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 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 infA Conserved open reading frames ycf1, ycf1_copy2, ycf2, ycf2_copy2, ycf4, ycf68, ycf68_copy2 Other genes None Possible missing protein coding genes: Group of genes Name of genes Subunits of ATP synthase None Subunits of NADH-dehydrogenase ndhK 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 ycf1 1257 [106679:107936](+) ycf1_copy2 5181 [121107:126288](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [12072:12215](-) [10848:11255](-) clpP (3/3) [69180:69248](-) [68058:68348](-) [67126:67365](-) ndhA (2/2) [118555:119103](-) [117018:117563](-) ndhB (2/2) [93952:94728](-) [92490:93245](-) ndhB_copy2 (2/2) [138240:139016](+) [139723:140478](+) petB (1/2) [73056:73715](+) petD (1/2) [74779:75273](+) rpl16 (1/2) [78815:79225](-) rpl2 (2/2) [83264:83647](-) [82156:82587](-) rpl2_copy2 (2/2) [149321:149704](+) [150381:150812](+) rpoC1 (2/2) [23058:23486](-) [20683:22302](-) rps12 (3/3) [66896:67009](-) [96147:96386](-) [95557:95583](-) rps12_copy2 (3/3) [66896:67009](-) [136582:136821](+) [137385:137411](+) rps16 (2/2) [5687:5728](-) [4641:4886](-) ycf3 (3/3) [42561:42692](-) [41609:41830](-) [40721:40879](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: psbA 2 [1:1058](-) [151431:151434](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon petB TTG rpl16 ATC rpl22 ATC rps19 GTG rpl2 ATA rpl2_copy2 ATA rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 133 genes (112 unique genes). Including: 88 protein-coding genes (79 are unique) 37 tRNA genes (29 are unique) 8 rRNA genes (4 are unique) Details are as follows: 88 protein-coding genes (79 are unique) Genes Length Location accD 1446 [55225:56670](+) atpA 1533 [9222:10754](-) atpB 1497 [50844:52340](-) atpE 408 [50440:50847](-) atpF 552 [12072:12215](-) [10848:11255](-) atpH 246 [12627:12872](-) atpI 747 [14292:15038](-) ccsA 894 [111282:112175](+) cemA 690 [58967:59656](+) clpP 600 [69180:69248](-) [68058:68348](-) [67126:67365](-) infA 234 [77430:77663](-) matK 1539 [1620:3158](-) ndhA 1095 [118555:119103](-) [117018:117563](-) ndhB 1533 [93952:94728](-) [92490:93245](-) ndhB_copy2 1533 [138240:139016](+) [139723:140478](+) ndhC 363 [48246:48608](-) ndhD 1500 [112433:113932](-) ndhE 306 [114893:115198](-) ndhF 2211 [107904:110114](-) ndhG 531 [115420:115950](-) ndhH 1188 [119105:120292](-) ndhI 522 [116410:116931](-) ndhJ 480 [46919:47398](-) petA 963 [59906:60868](+) petB 660 [73056:73715](+) petD 495 [74779:75273](+) petG 114 [63397:63510](+) petL 96 [63144:63239](+) petN 90 [27901:27990](+) psaA 2253 [37927:40179](-) psaB 2205 [35697:37901](-) psaC 246 [114073:114318](-) psaI 111 [57255:57365](+) psaJ 135 [64276:64410](+) psbA 1062 [1:1058](-) [151431:151434](-) psbB 1527 [69711:71237](+) psbC 1422 [32336:33757](+) psbD 1062 [31327:32388](+) psbE 252 [62035:62286](-) psbF 120 [61905:62024](-) psbH 222 [71884:72105](+) psbI 111 [6964:7074](+) psbJ 123 [61517:61639](-) psbK 186 [6538:6723](+) psbL 117 [61758:61874](-) psbM 105 [28608:28712](-) psbN 132 [71631:71762](-) psbT 108 [71452:71559](+) psbZ 189 [34359:34547](+) rbcL 1446 [53242:54687](+) rpl14 369 [78340:78708](-) rpl16 411 [78815:79225](-) rpl2 816 [83264:83647](-) [82156:82587](-) rpl20 354 [65848:66201](-) rpl22 324 [81122:81445](-) rpl23 261 [83672:83932](-) rpl23_copy2 261 [149036:149296](+) rpl2_copy2 816 [149321:149704](+) [150381:150812](+) rpl32 162 [110531:110692](+) rpl33 207 [64811:65017](+) rpl36 114 [77212:77325](-) rpoA 1014 [75540:76553](-) rpoB 3219 [23511:26729](-) rpoC1 2049 [23058:23486](-) [20683:22302](-) rpoC2 4041 [16463:20503](-) rps11 405 [76618:77022](-) rps12 381 [66896:67009](-) [96147:96386](-) [95557:95583](-) rps12_copy2 381 [66896:67009](-) [136582:136821](+) [137385:137411](+) rps14 303 [35290:35592](-) rps15 273 [120387:120659](-) rps16 288 [5687:5728](-) [4641:4886](-) rps18 306 [65299:65604](+) rps19 279 [81625:81903](-) rps19_copy2 279 [151065:151343](+) rps2 726 [15377:16102](-) rps3 660 [80300:80959](-) rps4 612 [43673:44284](-) rps7 468 [95031:95498](-) rps7_copy2 468 [137470:137937](+) rps8 405 [77783:78187](-) ycf1 1257 [106680:107936](+) ycf1_copy2 5181 [121108:126288](-) ycf2 6906 [84236:91141](+) ycf2_copy2 6906 [141827:148732](-) ycf3 513 [42561:42692](-) [41609:41830](-) [40721:40879](-) ycf4 558 [57812:58369](+) ycf68 372 [100147:100518](+) ycf68_copy2 372 [132450:132821](-) 37 tRNA genes (29 are unique) Genes Location trnK-UUU [3992:4028](-) [1284:1312](-) trnQ-UUG [6116:6188](-) trnS-GGA [7199:7285](-) trnR-UCU [9019:9090](+) trnC-GCA [27516:27586](+) trnD-GUC [29217:29290](-) trnY-GUA [29678:29761](-) trnE-UUC [29824:29896](-) trnT-GGU [30525:30596](+) trnS-UGA [33921:34013](-) trnG-UCC [34832:34902](+) trnfM-CAU [35056:35129](-) trnS-GCU [43292:43379](+) trnT-UGU [44554:44626](-) trnL-UAA [45235:45269](+) [45868:45917](+) trnF-GAA [46262:46334](+) trnV-UAC [49982:50020](-) [49370:49406](-) trnM-CAU [50191:50263](+) trnW-CCA [63632:63705](-) trnP-UGG [63828:63901](-) trnH-GUG [82039:82113](+) trnI-CAU [84094:84167](-) trnL-CAA [91845:91925](-) trnV-GAC [97889:97960](+) trnI-GAU [100006:100047](+) [101006:101040](+) trnA-UGC [101103:101140](+) [101913:101947](+) trnR-ACG [105697:105770](+) trnN-GUU [106292:106363](-) trnL-UAG [111109:111188](+) trnN-GUU_copy2 [126605:126676](+) trnR-ACG_copy2 [127198:127271](-) trnA-UGC_copy2 [131828:131865](-) [131021:131055](-) trnI-GAU_copy2 [132921:132962](-) [131928:131962](-) trnV-GAC_copy2 [135008:135079](-) trnL-CAA_copy2 [141043:141123](+) trnI-CAU_copy2 [148801:148874](+) trnH-GUG_copy2 [150855:150929](-) 8 rRNA genes (4 are unique) Genes Location rrn16 [98203:99693](+) rrn23 [102093:104902](+) rrn4.5 [105002:105104](+) rrn5 [105333:105453](+) rrn5_copy2 [127515:127635](-) rrn4.5_copy2 [127864:127966](-) rrn23_copy2 [128065:130874](-) rrn16_copy2 [133274:134764](-) This genome has 20 genes with intron(s). Details are as follows: 16 gene(s) have 1 intron(s) Genes Exons psbA [1:1058](-) [151431:151434](-) rps16 [5687:5728](-) [4641:4886](-) atpF [12072:12215](-) [10848:11255](-) rpoC1 [23058:23486](-) [20683:22302](-) rpl2 [83264:83647](-) [82156:82587](-) ndhB [93952:94728](-) [92490:93245](-) ndhA [118555:119103](-) [117018:117563](-) ndhB_copy2 [138240:139016](+) [139723:140478](+) rpl2_copy2 [149321:149704](+) [150381:150812](+) trnK-UUU [3992:4028](-) [1284:1312](-) trnL-UAA [45235:45269](+) [45868:45917](+) trnV-UAC [49982:50020](-) [49370:49406](-) trnI-GAU [100006:100047](+) [101006:101040](+) trnA-UGC [101103:101140](+) [101913:101947](+) trnA-UGC_copy2 [131828:131865](-) [131021:131055](-) trnI-GAU_copy2 [132921:132962](-) [131928:131962](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [66896:67009](-) [96147:96386](-) [95557:95583](-) ycf3 [42561:42692](-) [41609:41830](-) [40721:40879](-) rps12_copy2 [66896:67009](-) [136582:136821](+) [137385:137411](+) clpP [69180:69248](-) [68058:68348](-) [67126:67365](-)