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 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) [16724:16867](-) [15559:15969](-) clpP (3/3) [71678:71748](-) [70593:70881](-) [69646:69891](-) ndhA (2/2) [122020:122572](-) [120467:121005](-) ndhB (2/2) [95608:96384](-) [94150:94905](-) ndhB_copy2 (2/2) [142525:143301](+) [144004:144759](+) petB (2/2) [74643:74647](+) [75430:76072](+) petD (2/2) [76255:76261](+) [76993:77489](+) rpl16 (2/2) [82200:82208](-) [80824:81222](-) rpl16_copy2 (2/2) [156701:156709](+) [157687:158085](+) rpl2 (2/2) [85037:85427](-) [83952:84385](-) rpl2_copy2 (2/2) [153482:153872](+) [154524:154957](+) rpoC1 (2/2) [27242:27673](-) [24863:26473](-) rps12 (3/3) [69377:69490](-) [97796:98027](-) [97229:97254](-) rps12_copy2 (3/3) [69377:69490](-) [140882:141113](+) [141655:141680](+) rps16 (2/2) [1196:1236](+) [2122:2341](+) ycf3 (3/3) [49195:49319](-) [48240:48468](-) [47341:47493](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: rps4 2 [159523:159523](+) [1:632](+)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon rps19 GTG rpl2 ACG ndhD ACG rpl2_copy2 ACG rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 135 genes (112 unique genes). Including: 91 protein-coding genes (79 are unique) 36 tRNA genes (29 are unique) 8 rRNA genes (4 are unique) Details are as follows: 91 protein-coding genes (79 are unique) Genes Length Location accD 1443 [57487:58929](+) atpA 1524 [13969:15492](-) atpB 1503 [52957:54459](-) atpE 402 [52559:52960](-) atpF 555 [16724:16867](-) [15559:15969](-) atpH 246 [17304:17549](-) atpI 744 [18659:19402](-) ccsA 966 [114879:115844](+) cemA 690 [61176:61865](+) clpP 606 [71678:71748](-) [70593:70881](-) [69646:69891](-) infA 204 [79373:79576](-) matK 1530 [3786:5315](+) ndhA 1092 [122020:122572](-) [120467:121005](-) ndhB 1533 [95608:96384](-) [94150:94905](-) ndhB_copy2 1533 [142525:143301](+) [144004:144759](+) ndhC 363 [12167:12529](-) ndhD 1503 [116073:117575](-) ndhE 306 [118228:118533](-) ndhF 2229 [110409:112637](-) ndhG 534 [118817:119350](-) ndhH 1182 [122574:123755](-) ndhI 543 [119851:120393](-) ndhJ 477 [10817:11293](-) ndhK 678 [11430:12107](-) petA 969 [62073:63041](+) petB 648 [74643:74647](+) [75430:76072](+) petD 504 [76255:76261](+) [76993:77489](+) petG 114 [65857:65970](+) petL 96 [65574:65669](+) petN 90 [32524:32613](+) psaA 2253 [44345:46597](-) psaB 2205 [42115:44319](-) psaC 246 [117738:117983](-) psaI 111 [59466:59576](+) psaJ 135 [66752:66886](+) psbA 1062 [5888:6949](+) psbB 1527 [72158:73684](+) psbC 1422 [38636:40057](+) psbD 1062 [37627:38688](+) psbE 252 [63960:64211](-) psbF 120 [63831:63950](-) psbH 222 [74302:74523](+) psbI 111 [8468:8578](+) psbJ 123 [63450:63572](-) psbK 186 [7880:8065](+) psbL 117 [63692:63808](-) psbM 105 [33407:33511](-) psbN 132 [74068:74199](-) psbT 108 [73874:73981](+) psbZ 189 [40672:40860](+) rbcL 1428 [55325:56752](+) rpl14 369 [80313:80681](-) rpl14_copy2 369 [158228:158596](+) rpl16 408 [82200:82208](-) [80824:81222](-) rpl16_copy2 408 [156701:156709](+) [157687:158085](+) rpl2 825 [85037:85427](-) [83952:84385](-) rpl20 354 [68237:68590](-) rpl22 540 [83014:83553](-) rpl22_copy2 540 [155356:155895](+) rpl23 282 [85446:85727](-) rpl23_copy2 282 [153182:153463](+) rpl2_copy2 825 [153482:153872](+) [154524:154957](+) rpl32 255 [113675:113929](+) rpl33 201 [67287:67487](+) rpl36 114 [79270:79383](-) rpoA 1020 [77643:78662](-) rpoB 3213 [27700:30912](-) rpoC1 2043 [27242:27673](-) [24863:26473](-) rpoC2 4152 [20544:24695](-) rps11 417 [78735:79151](-) rps12 372 [69377:69490](-) [97796:98027](-) [97229:97254](-) rps12_copy2 372 [69377:69490](-) [140882:141113](+) [141655:141680](+) rps14 303 [41682:41984](-) rps15 273 [123878:124150](-) rps16 261 [1196:1236](+) [2122:2341](+) rps18 306 [67676:67981](+) rps19 279 [83613:83891](-) rps19_copy2 279 [155018:155296](+) rps2 711 [19622:20332](-) rps3 657 [82373:83029](-) rps3_copy2 657 [155880:156536](+) rps4 633 [159523:159523](+) [1:632](+) rps7 468 [96708:97175](-) rps7_copy2 468 [141734:142201](+) rps8 399 [79697:80095](-) rps8_copy2 399 [158814:159212](+) ycf1 5634 [124557:130190](-) ycf2 6834 [86035:92868](+) ycf2_copy2 6834 [146041:152874](-) ycf3 507 [49195:49319](-) [48240:48468](-) [47341:47493](-) ycf4 555 [60022:60576](+) 36 tRNA genes (29 are unique) Genes Location trnK-UUU [2990:3026](+) [5572:5606](+) trnH-GUG [7269:7343](+) trnQ-UUG [7472:7543](-) trnS-GCU [8665:8752](-) trnL-UAA [9300:9334](+) [9827:9876](+) trnF-GAA [10027:10099](+) trnG-UCC [12830:12852](+) [13564:13611](+) trnR-UCU [13768:13839](+) trnC-GCA [32002:32072](+) trnD-GUC [34629:34702](-) trnY-GUA [35080:35163](-) trnE-UUC [35223:35295](-) trnT-GGU [36015:36086](+) trnS-UGA [40254:40346](-) trnG-GCC [41196:41266](+) trnfM-CAU [41446:41519](-) trnS-GGA [50197:50283](+) trnV-UAC [52014:52051](-) [51395:51429](-) trnM-CAU [52231:52303](+) trnW-CCA [66116:66189](-) trnP-UGG [66353:66426](-) trnI-CAU [85893:85966](-) trnL-CAA [93509:93589](-) trnV-GAC [99854:99925](+) trnI-GAU [101935:101971](+) [102919:102953](+) trnA-UGC [103018:103055](+) [103869:103903](+) trnR-ACG [107645:107718](+) trnN-GUU [108324:108395](-) trnL-UAG [114684:114763](+) trnN-GUU_copy2 [130514:130585](+) trnR-ACG_copy2 [131191:131264](-) trnA-UGC_copy2 [135854:135891](-) [135006:135040](-) trnI-GAU_copy2 [136938:136974](-) [135956:135990](-) trnV-GAC_copy2 [138984:139055](-) trnL-CAA_copy2 [145320:145400](+) trnI-CAU_copy2 [152943:153016](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [100154:101644](+) rrn23 [104056:106865](+) rrn4.5 [106964:107066](+) rrn5 [107291:107411](+) rrn5_copy2 [131498:131618](-) rrn4.5_copy2 [131843:131945](-) rrn23_copy2 [132044:134853](-) rrn16_copy2 [137265:138755](-) This genome has 25 genes with intron(s). Details are as follows: 21 gene(s) have 1 intron(s) Genes Exons rps4 [159523:159523](+) [1:632](+) rps16 [1196:1236](+) [2122:2341](+) atpF [16724:16867](-) [15559:15969](-) rpoC1 [27242:27673](-) [24863:26473](-) petB [74643:74647](+) [75430:76072](+) petD [76255:76261](+) [76993:77489](+) rpl16 [82200:82208](-) [80824:81222](-) rpl2 [85037:85427](-) [83952:84385](-) ndhB [95608:96384](-) [94150:94905](-) ndhA [122020:122572](-) [120467:121005](-) ndhB_copy2 [142525:143301](+) [144004:144759](+) rpl2_copy2 [153482:153872](+) [154524:154957](+) rpl16_copy2 [156701:156709](+) [157687:158085](+) trnK-UUU [2990:3026](+) [5572:5606](+) trnL-UAA [9300:9334](+) [9827:9876](+) trnG-UCC [12830:12852](+) [13564:13611](+) trnV-UAC [52014:52051](-) [51395:51429](-) trnI-GAU [101935:101971](+) [102919:102953](+) trnA-UGC [103018:103055](+) [103869:103903](+) trnA-UGC_copy2 [135854:135891](-) [135006:135040](-) trnI-GAU_copy2 [136938:136974](-) [135956:135990](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [69377:69490](-) [97796:98027](-) [97229:97254](-) ycf3 [49195:49319](-) [48240:48468](-) [47341:47493](-) rps12_copy2 [69377:69490](-) [140882:141113](+) [141655:141680](+) clpP [71678:71748](-) [70593:70881](-) [69646:69891](-)