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, psbK, psbL, psbM, psbN, psbT, psbZ, ycf3 Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, 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 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 orf42, orf42_copy2 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 psbJ Large subunit of ribosome rpl22 Small subunit of ribosome rps16 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) [50786:50944](+) [51702:52109](+) clpP (3/3) [75280:75348](-) [74175:74465](-) [73355:73582](-) ndhA (2/2) [125904:126456](-) [124121:124665](-) ndhB (2/2) [100458:101180](-) [99017:99772](-) ndhB_copy2 (2/2) [146246:146968](+) [147654:148409](+) petB (2/2) [78320:78325](+) [79143:79784](+) petD (2/2) [79997:80004](+) [80714:81188](+) rpl16 (2/2) [86819:86827](-) [85259:85660](-) rpl2 (2/2) [89618:90010](-) [88521:88955](-) rpl2_copy2 (2/2) [157416:157808](+) [158471:158905](+) rpoC1 (2/2) [39919:40351](+) [41162:42717](+) rps12 (2/3) [73026:73139](-) [102625:102867](-) rps12_copy2 (2/3) [73026:73139](-) [144559:144801](+) ycf3 (3/3) [17138:17263](+) [17986:18213](+) [18995:19147](+) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: ycf68 2 [106935:106976](+) [107005:107424](+)] ndhI 2 [123560:124041](-) [123194:123230](-)] ycf1 2 [130554:133740](-) [128407:130514](-)] ycf68_copy2 2 [140450:140491](-) [140002:140421](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon psbL ACG rps19 GTG orf42 ATC ndhD ATC orf42_copy2 ATC 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 129 genes (110 unique genes). Including: 85 protein-coding genes (77 are unique) 36 tRNA genes (29 are unique) 8 rRNA genes (4 are unique) Details are as follows: 85 protein-coding genes (77 are unique) Genes Length Location accD 1506 [60176:61681](+) atpA 1533 [52185:53717](+) atpB 1488 [7331:8818](+) atpE 402 [8815:9216](+) atpF 567 [50786:50944](+) [51702:52109](+) atpH 246 [50123:50368](+) atpI 744 [48266:49009](+) ccsA 972 [118409:119380](+) cemA 690 [63530:64219](+) clpP 588 [75280:75348](-) [74175:74465](-) [73355:73582](-) matK 1326 [2253:3578](-) ndhA 1098 [125904:126456](-) [124121:124665](-) ndhB 1479 [100458:101180](-) [99017:99772](-) ndhB_copy2 1479 [146246:146968](+) [147654:148409](+) ndhC 363 [10821:11183](+) ndhD 1500 [119696:121195](-) ndhE 306 [121836:122141](-) ndhF 2256 [114150:116405](-) ndhG 531 [122377:122907](-) ndhH 1182 [126458:127639](-) ndhI 519 [123560:124041](-) [123194:123230](-) ndhJ 477 [12053:12529](+) ndhK 672 [11225:11896](+) orf42 129 [108044:108172](-) orf42_copy2 129 [139254:139382](+) petA 963 [64436:65398](+) petB 648 [78320:78325](+) [79143:79784](+) petD 483 [79997:80004](+) [80714:81188](+) petG 114 [68950:69063](+) petL 96 [68689:68784](+) petN 90 [34223:34312](-) psaA 2253 [20016:22268](+) psaB 2205 [22294:24498](+) psaC 246 [121324:121569](-) psaI 105 [62223:62327](+) psaJ 135 [70142:70276](+) psbA 1062 [312:1373](-) psbB 1527 [75816:77342](+) psbC 1422 [26828:28249](-) psbD 1062 [28197:29258](-) psbE 252 [67155:67406](-) psbF 120 [67026:67145](-) psbH 222 [77953:78174](+) psbI 111 [56131:56241](-) psbK 186 [56755:56940](-) psbL 117 [66887:67003](-) psbM 105 [32839:32943](+) psbN 132 [77711:77842](-) psbT 117 [77529:77645](+) psbZ 189 [25943:26131](-) rbcL 1428 [5127:6554](-) rpl14 369 [84757:85125](-) rpl16 411 [86819:86827](-) [85259:85660](-) rpl2 828 [89618:90010](-) [88521:88955](-) rpl20 360 [71804:72163](-) rpl23 276 [90035:90310](-) rpl23_copy2 276 [157116:157391](+) rpl2_copy2 828 [157416:157808](+) [158471:158905](+) rpl32 147 [117190:117336](+) rpl33 201 [70781:70981](+) rpl36 114 [83435:83548](-) rpoA 996 [81419:82414](-) rpoB 3213 [36680:39892](+) rpoC1 1989 [39919:40351](+) [41162:42717](+) rpoC2 4167 [42888:47054](+) rps11 417 [82497:82913](-) rps12 357 [73026:73139](-) [102625:102867](-) rps12_copy2 357 [73026:73139](-) [144559:144801](+) rps14 303 [24622:24924](+) rps15 273 [127751:128023](-) rps18 327 [71243:71569](+) rps19 279 [88182:88460](-) rps2 711 [47307:48017](+) rps3 657 [86989:87645](-) rps4 606 [15958:16563](+) rps7 468 [101553:102020](-) rps7_copy2 468 [145406:145873](+) rps8 405 [83985:84389](-) ycf1 5295 [130554:133740](-) [128407:130514](-) ycf2 6861 [90917:97777](+) ycf2_copy2 6861 [149649:156509](-) ycf3 507 [17138:17263](+) [17986:18213](+) [18995:19147](+) ycf4 555 [62512:63066](+) ycf68 462 [106935:106976](+) [107005:107424](+) ycf68_copy2 462 [140450:140491](-) [140002:140421](-) 36 tRNA genes (29 are unique) Genes Location trnH-GUG [42:116](-) trnK-UUU [4298:4334](-) [1690:1718](-) trnM-CAU [9374:9445](-) trnV-UAC [9629:9667](+) [10259:10295](+) trnF-GAA [13342:13414](-) trnL-UAA [14388:14424](-) [13802:13851](-) trnT-UGU [15609:15681](+) trnS-GGA [16790:16877](-) trnfM-CAU [25092:25165](+) trnG-UCC [25216:25286](-) trnS-UGA [26492:26584](+) trnT-GGU [30733:30804](-) trnE-UUC [31613:31685](+) trnY-GUA [31746:31829](+) trnD-GUC [32339:32412](+) trnC-GCA [35448:35518](-) trnR-UCU [53952:54023](-) trnS-GCU [55883:55969](+) trnQ-UUG [57577:57648](+) trnW-CCA [69196:69269](-) trnP-UGG [69445:69518](-) trnI-CAU [90755:90828](-) trnL-CAA [98359:98439](-) trnV-GAC [104723:104794](+) trnI-GAU [106794:106835](+) [107783:107817](+) trnA-UGC [107877:107914](+) [108715:108749](+) trnR-ACG [112530:112603](+) trnN-GUU [113233:113304](-) trnL-UAG [118203:118282](+) trnN-GUU_copy2 [134122:134193](+) trnR-ACG_copy2 [134823:134896](-) trnA-UGC_copy2 [139512:139549](-) [138677:138711](-) trnI-GAU_copy2 [140591:140632](-) [139609:139643](-) trnV-GAC_copy2 [142632:142703](-) trnL-CAA_copy2 [148987:149067](+) trnI-CAU_copy2 [156598:156671](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [105017:106507](+) rrn23 [108907:111721](+) rrn4.5 [111821:111924](+) rrn5 [112149:112269](+) rrn5_copy2 [135157:135277](-) rrn4.5_copy2 [135502:135605](-) rrn23_copy2 [135704:138518](-) rrn16_copy2 [140919:142409](-) This genome has 25 genes with intron(s). Details are as follows: 23 gene(s) have 1 intron(s) Genes Exons rps12 [73026:73139](-) [102625:102867](-) rpoC1 [39919:40351](+) [41162:42717](+) atpF [50786:50944](+) [51702:52109](+) rps12_copy2 [73026:73139](-) [144559:144801](+) petB [78320:78325](+) [79143:79784](+) petD [79997:80004](+) [80714:81188](+) rpl16 [86819:86827](-) [85259:85660](-) rpl2 [89618:90010](-) [88521:88955](-) ndhB [100458:101180](-) [99017:99772](-) ycf68 [106935:106976](+) [107005:107424](+) ndhI [123560:124041](-) [123194:123230](-) ndhA [125904:126456](-) [124121:124665](-) ycf1 [130554:133740](-) [128407:130514](-) ycf68_copy2 [140450:140491](-) [140002:140421](-) ndhB_copy2 [146246:146968](+) [147654:148409](+) rpl2_copy2 [157416:157808](+) [158471:158905](+) trnK-UUU [4298:4334](-) [1690:1718](-) trnV-UAC [9629:9667](+) [10259:10295](+) trnL-UAA [14388:14424](-) [13802:13851](-) trnI-GAU [106794:106835](+) [107783:107817](+) trnA-UGC [107877:107914](+) [108715:108749](+) trnA-UGC_copy2 [139512:139549](-) [138677:138711](-) trnI-GAU_copy2 [140591:140632](-) [139609:139643](-) 2 gene(s) have 2 intron(s) Genes Exons ycf3 [17138:17263](+) [17986:18213](+) [18995:19147](+) clpP [75280:75348](-) [74175:74465](-) [73355:73582](-)