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, petB_copy2, petD, petD_copy2, petG, petL, petN Subunits of photosystem I psaA, psaB, psaC, psaI, psaJ Subunits of photosystem II psbA, psbB, psbB_copy2, psbC, psbD, psbE, psbF, psbH, psbH_copy2, psbI, psbJ, psbK, psbL, psbM, psbN, psbN_copy2, psbT, psbT_copy2, ycf3 Large subunit of ribosome rpl14, rpl14_copy2, rpl16, rpl16_copy2, rpl2, rpl20, rpl22, rpl22_copy2, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36, rpl36_copy2 Small subunit of ribosome rps11, rps11_copy2, rps12, rps12_copy2, rps14, rps15, rps16, rps18, rps19, rps19_copy2, rps2, rps3, rps3_copy2, rps4, rps7, rps7_copy2, rps8, rps8_copy2 DNA dependent RNA polymerase 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 None Translational initiation factor infA, infA_copy2 Conserved open reading frames ycf15, ycf15_copy2, ycf2, ycf2_copy2, ycf4 Other genes lhbA, psbG 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 psbZ Large subunit of ribosome None Small subunit of ribosome None DNA dependent RNA polymerase rpoA Subunit of rubisco None c-type cytochrom synthesis gene None Envelop membrane protein None Maturase None Protease None Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor None Conserved open reading frames ycf1 Other genes None 2. Multicopy genes with different lengths: Genes Length Location rpl2 819 join{[86383:86767](-), [85292:85727](-)} rpl2_copy2 933 join{[152812:153214](+), [153774:154305](+)} 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [12614:12773](-) [11497:11906](-) clpP (3/3) [73060:73128](-) [72035:72331](-) [71038:71313](-) ndhA (2/2) [116792:117358](+) [118395:118934](+) ndhB (2/2) [95940:96716](-) [94490:95248](-) ndhB_copy2 (2/2) [142882:143658](+) [144350:145108](+) petB (2/2) [76059:76064](+) [76837:77490](+) petB_copy2 (2/2) [163534:163539](-) [162108:162761](-) petD (2/2) [77688:77695](+) [78379:78877](+) petD_copy2 (2/2) [161903:161910](-) [160721:161219](-) rpl16 (2/2) [83557:83565](-) [82328:82726](-) rpl16_copy2 (2/2) [156033:156041](+) [156872:157270](+) rpl2 (2/2) [86384:86767](-) [85293:85727](-) rpl2_copy2 (2/2) [152813:153214](+) [153775:154305](+) rpoC1 (2/2) [22798:23232](-) [20431:22050](-) rps12 (3/3) [70436:70549](-) [98127:98358](-) [97565:97590](-) rps12_copy2 (3/3) [70436:70549](-) [141240:141471](+) [142008:142033](+) rps16 (2/2) [6071:6110](-) [4954:5150](-) ycf3 (3/3) [44873:45001](-) [43922:44149](-) [43024:43176](-) ### 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 psbH ATC rps19 GTG rpl2 ACG rpl2_copy2 ATC rps19_copy2 GTG psbH_copy2 ATC 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 145 genes (111 unique genes). Including: 100 protein-coding genes (78 are unique) 37 tRNA genes (29 are unique) 8 rRNA genes (4 are unique) Details are as follows: 100 protein-coding genes (78 are unique) Genes Length Location atpA 1524 [9911:11434](-) atpB 1497 [54665:56161](-) atpE 402 [54267:54668](-) atpF 570 [12614:12773](-) [11497:11906](-) atpH 246 [13232:13477](-) atpI 744 [14249:14992](-) ccsA 966 [123489:124454](-) cemA 690 [62419:63108](+) clpP 642 [73060:73128](-) [72035:72331](-) [71038:71313](-) infA 246 [80905:81150](-) infA_copy2 246 [158448:158693](+) lhbA 189 [36651:36839](+) matK 1530 [2085:3614](-) ndhA 1107 [116792:117358](+) [118395:118934](+) ndhB 1536 [95940:96716](-) [94490:95248](-) ndhB_copy2 1536 [142882:143658](+) [144350:145108](+) ndhC 363 [51179:51541](-) ndhD 1554 [121679:123232](+) ndhE 306 [120745:121050](+) ndhF 2235 [126333:128567](+) ndhG 531 [119984:120514](+) ndhH 1182 [115609:116790](+) ndhI 507 [119013:119519](+) ndhJ 477 [49859:50335](-) ndhK 858 [50442:51299](-) petA 969 [63330:64298](+) petB 660 [76059:76064](+) [76837:77490](+) petB_copy2 660 [163534:163539](-) [162108:162761](-) petD 507 [77688:77695](+) [78379:78877](+) petD_copy2 507 [161903:161910](-) [160721:161219](-) petG 114 [66935:67048](+) petL 96 [66657:66752](+) petN 90 [28639:28728](+) psaA 2253 [40320:42572](-) psaB 2205 [38090:40294](-) psaC 246 [121346:121591](+) psaI 111 [61191:61301](+) psaJ 135 [67843:67977](+) psbA 1062 [526:1587](-) psbB 1527 [73545:75071](+) psbB_copy2 1527 [164527:166053](-) psbC 1422 [34552:35973](+) psbD 1062 [33543:34604](+) psbE 252 [65170:65421](-) psbF 120 [65041:65160](-) psbG 747 [50442:51188](-) psbH 246 [75694:75939](+) psbH_copy2 246 [163659:163904](-) psbI 111 [7652:7762](+) psbJ 123 [64664:64786](-) psbK 186 [7040:7225](+) psbL 117 [64902:65018](-) psbM 105 [29377:29481](-) psbN 132 [75478:75609](-) psbN_copy2 132 [163989:164120](+) psbT 102 [75258:75359](+) psbT_copy2 102 [164239:164340](-) rbcL 1428 [56904:58331](+) rpl14 369 [81833:82201](-) rpl14_copy2 369 [157397:157765](+) rpl16 408 [83557:83565](-) [82328:82726](-) rpl16_copy2 408 [156033:156041](+) [156872:157270](+) rpl2 819 [86384:86767](-) [85293:85727](-) rpl20 354 [69284:69637](-) rpl22 519 [84362:84880](-) rpl22_copy2 519 [154718:155236](+) rpl23 282 [86786:87067](-) rpl23_copy2 282 [152531:152812](+) rpl2_copy2 933 [152813:153214](+) [153775:154305](+) rpl32 159 [125158:125316](-) rpl33 198 [68424:68621](+) rpl36 114 [80674:80787](-) rpl36_copy2 114 [158811:158924](+) rpoB 3213 [23259:26471](-) rpoC1 2055 [22798:23232](-) [20431:22050](-) rpoC2 4143 [16121:20263](-) rps11 465 [80086:80550](-) rps11_copy2 465 [159048:159512](+) rps12 372 [70436:70549](-) [98127:98358](-) [97565:97590](-) rps12_copy2 372 [70436:70549](-) [141240:141471](+) [142008:142033](+) rps14 303 [37658:37960](-) rps15 273 [115211:115483](+) rps16 237 [6071:6110](-) [4954:5150](-) rps18 303 [68796:69098](+) rps19 288 [84934:85221](-) rps19_copy2 288 [154377:154664](+) rps2 711 [15200:15910](-) rps3 657 [83721:84377](-) rps3_copy2 657 [155221:155877](+) rps4 606 [46245:46850](-) rps7 468 [97049:97516](-) rps7_copy2 468 [142082:142549](+) rps8 399 [81285:81683](-) rps8_copy2 399 [157915:158313](+) ycf15 228 [93844:94071](+) ycf15_copy2 228 [145527:145754](-) ycf2 6087 [87637:93723](+) ycf2_copy2 6087 [145875:151961](-) ycf3 510 [44873:45001](-) [43922:44149](-) [43024:43176](-) ycf4 555 [61709:62263](+) 37 tRNA genes (29 are unique) Genes Location trnH-GUG [1:75](-) trnK-UUU [4334:4370](-) [1799:1833](-) trnQ-UUG [6638:6709](-) trnS-GCU [7912:7999](-) trnR-UCU [9716:9787](+) trnC-GCA [27693:27773](+) trnD-GUC [30691:30764](-) trnY-GUA [31151:31234](-) trnE-UUC [31294:31365](-) trnT-GGU [32023:32094](+) trnS-UGA [36203:36295](-) trnG-UCC [37180:37250](+) trnfM-CAU [37421:37494](-) trnS-GGA [45864:45950](+) trnT-UGU [47247:47319](-) trnL-UAA [48076:48110](+) [48602:48651](+) trnF-GAA [49073:49145](+) trnV-UAC [53755:53793](-) [53131:53167](-) trnM-CAU [53986:54057](+) trnT-GGU_copy2 [53991:54049](+) trnW-CCA [67173:67246](-) trnP-UGG [67398:67471](-) trnI-CAU [87250:87323](-) trnL-CAA [94087:94167](-) trnV-GAC [100053:100124](+) trnI-GAU [102143:102184](+) [103124:103158](+) trnA-UGC [103223:103260](+) [104061:104095](+) trnR-ACG [107839:107912](+) trnN-GUU [108531:108602](-) trnL-UAG [124550:124629](-) trnN-GUU_copy2 [130996:131067](+) trnR-ACG_copy2 [131686:131759](-) trnA-UGC_copy2 [136338:136375](-) [135503:135537](-) trnI-GAU_copy2 [137414:137455](-) [136440:136474](-) trnV-GAC_copy2 [139474:139545](-) trnL-CAA_copy2 [145431:145511](+) trnI-CAU_copy2 [152275:152348](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [100352:101842](+) rrn23 [104224:107027](+) rrn4.5 [107126:107228](+) rrn5 [107454:107574](+) rrn5_copy2 [132024:132144](-) rrn4.5_copy2 [132370:132472](-) rrn23_copy2 [132571:135374](-) rrn16_copy2 [137756:139246](-) This genome has 25 genes with intron(s). Details are as follows: 21 gene(s) have 1 intron(s) Genes Exons rps16 [6071:6110](-) [4954:5150](-) atpF [12614:12773](-) [11497:11906](-) rpoC1 [22798:23232](-) [20431:22050](-) petB [76059:76064](+) [76837:77490](+) petD [77688:77695](+) [78379:78877](+) rpl16 [83557:83565](-) [82328:82726](-) rpl2 [86384:86767](-) [85293:85727](-) ndhB [95940:96716](-) [94490:95248](-) ndhA [116792:117358](+) [118395:118934](+) ndhB_copy2 [142882:143658](+) [144350:145108](+) rpl2_copy2 [152813:153214](+) [153775:154305](+) rpl16_copy2 [156033:156041](+) [156872:157270](+) petD_copy2 [161903:161910](-) [160721:161219](-) petB_copy2 [163534:163539](-) [162108:162761](-) trnK-UUU [4334:4370](-) [1799:1833](-) trnL-UAA [48076:48110](+) [48602:48651](+) trnV-UAC [53755:53793](-) [53131:53167](-) trnI-GAU [102143:102184](+) [103124:103158](+) trnA-UGC [103223:103260](+) [104061:104095](+) trnA-UGC_copy2 [136338:136375](-) [135503:135537](-) trnI-GAU_copy2 [137414:137455](-) [136440:136474](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [70436:70549](-) [98127:98358](-) [97565:97590](-) ycf3 [44873:45001](-) [43922:44149](-) [43024:43176](-) rps12_copy2 [70436:70549](-) [141240:141471](+) [142008:142033](+) clpP [73060:73128](-) [72035:72331](-) [71038:71313](-)