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, rpl16, rpl2, rpl20, rpl22, 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, 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, ycf15, ycf15_copy2, ycf2, ycf2_copy2, ycf4 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 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 infA Conserved open reading frames None Other genes None 2. Multicopy genes with different lengths: Genes Length Location rpl2 828 join{[88915:89308](-), [87813:88248](-)} rpl2_copy2 825 join{[157393:157783](+), [158453:158888](+)} 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [14029:14187](-) [12863:13273](-) clpP (3/3) [75516:75584](-) [74370:74660](-) [73483:73710](-) ndhA (2/2) [125796:126347](-) [124158:124697](-) ndhB (2/2) [99858:100634](-) [98421:99176](-) ndhB_copy2 (2/2) [146068:146844](+) [147526:148281](+) petB (2/2) [78465:78470](+) [79270:79926](+) petD (2/2) [80121:80129](+) [80805:81329](+) rpl16 (2/2) [86126:86134](-) [84813:85214](-) rpl2 (2/2) [88916:89308](-) [87814:88248](-) rpl2_copy2 (2/2) [157394:157783](+) [158454:158888](+) rpoC1 (2/2) [24764:25198](-) [22392:24011](-) rps12 (3/3) [73218:73331](-) [102040:102271](-) [101478:101503](-) rps12_copy2 (3/3) [73218:73331](-) [144431:144662](+) [145199:145224](+) rps16 (2/2) [6317:6356](-) [5226:5452](-) ycf3 (3/3) [46818:46946](-) [45863:46090](-) [44923:45075](-) ### 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 psbC ATC rps19 GTG orf42 ATC ndhD ATA orf42_copy2 ATC rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 137 genes (115 unique genes). Including: 89 protein-coding genes (80 are unique) 40 tRNA genes (31 are unique) 8 rRNA genes (4 are unique) Details are as follows: 89 protein-coding genes (80 are unique) Genes Length Location accD 1476 [60199:61674](+) atpA 1518 [11288:12805](-) atpB 1497 [55933:57429](-) atpE 402 [55535:55936](-) atpF 570 [14029:14187](-) [12863:13273](-) atpH 246 [14665:14910](-) atpI 744 [16130:16873](-) ccsA 960 [118770:119729](+) cemA 699 [64382:65080](+) clpP 588 [75516:75584](-) [74370:74660](-) [73483:73710](-) matK 1518 [2169:3686](-) ndhA 1092 [125796:126347](-) [124158:124697](-) ndhB 1533 [99858:100634](-) [98421:99176](-) ndhB_copy2 1533 [146068:146844](+) [147526:148281](+) ndhC 363 [53074:53436](-) ndhD 1476 [120040:121515](-) ndhE 306 [122183:122488](-) ndhF 2211 [114154:116364](-) ndhG 537 [122747:123283](-) ndhH 1182 [126349:127530](-) ndhI 504 [123573:124076](-) ndhJ 477 [51726:52202](-) ndhK 684 [52333:53016](-) orf42 129 [107445:107573](-) orf42_copy2 129 [139129:139257](+) petA 963 [65300:66262](+) petB 663 [78465:78470](+) [79270:79926](+) petD 534 [80121:80129](+) [80805:81329](+) petG 114 [69644:69757](+) petL 96 [69381:69476](+) petN 90 [30281:30370](+) psaA 2253 [42018:44270](-) psaB 2205 [39788:41992](-) psaC 246 [121704:121949](-) psaI 114 [62339:62452](+) psaJ 135 [70584:70718](+) psbA 1062 [520:1581](-) psbB 1527 [76010:77536](+) psbC 1431 [36021:37451](+) psbD 1062 [35021:36082](+) psbE 252 [67849:68100](-) psbF 120 [67720:67839](-) psbH 222 [78125:78346](+) psbI 111 [8945:9055](+) psbJ 123 [67316:67438](-) psbK 186 [8391:8576](+) psbL 117 [67581:67697](-) psbM 105 [31496:31600](-) psbN 132 [77889:78020](-) psbT 108 [77721:77828](+) psbZ 189 [38134:38322](+) rbcL 1428 [58210:59637](+) rpl14 369 [84320:84688](-) rpl16 411 [86126:86134](-) [84813:85214](-) rpl2 828 [88916:89308](-) [87814:88248](-) rpl20 354 [72115:72468](-) rpl22 486 [86936:87421](-) rpl23 282 [89327:89608](-) rpl23_copy2 282 [157094:157375](+) rpl2_copy2 825 [157394:157783](+) [158454:158888](+) rpl32 159 [117349:117507](+) rpl33 201 [71157:71357](+) rpl36 114 [83163:83276](-) rpoA 984 [81581:82564](-) rpoB 3213 [25225:28437](-) rpoC1 2055 [24764:25198](-) [22392:24011](-) rpoC2 4194 [18015:22208](-) rps11 417 [82629:83045](-) rps12 372 [73218:73331](-) [102040:102271](-) [101478:101503](-) rps12_copy2 372 [73218:73331](-) [144431:144662](+) [145199:145224](+) rps14 303 [39339:39641](-) rps15 273 [127633:127905](-) rps16 267 [6317:6356](-) [5226:5452](-) rps18 306 [71551:71856](+) rps19 279 [87467:87745](-) rps19_copy2 279 [158957:159235](+) rps2 711 [17108:17818](-) rps3 660 [86292:86951](-) rps4 606 [48211:48816](-) rps7 468 [100957:101424](-) rps7_copy2 468 [145278:145745](+) rps8 405 [83754:84158](-) ycf1 5370 [128255:133624](-) ycf15 192 [103289:103480](-) ycf15_copy2 192 [143222:143413](+) ycf2 6858 [89936:96793](+) ycf2_copy2 6858 [149909:156766](-) ycf3 510 [46818:46946](-) [45863:46090](-) [44923:45075](-) ycf4 555 [62885:63439](+) 40 tRNA genes (31 are unique) Genes Location trnH-GUG [5:77](-) trnK-UUU [4405:4441](-) [1847:1881](-) trnQ-UUG [7966:8037](-) trnS-GCU [9192:9279](-) trnG-UCC [10071:10093](+) [10816:10864](+) trnR-UCU [11020:11091](+) trnC-GCA [29497:29577](+) trnD-GUC [32156:32229](-) trnY-GUA [32686:32769](-) trnE-UUC [32829:32901](-) trnT-GGU [33707:33778](+) trnM-CAU [33713:33771](+) trnS-UGA [37689:37780](-) trnG-GCC [38863:38933](+) trnfM-CAU [39103:39176](-) trnS-GGA [47823:47909](+) trnT-UGU [49176:49248](-) trnL-UAA [50206:50242](+) [50762:50810](+) trnF-GAA [51182:51254](+) trnV-UAC [54980:55018](-) [54344:54380](-) trnM-CAU_copy2 [55212:55283](+) trnT-GGU_copy2 [55217:55275](+) trnW-CCA [69899:69972](-) trnP-UGG [70148:70221](-) trnP-GGG [70150:70220](-) trnI-CAU [89774:89847](-) trnL-CAA [97762:97842](-) trnV-GAC [104080:104151](+) trnI-GAU [106177:106218](+) [107173:107207](+) trnA-UGC [107278:107315](+) [108156:108190](+) trnR-ACG [111984:112057](+) trnN-GUU [112671:112742](-) trnL-UAG [118587:118666](+) trnN-GUU_copy2 [133960:134031](+) trnR-ACG_copy2 [134645:134718](-) trnA-UGC_copy2 [139387:139424](-) [138512:138546](-) trnI-GAU_copy2 [140484:140525](-) [139495:139529](-) trnV-GAC_copy2 [142551:142622](-) trnL-CAA_copy2 [148860:148940](+) trnI-CAU_copy2 [156855:156928](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [104392:105881](+) rrn23 [108354:111163](+) rrn4.5 [111262:111364](+) rrn5 [111621:111741](+) rrn5_copy2 [134961:135081](-) rrn4.5_copy2 [135338:135440](-) rrn23_copy2 [135539:138348](-) rrn16_copy2 [140820:142309](-) This genome has 23 genes with intron(s). Details are as follows: 19 gene(s) have 1 intron(s) Genes Exons rps16 [6317:6356](-) [5226:5452](-) atpF [14029:14187](-) [12863:13273](-) rpoC1 [24764:25198](-) [22392:24011](-) petB [78465:78470](+) [79270:79926](+) petD [80121:80129](+) [80805:81329](+) rpl16 [86126:86134](-) [84813:85214](-) rpl2 [88916:89308](-) [87814:88248](-) ndhB [99858:100634](-) [98421:99176](-) ndhA [125796:126347](-) [124158:124697](-) ndhB_copy2 [146068:146844](+) [147526:148281](+) rpl2_copy2 [157394:157783](+) [158454:158888](+) trnK-UUU [4405:4441](-) [1847:1881](-) trnG-UCC [10071:10093](+) [10816:10864](+) trnL-UAA [50206:50242](+) [50762:50810](+) trnV-UAC [54980:55018](-) [54344:54380](-) trnI-GAU [106177:106218](+) [107173:107207](+) trnA-UGC [107278:107315](+) [108156:108190](+) trnA-UGC_copy2 [139387:139424](-) [138512:138546](-) trnI-GAU_copy2 [140484:140525](-) [139495:139529](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [73218:73331](-) [102040:102271](-) [101478:101503](-) ycf3 [46818:46946](-) [45863:46090](-) [44923:45075](-) rps12_copy2 [73218:73331](-) [144431:144662](+) [145199:145224](+) clpP [75516:75584](-) [74370:74660](-) [73483:73710](-)