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, ndhA_copy2, ndhB, ndhC, ndhD, ndhD_copy2, ndhE, ndhE_copy2, ndhF, ndhG, ndhG_copy2, ndhH, ndhH_copy2, ndhI, ndhI_copy2, ndhJ, ndhK Subunits of cytochrome b/f complex petA, petB, petD, petG, petL, petN Subunits of photosystem I psaA, psaB, psaC, psaC_copy2, psaI, psaJ Subunits of photosystem II psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbT, psbZ Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, rpl22, rpl23, rpl32, rpl32_copy2, rpl32_copy3, rpl32_copy4, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps14, rps15, rps15_copy2, rps16, rps16_copy2, rps16_copy3, rps16_copy4, rps18, rps19, rps2, rps3, rps4, rps7, rps8 DNA dependent RNA polymerase rpoA, rpoB, rpoC1, rpoC2 Subunit of rubisco rbcL c-type cytochrom synthesis gene ccsA, ccsA_copy2 Envelop membrane protein cemA Maturase matK Protease None Subunit of Acetyl-CoA-carboxylase None Translational initiation factor None Conserved open reading frames ycf3/pafI, ycf4/pafII Other genes psbN/pbf1 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 psbN, ycf3 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 clpP Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor infA Conserved open reading frames ycf1, ycf15, ycf2, ycf4 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) [67431:67574](-) [66304:66714](-) ndhA (2/2) [134558:135109](+) [136214:136753](+) ndhA_copy2 (2/2) [163770:164321](-) [162126:162665](-) ndhB (2/2) [103002:103778](-) [101561:102316](-) petB (2/2) [41884:41889](+) [42597:43277](+) petD (2/2) [43468:43473](+) [44237:44713](+) rpl16 (2/2) [91806:91814](-) [90348:90773](-) rpl2 (1/2) [95107:95910](-) rpoC1 (2/2) [77929:78360](-) [75569:77200](-) rps12 (3/3) [30560:30673](+) [105194:105424](-) [104631:104657](-) rps16 (2/2) [109595:109633](+) [110518:110739](+) rps16_copy2 (2/2) [112245:112283](+) [113168:113389](+) rps16_copy3 (2/2) [186596:186634](-) [185490:185711](-) rps16_copy4 (2/2) [189246:189284](-) [188140:188361](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: psbA 2 [1:236](-) [190919:191744](-)] ycf3/pafI 3 [6262:6387](-) [5315:5542](-) [4430:4582](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon rps2 GTG rps19 GTG ndhD GTG ndhD_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 145 genes (112 unique genes). Including: 89 protein-coding genes (74 are unique) 48 tRNA genes (34 are unique) 8 rRNA genes (4 are unique) Details are as follows: 89 protein-coding genes (74 are unique) Genes Length Location atpA 1524 [64711:66234](-) atpB 1497 [15667:17163](+) atpE 414 [17160:17573](+) atpF 555 [67431:67574](-) [66304:66714](-) atpH 246 [67957:68202](-) atpI 744 [69348:70091](-) ccsA 963 [143752:144714](-) ccsA_copy2 963 [154165:155127](+) cemA 684 [21501:22184](+) matK 1521 [730:2250](-) ndhA 1092 [134558:135109](+) [136214:136753](+) ndhA_copy2 1092 [163770:164321](-) [162126:162665](-) ndhB 1533 [103002:103778](-) [101561:102316](-) ndhC 363 [11775:12137](-) ndhD 1521 [141986:143506](+) ndhD_copy2 1521 [155373:156893](-) ndhE 306 [141081:141386](+) ndhE_copy2 306 [157493:157798](-) ndhF 2244 [148016:150259](-) ndhG 534 [140327:140860](+) ndhG_copy2 534 [158019:158552](-) ndhH 1182 [133375:134556](+) ndhH_copy2 1182 [164323:165504](-) ndhI 534 [136854:137387](+) ndhI_copy2 534 [161492:162025](-) ndhJ 477 [10458:10934](-) ndhK 678 [11040:11717](-) petA 963 [22415:23377](+) petB 687 [41884:41889](+) [42597:43277](+) petD 483 [43468:43473](+) [44237:44713](+) petG 114 [34213:34326](-) petL 96 [34506:34601](-) petN 90 [28029:28118](-) psaA 2253 [57306:59558](-) psaB 2205 [55076:57280](-) psaC 246 [141631:141876](+) psaC_copy2 246 [157003:157248](-) psaI 111 [20174:20284](+) psaJ 135 [33193:33327](-) psbA 1062 [1:236](-) [190919:191744](-) psbB 1527 [39504:41030](+) psbC 1464 [50072:51535](+) psbD 1062 [49105:50166](+) psbE 252 [35884:36135](+) psbF 120 [36145:36264](+) psbH 222 [41540:41761](+) psbI 111 [62506:62616](+) psbJ 123 [36539:36661](+) psbK 186 [61902:62087](+) psbL 117 [36287:36403](+) psbM 105 [26798:26902](+) psbN/pbf1 132 [41301:41432](-) psbT 108 [41133:41240](+) psbZ 189 [52209:52397](+) rbcL 1428 [13465:14892](-) rpl14 396 [89854:90249](-) rpl16 435 [91806:91814](-) [90348:90773](-) rpl2 804 [95107:95910](-) rpl20 354 [31455:31808](+) rpl22 468 [94262:94729](-) rpl23 288 [95917:96204](-) rpl32 204 [145393:145596](-) rpl32_copy2 204 [147140:147343](-) rpl32_copy3 204 [151536:151739](+) rpl32_copy4 204 [153283:153486](+) rpl33 207 [32534:32740](-) rpl36 114 [88454:88567](-) rpoA 828 [86994:87821](-) rpoB 3207 [79064:82270](-) rpoC1 2064 [77929:78360](-) [75569:77200](-) rpoC2 4116 [71278:75393](-) rps11 420 [87921:88340](-) rps12 372 [30560:30673](+) [105194:105424](-) [104631:104657](-) rps14 303 [54634:54936](-) rps15 279 [133010:133288](+) rps15_copy2 279 [165591:165869](-) rps16 261 [109595:109633](+) [110518:110739](+) rps16_copy2 261 [112245:112283](+) [113168:113389](+) rps16_copy3 261 [186596:186634](-) [185490:185711](-) rps16_copy4 261 [189246:189284](-) [188140:188361](-) rps18 321 [32100:32420](-) rps19 279 [94775:95053](-) rps2 714 [70302:71015](-) rps3 687 [93591:94277](-) rps4 636 [7090:7725](-) rps7 471 [104106:104576](-) rps8 399 [89267:89665](-) ycf3/pafI 507 [6262:6387](-) [5315:5542](-) [4430:4582](-) ycf4/pafII 555 [20722:21276](+) 48 tRNA genes (34 are unique) Genes Location trnK-UUU [2967:3003](-) [427:461](-) trnS-GGA [6719:6805](+) trnT-UGU [8093:8165](-) trnL-UAA [8900:8936](+) [9429:9478](+) trnF-GAA [9860:9932](+) trnV-UAC [13219:13257](-) [12596:12630](-) trnM-CAU [17782:17853](-) trnE-UUC [24892:24964](+) trnY-GUA [25024:25107](+) trnD-GUC [25217:25290](+) trnC-GCA [28851:28921](-) trnP-UGG [33748:33821](+) trnP-GGG [33749:33819](+) trnW-CCA [34016:34089](+) trnT-GGU [47567:47638](+) trnS-UGA [51769:51861](-) trnG-GCC [52646:52716](+) trnG-GCC_copy2 [53061:53131](+) trnfM-CAU [53186:53259](-) trnG-GCC_copy3 [53457:53527](+) trnG-GCC_copy4 [53872:53942](+) trnfM-CAU_copy2 [53997:54070](-) trnG-GCC_copy5 [54268:54338](+) trnfM-CAU_copy3 [54393:54466](-) trnQ-UUG [61490:61561](-) trnS-GCU [62757:62844](-) trnS-GCA [63568:63599](+) [64261:64320](+) trnT-CGU [63569:63602](+) [64278:64320](+) trnS-CGA [63569:63591](+) [64282:64319](+) trnG-UCC [63570:63592](+) [64272:64319](+) trnR-UCU [64525:64596](+) trnI-CAU [96910:96983](-) trnL-CAA [100908:100988](-) trnV-GAC [107003:107074](+) trnH-GUG [108311:108384](+) trnI-GAU [119856:119897](+) [120839:120873](+) trnA-UGC [120938:120975](+) [121783:121817](+) trnR-ACG [125627:125700](+) trnN-GUU [126214:126285](-) trnL-UAG [144816:144895](-) trnL-UAG_copy2 [146563:146642](-) trnL-UAG_copy3 [152237:152316](+) trnL-UAG_copy4 [153984:154063](+) trnN-GUU_copy2 [172594:172665](+) trnR-ACG_copy2 [173179:173252](-) trnA-UGC_copy2 [177904:177941](-) [177062:177096](-) trnI-GAU_copy2 [178982:179023](-) [178006:178040](-) trnH-GUG_copy2 [190495:190568](-) 8 rRNA genes (4 are unique) Genes Location rrn16S [118065:119565](+) rrn23S [121970:124796](+) rrn4.5S [124897:125016](+) rrn5S [125259:125376](+) rrn5S_copy2 [173503:173620](-) rrn4.5S_copy2 [173863:173982](-) rrn23S_copy2 [174083:176909](-) rrn16S_copy2 [179314:180814](-) This genome has 26 genes with intron(s). Details are as follows: 24 gene(s) have 1 intron(s) Genes Exons psbA [1:236](-) [190919:191744](-) petB [41884:41889](+) [42597:43277](+) petD [43468:43473](+) [44237:44713](+) atpF [67431:67574](-) [66304:66714](-) rpoC1 [77929:78360](-) [75569:77200](-) rpl16 [91806:91814](-) [90348:90773](-) ndhB [103002:103778](-) [101561:102316](-) rps16 [109595:109633](+) [110518:110739](+) rps16_copy2 [112245:112283](+) [113168:113389](+) ndhA [134558:135109](+) [136214:136753](+) ndhA_copy2 [163770:164321](-) [162126:162665](-) rps16_copy3 [186596:186634](-) [185490:185711](-) rps16_copy4 [189246:189284](-) [188140:188361](-) trnK-UUU [2967:3003](-) [427:461](-) trnL-UAA [8900:8936](+) [9429:9478](+) trnV-UAC [13219:13257](-) [12596:12630](-) trnS-GCA [63568:63599](+) [64261:64320](+) trnT-CGU [63569:63602](+) [64278:64320](+) trnS-CGA [63569:63591](+) [64282:64319](+) trnG-UCC [63570:63592](+) [64272:64319](+) trnI-GAU [119856:119897](+) [120839:120873](+) trnA-UGC [120938:120975](+) [121783:121817](+) trnA-UGC_copy2 [177904:177941](-) [177062:177096](-) trnI-GAU_copy2 [178982:179023](-) [178006:178040](-) 2 gene(s) have 2 intron(s) Genes Exons ycf3/pafI [6262:6387](-) [5315:5542](-) [4430:4582](-) rps12 [30560:30673](+) [105194:105424](-) [104631:104657](-)