are unique) Genes Location 16SrRNA [103203:104694](+) 23SrRNA [106977:109786](+) 4.5SrRNA [109885:109987](+) 5SrRNA [110248:110368](+) 5SrRNA_copy2 [133432:133552](-) 4.5SrRNA_copy2 [133813:133915](-) 23SrRNA_copy2 [134014:136823](-) 16SrRNA_copy2 [139107:140597](-) This genome has 23 genes with intron(s). Details are as follows: 19 gene(s) have 1 intron(s) Genes Exons rps16 [6007:6046](-) [4939:5153](-) atpF [13956:14100](-) [12769:13178](-) rpoC1 [24132:24562](-) [21833:23444](-) petB [77318:77323](+) [78109:78750](+) petD [78943:78950](+) [79677:80151](+) rpl16 [85127:85135](-) [83634:84032](-) rpl2 [87927:88317](-) [86828:87261](-) ndhB [98817:99593](-) [97375:98130](-) ndhA [124021:124573](-) [122343:122881](-) ndhB_copy2 [144207:144983](+) [145670:146425](+) rpl2_copy2 [155483:155873](+) [156539:156972](+) trnK [4175:4211](-) [1636:1670](-) trnG [9482:9504](+) [10189:10236](+) trnL [49556:49590](+) [50099:50148](+) trnV [54350:54387](-) [53708:53742](-) trnI_copy2 [104990:105026](+) [105843:105877](+) trnA [105950:105987](+) [106790:106824](+) trnA_copy2 [137813:137850](-) [136976:137010](-) trnI_copy3 [138774:138810](-) [137923:137957](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [72056:72169](-) [101014:101245](-) [100448:100473](-) ycf3 [46380:46506](-) [45403:45632](-) [44513:44665](-) rps12_copy2 [72056:72169](-) [142555:142786](+) [143327:143352](+) clpP [74297:74367](-) [73172:73463](-) [72343:72570](-)