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, 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, 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, rps19_copy2, rps2, rps3, rps4, rps7, rps7_copy2, rps8 DNA dependent RNA polymerase rpoA, rpoC1, rpoC2 Subunit of rubisco rbcL c-type cytochrom synthesis gene ccsA Envelop membrane protein cemA Maturase matK Protease None Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor infA Conserved open reading frames ycf1, ycf15, ycf15_copy2, ycf15_copy3, ycf15_copy4, 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 ndhF Subunits of cytochrome b/f complex None Subunits of photosystem I None Subunits of photosystem II psbM, psbN Large subunit of ribosome None Small subunit of ribosome rps16 DNA dependent RNA polymerase rpoB Subunit of rubisco None c-type cytochrom synthesis gene None Envelop membrane protein None Maturase None Protease clpP Subunit of Acetyl-CoA-carboxylase None Translational initiation factor None Conserved open reading frames None Other genes None 2. Multicopy genes with different lengths: Genes Length Location rpl2 855 join{[90397:90785](-), [89304:89771](-)} rpl2_copy2 852 join{[157905:158290](+), [158919:159386](+)} ycf2 4272 join{[94053:95386](+), [95416:98355](+)} ycf2_copy2 4275 join{[153301:154637](-), [150335:153274](-)} ycf15 327 join{[98419:98578](+), [98884:99052](+)} ycf15_copy2 192 [104849:105041](-) ycf15_copy3 192 [143649:143841](+) ycf15_copy4 330 join{[150109:150271](-), [149638:149806](-)} ndhB 1626 join{[101352:102222](-), [99981:100737](-)} ndhB_copy2 1623 join{[146468:147335](+), [147953:148709](+)} ycf1 1392 [114619:116011](+) ycf1_copy2 5568 join{[129387:134071](-), [128473:129357](-)} 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [12884:13046](-) [11740:12149](-) ndhA (2/2) [125965:126520](-) [124318:124856](-) ndhB (2/2) [101353:102222](-) [99982:100737](-) ndhB_copy2 (2/2) [146469:147335](+) [147954:148709](+) petB (1/2) [80535:81233](+) petD (1/2) [82106:82645](+) rpl16 (1/2) [86173:86583](-) rpl2 (2/2) [90398:90785](-) [89305:89771](-) rpl2_copy2 (2/2) [157906:158290](+) [158920:159386](+) rpoC1 (2/2) [24038:24472](-) [21686:23302](-) rps12 (3/3) [74640:74753](-) [103634:103865](-) [103068:103096](-) rps12_copy2 (3/3) [74640:74753](-) [144826:145057](+) [145595:145623](+) ycf3 (3/3) [46430:46556](-) [45380:45609](-) [44489:44641](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: psbA 2 [1:648](-) [159930:159944](-)] ycf2 2 [94054:95386](+) [95417:98355](+)] ycf15 2 [98420:98578](+) [98885:99052](+)] ycf1_copy2 2 [129388:134071](-) [128474:129357](-)] ycf15_copy4 2 [150110:150271](-) [149639:149806](-)] ycf2_copy2 2 [153302:154637](-) [150336:153274](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon psbI ATA petN ATA psbC GTG atpE CTG cemA GTG psbL TTG psbH ATA rpl36 TTG rpl16 ATC rps19 GTG rpl2 ATA ycf2 TTG ycf15 GTG ndhD ATA ycf15_copy4 GTG ycf2_copy2 TTG rpl2_copy2 ATA rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 127 genes (103 unique genes). Including: 85 protein-coding genes (74 are unique) 34 tRNA genes (25 are unique) 8 rRNA genes (4 are unique) Details are as follows: 85 protein-coding genes (74 are unique) Genes Length Location accD 1485 [61530:63014](+) atpA 1524 [10149:11672](-) atpB 1497 [57055:58551](-) atpE 384 [56645:57028](-) atpF 573 [12884:13046](-) [11740:12149](-) atpH 246 [14035:14280](-) atpI 744 [15486:16229](-) ccsA 960 [118791:119750](+) cemA 690 [65690:66379](+) infA 234 [84735:84968](-) matK 1527 [1413:2939](-) ndhA 1095 [125965:126520](-) [124318:124856](-) ndhB 1626 [101353:102222](-) [99982:100737](-) ndhB_copy2 1623 [146469:147335](+) [147954:148709](+) ndhC 363 [53080:53442](-) ndhD 1488 [119963:121450](-) ndhE 306 [122192:122497](-) ndhG 531 [122861:123391](-) ndhH 1182 [126522:127703](-) ndhI 516 [123724:124239](-) ndhJ 477 [51756:52232](-) ndhK 858 [52343:53200](-) petA 963 [66589:67551](+) petB 699 [80535:81233](+) petD 540 [82106:82645](+) petG 114 [70969:71082](+) petL 96 [70691:70786](+) petN 99 [29607:29705](+) psaA 2253 [41565:43817](-) psaB 2205 [39335:41539](-) psaC 246 [121602:121847](-) psaI 111 [63638:63748](+) psaJ 135 [71966:72100](+) psbA 663 [1:648](-) [159930:159944](-) psbB 1527 [77366:78892](+) psbC 1452 [35919:37370](+) psbD 1062 [34940:36001](+) psbE 252 [69149:69400](-) psbF 120 [69020:69139](-) psbH 231 [79492:79722](+) psbI 162 [8267:8428](+) psbJ 123 [68622:68744](-) psbK 186 [7716:7901](+) psbL 132 [68881:69012](-) psbT 108 [79084:79191](+) psbZ 189 [38116:38304](+) rbcL 1428 [59369:60796](+) rpl14 369 [85676:86044](-) rpl16 411 [86173:86583](-) rpl2 855 [90398:90785](-) [89305:89771](-) rpl20 360 [73479:73838](-) rpl22 543 [88347:88889](-) rpl23 303 [90810:91112](-) rpl23_copy2 303 [157579:157881](+) rpl2_copy2 852 [157906:158290](+) [158920:159386](+) rpl32 165 [117262:117426](+) rpl33 201 [72513:72713](+) rpl36 129 [84512:84640](+) rpoA 1008 [82896:83903](-) rpoC1 2052 [24038:24472](-) [21686:23302](-) rpoC2 4146 [17391:21536](-) rps11 417 [83977:84393](-) rps12 375 [74640:74753](-) [103634:103865](-) [103068:103096](-) rps12_copy2 375 [74640:74753](-) [144826:145057](+) [145595:145623](+) rps14 303 [38901:39203](-) rps15 273 [127802:128074](-) rps18 318 [72889:73206](+) rps19 279 [88938:89216](-) rps19_copy2 279 [159475:159753](+) rps2 711 [16473:17183](-) rps3 657 [87746:88402](-) rps4 606 [47776:48381](-) rps7 468 [102546:103013](-) rps7_copy2 468 [145678:146145](+) rps8 399 [85090:85488](-) ycf1 1392 [114620:116011](+) ycf15 327 [98420:98578](+) [98885:99052](+) ycf15_copy2 192 [104850:105041](-) ycf15_copy3 192 [143650:143841](+) ycf15_copy4 330 [150110:150271](-) [149639:149806](-) ycf1_copy2 5568 [129388:134071](-) [128474:129357](-) ycf2 4272 [94054:95386](+) [95417:98355](+) ycf2_copy2 4275 [153302:154637](-) [150336:153274](-) ycf3 510 [46430:46556](-) [45380:45609](-) [44489:44641](-) ycf4 555 [64125:64679](+) 34 tRNA genes (25 are unique) Genes Location trnK-UUU [3685:3721](-) [1108:1142](-) trnQ-UUG [7312:7387](-) trnS-GCU [8597:8684](-) trnS-CGA [8994:9024](+) [9740:9801](+) trnR-UCU [9957:10028](+) trnC-GCA [29095:29165](+) trnD-GUC [31724:31801](-) trnT-GGU [33099:33172](+) trnS-UGA [37653:37745](-) trnG-GCC [38472:38543](+) trnM-CAU [38665:38739](-) trnS-GGA [47394:47480](+) trnT-UGU [48804:48878](-) trnL-UAA [50002:50036](+) [50560:50609](+) trnF-GAA [50968:51041](+) trnV [56118:56156](-) [55440:55465](-) trnM-CAU_copy2 [56339:56411](+) trnW-CCA [71215:71288](-) trnP-UGG [71451:71526](-) trnM-CAU_copy3 [91277:91351](-) trnL-CAA [99387:99469](-) trnV-GAC [105738:105809](+) trnE-UUC [107818:107849](+) [108792:108831](+) trnA-UGC [108896:108932](+) [109737:109772](+) trnR-ACG [113537:113611](+) trnN-GUU [114230:114303](-) trnL-UAG [118585:118664](+) trnN-GUU_copy2 [134388:134461](+) trnR-ACG_copy2 [135080:135154](-) trnA-UGC_copy2 [139759:139795](-) [138919:138954](-) trnE-UUC_copy2 [140842:140873](-) [139860:139899](-) trnV-GAC_copy2 [142882:142953](-) trnL-CAA_copy2 [149222:149304](+) trnM-CAU_copy4 [157340:157414](+) 8 rRNA genes (4 are unique) Genes Location rrn16S [106037:107527](-) rrn23S [109773:112739](+) rrn4.5S [112839:112941](-) rrn5S [113165:113295](+) rrn5S_copy2 [135396:135526](-) rrn4.5S_copy2 [135750:135852](+) rrn23S_copy2 [135952:138918](-) rrn16S_copy2 [141164:142654](+) This genome has 24 genes with intron(s). Details are as follows: 21 gene(s) have 1 intron(s) Genes Exons psbA [1:648](-) [159930:159944](-) atpF [12884:13046](-) [11740:12149](-) rpoC1 [24038:24472](-) [21686:23302](-) rpl2 [90398:90785](-) [89305:89771](-) ycf2 [94054:95386](+) [95417:98355](+) ycf15 [98420:98578](+) [98885:99052](+) ndhB [101353:102222](-) [99982:100737](-) ndhA [125965:126520](-) [124318:124856](-) ycf1_copy2 [129388:134071](-) [128474:129357](-) ndhB_copy2 [146469:147335](+) [147954:148709](+) ycf15_copy4 [150110:150271](-) [149639:149806](-) ycf2_copy2 [153302:154637](-) [150336:153274](-) rpl2_copy2 [157906:158290](+) [158920:159386](+) trnK-UUU [3685:3721](-) [1108:1142](-) trnS-CGA [8994:9024](+) [9740:9801](+) trnL-UAA [50002:50036](+) [50560:50609](+) trnV [56118:56156](-) [55440:55465](-) trnE-UUC [107818:107849](+) [108792:108831](+) trnA-UGC [108896:108932](+) [109737:109772](+) trnA-UGC_copy2 [139759:139795](-) [138919:138954](-) trnE-UUC_copy2 [140842:140873](-) [139860:139899](-) 3 gene(s) have 2 intron(s) Genes Exons rps12 [74640:74753](-) [103634:103865](-) [103068:103096](-) ycf3 [46430:46556](-) [45380:45609](-) [44489:44641](-) rps12_copy2 [74640:74753](-) [144826:145057](+) [145595:145623](+)