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, 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, 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 None Maturase matK Protease clpP Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor infA Conserved open reading frames ycf15, ycf15_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 psbM Large subunit of ribosome None Small subunit of ribosome rps16 DNA dependent RNA polymerase None Subunit of rubisco None c-type cytochrom synthesis gene None Envelop membrane protein cemA Maturase None Protease None Subunit of Acetyl-CoA-carboxylase None Translational initiation factor None Conserved open reading frames ycf1 Other genes None 2. Multicopy genes with different lengths: Genes Length Location rps12 372 join{[74116:74230](-), [102586:102818](-), [102024:102050](-)} rps12_copy2 264 join{[74116:74230](-), [144506:144630](+), [145274:145300](+)} rpl2 855 join{[89903:90309](-), [88813:89262](-)} rpl2_copy2 846 join{[157027:157426](+), [158064:158511](+)} ycf2 4737 [93100:97837](+) ycf2_copy2 6936 [149487:156423](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [13464:13626](-) [12385:12794](-) clpP (3/3) [76299:76368](-) [75210:75507](-) [74319:74562](-) ndhA (2/2) [125541:126096](-) [123829:124367](-) ndhB (2/2) [100398:101174](-) [98948:99703](-) ndhB_copy2 (2/2) [146151:146927](+) [147622:148377](+) petB (1/2) [80072:80758](+) petD (1/2) [81612:82157](+) rpl16 (1/2) [85573:85983](-) rpl2 (2/2) [89904:90309](-) [88814:89262](-) rpl2_copy2 (2/2) [157028:157426](+) [158065:158511](+) rpoC1 (2/2) [24161:24595](-) [21786:23390](-) rps12 (3/3) [74117:74230](-) [102587:102818](-) [102025:102050](-) rps12_copy2 (3/3) [74117:74230](-) [144507:144630](+) [145275:145300](+) ycf3 (3/3) [47428:47561](-) [46473:46701](-) [45559:45711](-) ### 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 petB ATA rpl16 ATC rps19 GTG rpl2 ATA ycf2 TTG ndhD GTG rpl2_copy2 ACG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 119 genes (104 unique genes). Including: 83 protein-coding genes (76 are unique) 29 tRNA genes (24 are unique) 7 rRNA genes (4 are unique) Details are as follows: 83 protein-coding genes (76 are unique) Genes Length Location accD 1494 [61228:62721](+) atpA 1524 [10780:12303](-) atpB 1497 [56734:58230](-) atpE 402 [56336:56737](-) atpF 573 [13464:13626](-) [12385:12794](-) atpH 246 [14229:14474](-) atpI 744 [15552:16295](-) ccsA 972 [117942:118913](+) clpP 612 [76299:76368](-) [75210:75507](-) [74319:74562](-) infA 234 [84222:84455](-) matK 1536 [2429:3964](-) ndhA 1095 [125541:126096](-) [123829:124367](-) ndhB 1533 [100398:101174](-) [98948:99703](-) ndhB_copy2 1533 [146151:146927](+) [147622:148377](+) ndhC 363 [54258:54620](-) ndhD 1521 [119220:120740](-) ndhE 306 [121471:121776](-) ndhF 2217 [113779:115995](-) ndhG 531 [122033:122563](-) ndhH 1182 [126098:127279](-) ndhI 543 [123204:123746](-) ndhJ 477 [52867:53343](-) ndhK 684 [53496:54179](-) petA 963 [66203:67165](+) petB 687 [80072:80758](+) petD 546 [81612:82157](+) petG 114 [69993:70106](+) petL 96 [69705:69800](+) petN 90 [29759:29848](+) psaA 2253 [42669:44921](-) psaB 2205 [40439:42643](-) psaC 246 [120846:121091](-) psaI 111 [63507:63617](+) psaJ 135 [71353:71487](+) psbA 1062 [621:1682](-) psbB 1527 [76824:78350](+) psbC 1386 [36739:38124](+) psbD 1062 [35694:36755](+) psbE 252 [68139:68390](-) psbF 120 [68010:68129](-) psbH 222 [78946:79167](+) psbI 111 [8619:8729](+) psbJ 123 [67626:67748](-) psbK 186 [8006:8191](+) psbL 117 [67868:67984](-) psbN 132 [78705:78836](-) psbT 108 [78539:78646](+) psbZ 189 [38732:38920](+) rbcL 1449 [59017:60465](+) rpl14 369 [85052:85420](-) rpl16 411 [85573:85983](-) rpl2 855 [89904:90309](-) [88814:89262](-) rpl20 363 [72967:73329](-) rpl22 525 [87846:88370](-) rpl23 282 [90316:90597](-) rpl23_copy2 282 [156728:157009](+) rpl2_copy2 846 [157028:157426](+) [158065:158511](+) rpl32 174 [117054:117227](+) rpl33 201 [72008:72208](+) rpl36 114 [83993:84106](-) rpoA 1020 [82370:83389](-) rpoB 3213 [24622:27834](-) rpoC1 2040 [24161:24595](-) [21786:23390](-) rpoC2 2166 [17451:19616](+) rps11 417 [83455:83871](-) rps12 372 [74117:74230](-) [102587:102818](-) [102025:102050](-) rps12_copy2 264 [74117:74230](-) [144507:144630](+) [145275:145300](+) rps14 303 [40000:40302](-) rps15 273 [127396:127668](-) rps18 306 [72373:72678](+) rps19 279 [88432:88710](-) rps2 711 [16519:17229](-) rps3 657 [87205:87861](-) rps4 606 [48865:49470](-) rps7 468 [101504:101971](-) rps7_copy2 468 [145354:145821](+) rps8 399 [84462:84860](-) ycf15 399 [103638:104036](-) ycf15_copy2 399 [143289:143687](+) ycf2 4737 [93101:97837](+) ycf2_copy2 6936 [149488:156423](-) ycf3 516 [47428:47561](-) [46473:46701](-) [45559:45711](-) ycf4 555 [64024:64578](+) 29 tRNA genes (24 are unique) Genes Location trnH-GTG [17:90](-) trnQ-TTG [7609:7680](-) trnS-GCT [8871:8958](-) trnR-TCT [10590:10661](+) trnC-GCA [29200:29270](+) trnD-GTC [32135:32208](-) trnY-GTA [32730:32813](-) trnE-TTC [32873:32945](-) trnT-GGT [34053:34124](+) trnS-TGA [38305:38397](-) trnG-GCC [39515:39585](+) trnfM-CAT [39747:39820](-) trnS-GGA [48480:48569](+) trnT-TGT [49840:49912](-) trnF-GAA [52020:52092](+) trnM-CAT [56008:56080](+) trnW-CCA [70253:70326](-) trnP-TGG [70498:70571](-) trnI-CAT [90760:90833](-) trnL-CAA [98313:98393](-) trnV-GAC [104722:104793](+) trnR-ACG [112492:112565](+) trnN-GTT [113218:113289](-) trnL-TAG [117750:117829](+) trnN-GTT_copy2 [134054:134125](+) trnR-ACG_copy2 [134760:134833](-) trnV-GAC_copy2 [142532:142603](-) trnL-CAA_copy2 [148932:149012](+) trnI-CAT_copy2 [156492:156565](+) 7 rRNA genes (4 are unique) Genes Location rrn23S [108303:111717](+) rrn4.5 [111817:111919](-) rrn5 [112142:112272](+) rrn5_copy2 [135053:135183](-) rrn4.5_copy2 [135406:135508](+) rrn23S_copy2 [135608:139022](-) rrn16S [140814:142304](+) This genome has 11 genes with intron(s). Details are as follows: 7 gene(s) have 1 intron(s) Genes Exons atpF [13464:13626](-) [12385:12794](-) rpoC1 [24161:24595](-) [21786:23390](-) rpl2 [89904:90309](-) [88814:89262](-) ndhB [100398:101174](-) [98948:99703](-) ndhA [125541:126096](-) [123829:124367](-) ndhB_copy2 [146151:146927](+) [147622:148377](+) rpl2_copy2 [157028:157426](+) [158065:158511](+) 4 gene(s) have 2 intron(s) Genes Exons rps12 [74117:74230](-) [102587:102818](-) [102025:102050](-) ycf3 [47428:47561](-) [46473:46701](-) [45559:45711](-) rps12_copy2 [74117:74230](-) [144507:144630](+) [145275:145300](+) clpP [76299:76368](-) [75210:75507](-) [74319:74562](-)