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 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 None None None 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [16604:16748](-) [15445:15854](-) clpP (3/3) [71534:71604](-) [70442:70730](-) [69503:69748](-) ndhA (2/2) [121820:122372](-) [120273:120811](-) ndhB (2/2) [95483:96259](-) [94025:94780](-) ndhB_copy2 (2/2) [142356:143132](+) [143835:144590](+) petB (2/2) [74499:74504](+) [75288:75929](+) petD (2/2) [76132:76139](+) [76872:77367](+) rpl16 (2/2) [82075:82083](-) [80699:81097](-) rpl16_copy2 (2/2) [156532:156540](+) [157518:157916](+) rpl2 (2/2) [84912:85314](-) [83827:84260](-) rpl2_copy2 (2/2) [153301:153703](+) [154355:154788](+) rpoC1 (2/2) [27114:27543](-) [24733:26345](-) rps12 (3/3) [69229:69342](-) [97671:97902](-) [97104:97129](-) rps12_copy2 (3/3) [69229:69342](-) [140713:140944](+) [141486:141511](+) rps16 (2/2) [1204:1243](+) [2132:2352](+) ycf3 (3/3) [49048:49171](-) [48092:48321](-) [47192:47344](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: rps4 2 [159353:159353](+) [1:632](+)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon rps19 GTG rpl2 ATA rpl32 GTG ndhD ATA rpl2_copy2 ATA rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 136 genes (112 unique genes). Including: 92 protein-coding genes (79 are unique) 36 tRNA genes (29 are unique) 8 rRNA genes (4 are unique) Details are as follows: 92 protein-coding genes (79 are unique) Genes Length Location accD 1443 [57387:58829](+) atpA 1524 [13855:15378](-) atpB 1503 [52860:54362](-) atpE 402 [52462:52863](-) atpF 555 [16604:16748](-) [15445:15854](-) atpH 246 [17184:17429](-) atpI 744 [18539:19282](-) ccsA 966 [114696:115661](+) cemA 690 [61087:61776](+) clpP 606 [71534:71604](-) [70442:70730](-) [69503:69748](-) infA 171 [79282:79452](-) infA_copy2 171 [159163:159333](+) matK 1530 [3805:5334](+) ndhA 1092 [121820:122372](-) [120273:120811](-) ndhB 1533 [95483:96259](-) [94025:94780](-) ndhB_copy2 1533 [142356:143132](+) [143835:144590](+) ndhC 363 [12054:12416](-) ndhD 1461 [115891:117351](-) ndhE 306 [118054:118359](-) ndhF 2235 [110314:112548](-) ndhG 534 [118642:119175](-) ndhH 1182 [122374:123555](-) ndhI 543 [119657:120199](-) ndhJ 477 [10700:11176](-) ndhK 678 [11313:11990](-) petA 969 [61984:62952](+) petB 648 [74499:74504](+) [75288:75929](+) petD 504 [76132:76139](+) [76872:77367](+) petG 114 [65721:65834](+) petL 96 [65441:65536](+) petN 90 [32378:32467](+) psaA 2253 [44200:46452](-) psaB 2205 [41970:44174](-) psaC 246 [117564:117809](-) psaI 111 [59367:59477](+) psaJ 135 [66617:66751](+) psbA 1062 [5909:6970](+) psbB 1527 [72014:73540](+) psbC 1422 [38499:39920](+) psbD 1062 [37490:38551](+) psbE 252 [63875:64126](-) psbF 120 [63746:63865](-) psbH 222 [74158:74379](+) psbI 111 [8498:8608](+) psbJ 123 [63365:63487](-) psbK 186 [7905:8090](+) psbL 117 [63607:63723](-) psbM 105 [33263:33367](-) psbN 132 [73924:74055](-) psbT 108 [73730:73837](+) psbZ 189 [40535:40723](+) rbcL 1428 [55231:56658](+) rpl14 369 [80188:80556](-) rpl14_copy2 369 [158059:158427](+) rpl16 408 [82075:82083](-) [80699:81097](-) rpl16_copy2 408 [156532:156540](+) [157518:157916](+) rpl2 837 [84912:85314](-) [83827:84260](-) rpl20 354 [68089:68442](-) rpl22 540 [82889:83428](-) rpl22_copy2 540 [155187:155726](+) rpl23 282 [85321:85602](-) rpl23_copy2 282 [153013:153294](+) rpl2_copy2 837 [153301:153703](+) [154355:154788](+) rpl32 153 [113569:113721](+) rpl33 201 [67144:67344](+) rpl36 114 [79146:79259](-) rpoA 1044 [77519:78562](-) rpoB 3213 [27570:30782](-) rpoC1 2043 [27114:27543](-) [24733:26345](-) rpoC2 4152 [20414:24565](-) rps11 417 [78611:79027](-) rps12 372 [69229:69342](-) [97671:97902](-) [97104:97129](-) rps12_copy2 372 [69229:69342](-) [140713:140944](+) [141486:141511](+) rps14 303 [41537:41839](-) rps15 273 [123681:123953](-) rps16 261 [1204:1243](+) [2132:2352](+) rps18 306 [67533:67838](+) rps19 279 [83488:83766](-) rps19_copy2 279 [154849:155127](+) rps2 711 [19502:20212](-) rps3 657 [82248:82904](-) rps3_copy2 657 [155711:156367](+) rps4 633 [159353:159353](+) [1:632](+) rps7 468 [96583:97050](-) rps7_copy2 468 [141565:142032](+) rps8 399 [79572:79970](-) rps8_copy2 399 [158645:159043](+) ycf1 5634 [124360:129993](-) ycf2 6834 [85910:92743](+) ycf2_copy2 6834 [145872:152705](-) ycf3 507 [49048:49171](-) [48092:48321](-) [47192:47344](-) ycf4 555 [59924:60478](+) 36 tRNA genes (29 are unique) Genes Location trnK-UUU [3008:3044](+) [5595:5629](+) trnH-GUG [7299:7372](+) trnQ-UUG [7497:7568](-) trnS-GCU [8695:8782](-) trnL-UAA [9359:9393](+) [9887:9936](+) trnF-GAA [10085:10157](+) trnG-UCC [12716:12738](+) [13449:13496](+) trnR-UCU [13654:13725](+) trnC-GCA [31864:31934](+) trnD-GUC [34491:34564](-) trnY-GUA [34942:35025](-) trnE-UUC [35085:35157](-) trnT-GGU [35881:35952](+) trnS-UGA [40117:40209](-) trnG-GCC [41052:41122](+) trnfM-CAU [41301:41374](-) trnS-GGA [50087:50173](+) trnV-UAC [51917:51954](-) [51298:51332](-) trnM-CAU [52134:52206](+) trnW-CCA [65980:66053](-) trnP-UGG [66218:66291](-) trnI-CAU [85768:85841](-) trnL-CAA [93384:93464](-) trnV-GAC [99746:99817](+) trnI-GAU [101827:101863](+) [102811:102845](+) trnA-UGC [102910:102947](+) [103761:103795](+) trnR-ACG [107538:107611](+) trnN-GUU [108227:108298](-) trnL-UAG [114501:114580](+) trnN-GUU_copy2 [130317:130388](+) trnR-ACG_copy2 [131004:131077](-) trnA-UGC_copy2 [135668:135705](-) [134820:134854](-) trnI-GAU_copy2 [136752:136788](-) [135770:135804](-) trnV-GAC_copy2 [138798:138869](-) trnL-CAA_copy2 [145151:145231](+) trnI-CAU_copy2 [152774:152847](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [100046:101536](+) rrn23 [103948:106758](+) rrn4.5 [106856:106958](+) rrn5 [107183:107303](+) rrn5_copy2 [131312:131432](-) rrn4.5_copy2 [131657:131759](-) rrn23_copy2 [131857:134667](-) rrn16_copy2 [137079:138569](-) This genome has 25 genes with intron(s). Details are as follows: 21 gene(s) have 1 intron(s) Genes Exons rps4 [159353:159353](+) [1:632](+) rps16 [1204:1243](+) [2132:2352](+) atpF [16604:16748](-) [15445:15854](-) rpoC1 [27114:27543](-) [24733:26345](-) petB [74499:74504](+) [75288:75929](+) petD [76132:76139](+) [76872:77367](+) rpl16 [82075:82083](-) [80699:81097](-) rpl2 [84912:85314](-) [83827:84260](-) ndhB [95483:96259](-) [94025:94780](-) ndhA [121820:122372](-) [120273:120811](-) ndhB_copy2 [142356:143132](+) [143835:144590](+) rpl2_copy2 [153301:153703](+) [154355:154788](+) rpl16_copy2 [156532:156540](+) [157518:157916](+) trnK-UUU [3008:3044](+) [5595:5629](+) trnL-UAA [9359:9393](+) [9887:9936](+) trnG-UCC [12716:12738](+) [13449:13496](+) trnV-UAC [51917:51954](-) [51298:51332](-) trnI-GAU [101827:101863](+) [102811:102845](+) trnA-UGC [102910:102947](+) [103761:103795](+) trnA-UGC_copy2 [135668:135705](-) [134820:134854](-) trnI-GAU_copy2 [136752:136788](-) [135770:135804](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [69229:69342](-) [97671:97902](-) [97104:97129](-) ycf3 [49048:49171](-) [48092:48321](-) [47192:47344](-) rps12_copy2 [69229:69342](-) [140713:140944](+) [141486:141511](+) clpP [71534:71604](-) [70442:70730](-) [69503:69748](-)