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, psbM, psbN, psbT, psbZ, ycf3 Large subunit of ribosome rpl14, rpl14_copy2, rpl16, rpl16_copy2, rpl2, rpl20, rpl22, rpl22_copy2, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36 Small subunit of ribosome rps11, 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 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 infA, infA_copy2 Conserved open reading frames ycf1, ycf2, ycf2_copy2, ycf4, ycf68 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 None 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 None Subunit of Acetyl-CoA-carboxylase None Translational initiation factor None Conserved open reading frames ycf15 Other genes None 2. Multicopy genes with different lengths: Genes Length Location rpl16 408 join{[82187:82196](-), [80811:81210](-)} rpl16_copy2 411 [157714:158125](+) rpl22 540 [83001:83541](-) rpl22_copy2 486 [155449:155935](+) ycf2 6834 [86022:92856](+) ycf2_copy2 6819 [146080:152899](-) ndhB 1479 join{[95595:96318](-), [94137:94893](-)} ndhB_copy2 1533 join{[142564:143341](+), [144043:144799](+)} 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [16581:16725](-) [15431:15840](-) clpP (3/3) [71650:71720](-) [70565:70856](-) [69611:69856](-) ndhA (2/2) [122031:122582](-) [120488:121027](-) ndhB (2/2) [95596:96318](-) [94138:94893](-) ndhB_copy2 (2/2) [142565:143341](+) [144044:144799](+) petB (2/2) [74615:74620](+) [75402:76043](+) petD (2/2) [76248:76255](+) [76988:77483](+) rpl16 (2/2) [82188:82196](-) [80812:81210](-) rpl16_copy2 (1/2) [157715:158125](+) rpl2 (2/2) [85025:85427](-) [83940:84373](-) rpl2_copy2 (2/2) [153510:153912](+) [154564:154997](+) rpoC1 (2/2) [27100:27552](-) [24721:26331](-) rps12 (3/3) [69337:69450](-) [97784:98012](-) [97217:97272](-) rps12_copy2 (3/3) [69337:69450](-) [140925:141153](+) [141665:141720](+) rps16 (2/2) [1194:1233](+) [2122:2342](+) ycf3 (3/3) [49097:49222](-) [48143:48370](-) [47243:47395](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: rps4 2 [159562:159564](+) [1:630](+)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon rps19 GTG rpl2 ATA ndhD ATA ycf68 CTG ycf2_copy2 GTG rpl2_copy2 ATA rps19_copy2 GTG rpl16_copy2 ATC 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 137 genes (113 unique genes). Including: 93 protein-coding genes (80 are unique) 36 tRNA genes (29 are unique) 8 rRNA genes (4 are unique) Details are as follows: 93 protein-coding genes (80 are unique) Genes Length Location accD 1443 [57442:58884](+) atpA 1524 [13841:15364](-) atpB 1503 [52908:54410](-) atpE 402 [52510:52911](-) atpF 555 [16581:16725](-) [15431:15840](-) atpH 246 [17162:17407](-) atpI 744 [18518:19261](-) ccsA 966 [114913:115878](+) cemA 690 [61131:61820](+) clpP 609 [71650:71720](-) [70565:70856](-) [69611:69856](-) infA 171 [79395:79565](-) infA_copy2 171 [159372:159542](+) matK 1530 [3790:5319](+) ndhA 1092 [122031:122582](-) [120488:121027](-) ndhB 1479 [95596:96318](-) [94138:94893](-) ndhB_copy2 1533 [142565:143341](+) [144044:144799](+) ndhC 363 [12036:12398](-) ndhD 1479 [116118:117596](-) ndhE 303 [118272:118574](-) ndhF 2232 [110416:112647](-) ndhG 534 [118859:119392](-) ndhH 1182 [122584:123765](-) ndhI 543 [119872:120414](-) ndhJ 477 [10683:11159](-) ndhK 678 [11295:11972](-) petA 969 [62028:62996](+) petB 648 [74615:74620](+) [75402:76043](+) petD 504 [76248:76255](+) [76988:77483](+) petG 114 [65826:65939](+) petL 96 [65546:65641](+) petN 90 [32366:32455](+) psaA 2253 [44251:46503](-) psaB 2205 [42021:44225](-) psaC 246 [117783:118028](-) psaI 111 [59422:59532](+) psaJ 165 [66691:66855](+) psbA 1062 [5891:6952](+) psbB 1527 [72130:73656](+) psbC 1422 [38549:39970](+) psbD 1062 [37540:38601](+) psbE 252 [63920:64171](-) psbF 120 [63791:63910](-) psbH 222 [74274:74495](+) psbI 111 [8483:8593](+) psbJ 123 [63410:63532](-) psbK 186 [7894:8079](+) psbL 117 [63652:63768](-) psbM 105 [33251:33355](-) psbN 132 [74040:74171](-) psbT 108 [73846:73953](+) psbZ 189 [40585:40773](+) rbcL 1428 [55279:56706](+) rpl14 369 [80301:80669](-) rpl14_copy2 369 [158268:158636](+) rpl16 408 [82188:82196](-) [80812:81210](-) rpl16_copy2 411 [157715:158125](+) rpl2 837 [85025:85427](-) [83940:84373](-) rpl20 354 [68192:68545](-) rpl22 540 [83002:83541](-) rpl22_copy2 486 [155450:155935](+) rpl23 282 [85434:85715](-) rpl23_copy2 282 [153222:153503](+) rpl2_copy2 837 [153510:153912](+) [154564:154997](+) rpl32 222 [113717:113938](+) rpl33 201 [67247:67447](+) rpl36 114 [79262:79375](-) rpoA 1044 [77635:78678](-) rpoB 3213 [27558:30770](-) rpoC1 2064 [27100:27552](-) [24721:26331](-) rpoC2 4152 [20402:24553](-) rps11 417 [78727:79143](-) rps12 399 [69337:69450](-) [97784:98012](-) [97217:97272](-) rps12_copy2 399 [69337:69450](-) [140925:141153](+) [141665:141720](+) rps14 303 [41587:41889](-) rps15 273 [123906:124178](-) rps16 261 [1194:1233](+) [2122:2342](+) rps18 306 [67636:67941](+) rps19 279 [83601:83879](-) rps19_copy2 279 [155058:155336](+) rps2 711 [19481:20191](-) rps3 657 [82361:83017](-) rps3_copy2 657 [155920:156576](+) rps4 633 [159562:159564](+) [1:630](+) rps7 468 [96696:97163](-) rps7_copy2 468 [141774:142241](+) rps8 399 [79685:80083](-) rps8_copy2 399 [158854:159252](+) ycf1 3909 [124584:128492](-) ycf2 6834 [86023:92856](+) ycf2_copy2 6819 [146081:152899](-) ycf3 507 [49097:49222](-) [48143:48370](-) [47243:47395](-) ycf4 555 [59980:60534](+) ycf68 285 [136575:136859](-) 36 tRNA genes (29 are unique) Genes Location trnK-UUU [2993:3029](+) [5576:5610](+) trnH-GUG [7286:7359](+) trnQ-UUG [7486:7557](-) trnS-GCU [8680:8767](-) trnL-UAA [9344:9378](+) [9871:9920](+) trnF-GAA [10070:10142](+) trnG-UCC [12700:12722](+) [13434:13481](+) trnR-UCU [13640:13711](+) trnC-GCA [31852:31922](+) trnD-GUC [34510:34583](-) trnY-GUA [34961:35044](-) trnE-UUC [35104:35176](-) trnT-GGU [35897:35968](+) trnS-UGA [40167:40259](-) trnG-GCC [41102:41172](+) trnfM-CAU [41351:41424](-) trnS-GGA [50141:50227](+) trnV-UAC [51965:52002](-) [51346:51380](-) trnM-CAU [52182:52254](+) trnW-CCA [66085:66158](-) trnP-UGG [66322:66395](-) trnI-CAU [85881:85954](-) trnL-CAA [93497:93577](-) trnV-GAC [99842:99913](+) trnI-GAU [101923:101959](+) [102907:102941](+) trnA-UGC [103006:103043](+) [103857:103891](+) trnR-ACG [107633:107706](+) trnN-GUU [108322:108393](-) trnL-UAG [114718:114797](+) trnN-GUU_copy2 [130544:130615](+) trnR-ACG_copy2 [131231:131304](-) trnA-UGC_copy2 [135894:135931](-) [135046:135080](-) trnI-GAU_copy2 [136978:137014](-) [135996:136030](-) trnV-GAC_copy2 [139024:139095](-) trnL-CAA_copy2 [145360:145440](+) trnI-CAU_copy2 [152983:153056](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [100142:101632](+) rrn23 [104044:106851](+) rrn4.5 [106952:107054](+) rrn5 [107279:107399](+) rrn5_copy2 [131538:131658](-) rrn4.5_copy2 [131883:131985](-) rrn23_copy2 [132086:134893](-) rrn16_copy2 [137305:138795](-) This genome has 24 genes with intron(s). Details are as follows: 20 gene(s) have 1 intron(s) Genes Exons rps4 [159562:159564](+) [1:630](+) rps16 [1194:1233](+) [2122:2342](+) atpF [16581:16725](-) [15431:15840](-) rpoC1 [27100:27552](-) [24721:26331](-) petB [74615:74620](+) [75402:76043](+) petD [76248:76255](+) [76988:77483](+) rpl16 [82188:82196](-) [80812:81210](-) rpl2 [85025:85427](-) [83940:84373](-) ndhB [95596:96318](-) [94138:94893](-) ndhA [122031:122582](-) [120488:121027](-) ndhB_copy2 [142565:143341](+) [144044:144799](+) rpl2_copy2 [153510:153912](+) [154564:154997](+) trnK-UUU [2993:3029](+) [5576:5610](+) trnL-UAA [9344:9378](+) [9871:9920](+) trnG-UCC [12700:12722](+) [13434:13481](+) trnV-UAC [51965:52002](-) [51346:51380](-) trnI-GAU [101923:101959](+) [102907:102941](+) trnA-UGC [103006:103043](+) [103857:103891](+) trnA-UGC_copy2 [135894:135931](-) [135046:135080](-) trnI-GAU_copy2 [136978:137014](-) [135996:136030](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [69337:69450](-) [97784:98012](-) [97217:97272](-) ycf3 [49097:49222](-) [48143:48370](-) [47243:47395](-) rps12_copy2 [69337:69450](-) [140925:141153](+) [141665:141720](+) clpP [71650:71720](-) [70565:70856](-) [69611:69856](-)