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, psbT, psbZ 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, 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 None Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor infA Conserved open reading frames ycf1, ycf15, ycf15_copy2, ycf1_copy2, ycf2, ycf2_copy2 Other genes clpP1, pafI, pafII, pbf1 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 psbN, ycf3 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 clpP Subunit of Acetyl-CoA-carboxylase None Translational initiation factor None Conserved open reading frames ycf4 Other genes None 2. Multicopy genes with different lengths: Genes Length Location ycf1 1920 [108275:110195](+) ycf1_copy2 5613 [123380:128993](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [12972:13116](-) [11870:12279](-) ndhA (2/2) [120889:121438](-) [119187:119725](-) ndhB (2/2) [95441:96217](-) [93993:94748](-) ndhB_copy2 (2/2) [141052:141828](+) [142521:143276](+) petB (2/2) [74396:74401](+) [75189:75830](+) petD (2/2) [76015:76022](+) [76761:77235](+) rpl16 (2/2) [82081:82089](-) [80648:81046](-) rpl2 (2/2) [84792:85182](-) [83695:84128](-) rpl2_copy2 (2/2) [152087:152477](+) [153141:153574](+) rpoC1 (2/2) [23295:23726](-) [20929:22539](-) rps12 (3/3) [69116:69229](-) [97584:97815](-) [97030:97055](-) rps12_copy2 (3/3) [69116:69229](-) [139454:139685](+) [140214:140239](+) rps16 (2/2) [5970:6009](-) [4913:5145](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: pafI 3 [44550:44673](-) [43568:43797](-) [42657:42809](-)] clpP1 3 [71342:71412](-) [70225:70516](-) [69343:69570](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon psbC GTG rpl33 ATA rps19 GTG ndhD ACG ndhA ATA 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 133 genes (114 unique genes). Including: 88 protein-coding genes (80 are unique) 37 tRNA genes (30 are unique) 8 rRNA genes (4 are unique) Details are as follows: 88 protein-coding genes (80 are unique) Genes Length Location accD 1467 [56518:57984](+) atpA 1524 [10286:11809](-) atpB 1497 [52252:53748](-) atpE 399 [51857:52255](-) atpF 555 [12972:13116](-) [11870:12279](-) atpH 246 [13466:13711](-) atpI 735 [14760:15494](-) ccsA 975 [113971:114945](+) cemA 690 [60670:61359](+) clpP1 591 [71342:71412](-) [70225:70516](-) [69343:69570](-) infA 195 [79221:79415](-) matK 1518 [1903:3420](-) ndhA 1089 [120889:121438](-) [119187:119725](-) ndhB 1533 [95441:96217](-) [93993:94748](-) ndhB_copy2 1533 [141052:141828](+) [142521:143276](+) ndhC 363 [49840:50202](-) ndhD 1500 [115197:116696](-) ndhE 306 [117313:117618](-) ndhF 2235 [110169:112403](-) ndhG 531 [117723:118253](-) ndhH 1182 [121452:122633](-) ndhI 504 [118591:119094](-) ndhJ 477 [48491:48967](-) ndhK 684 [49099:49782](-) pafI 507 [44550:44673](-) [43568:43797](-) [42657:42809](-) pafII 531 [59341:59871](+) pbf1 132 [73793:73924](-) petA 960 [61607:62566](+) petB 648 [74396:74401](+) [75189:75830](+) petD 483 [76015:76022](+) [76761:77235](+) petG 114 [65704:65817](+) petL 96 [65439:65534](+) petN 90 [28698:28787](+) psaA 2253 [39623:41875](-) psaB 2205 [37393:39597](-) psaC 246 [116817:117062](-) psaI 111 [58765:58875](+) psaJ 135 [66604:66738](+) psbA 1062 [345:1406](-) psbB 1527 [71881:73407](+) psbC 1386 [33971:35356](+) psbD 1062 [32926:33987](+) psbE 252 [64069:64320](-) psbF 120 [63940:64059](-) psbH 222 [74050:74271](+) psbI 111 [8256:8366](+) psbJ 123 [63538:63660](-) psbK 186 [7595:7780](+) psbL 117 [63800:63916](-) psbM 105 [29500:29604](-) psbT 108 [73625:73732](+) psbZ 189 [36002:36190](+) rbcL 1437 [54342:55778](+) rpl14 369 [80152:80520](-) rpl16 408 [82081:82089](-) [80648:81046](-) rpl2 825 [84792:85182](-) [83695:84128](-) rpl20 387 [68006:68392](-) rpl22 438 [82862:83299](-) rpl23 282 [85201:85482](-) rpl23_copy2 282 [151787:152068](+) rpl2_copy2 825 [152087:152477](+) [153141:153574](+) rpl32 162 [112984:113145](+) rpl33 78 [67244:67321](+) rpl36 114 [79003:79116](-) rpoA 1014 [77396:78409](-) rpoB 3213 [23753:26965](-) rpoC1 2043 [23295:23726](-) [20929:22539](-) rpoC2 4191 [16581:20771](-) rps11 408 [78484:78891](-) rps12 372 [69116:69229](-) [97584:97815](-) [97030:97055](-) rps12_copy2 372 [69116:69229](-) [139454:139685](+) [140214:140239](+) rps14 303 [36955:37257](-) rps15 255 [122753:123007](-) rps16 273 [5970:6009](-) [4913:5145](-) rps18 309 [67472:67780](+) rps19 279 [83365:83643](-) rps2 711 [15645:16355](-) rps3 657 [82221:82877](-) rps4 606 [45391:45996](-) rps7 468 [96510:96977](-) rps7_copy2 468 [140292:140759](+) rps8 405 [79592:79996](-) ycf1 1920 [108276:110195](+) ycf15 132 [92800:92931](+) ycf15_copy2 132 [144338:144469](-) ycf1_copy2 5613 [123381:128993](-) ycf2 6849 [85810:92658](+) ycf2_copy2 6849 [144611:151459](-) 37 tRNA genes (30 are unique) Genes Location trnH-GUG [2:75](-) trnK-UUU [4112:4148](-) [1607:1641](-) trnQ-UUG [7196:7267](-) trnS-GCU [8454:8541](-) trnG-UCC [9123:9145](+) [9831:9878](+) trnR-UCU [10095:10166](+) trnC-GCA [27998:28068](+) trnD-GUC [30231:30304](-) trnY-GUA [30420:30503](-) trnE-UUC [30563:30635](-) trnT-GGU [31550:31621](+) trnS-UGA [35591:35683](-) trnG-GCC [36504:36574](+) trnfM-CAU [36735:36808](-) trnS-GGA [44981:45067](+) trnT-UGU [46352:46424](-) trnL-UAA [47161:47195](+) [47477:47526](+) trnF-GAA [47876:47948](+) trnV-UAC [51365:51402](-) [50736:50770](-) trnM-CAU [51577:51649](+) trnW-CCA [65953:66026](-) trnP-UGG [66150:66223](-) trnI-CAU [85648:85721](-) trnL-CAA [93366:93446](-) trnV-GAC [99399:99470](+) trnI-GAU [101495:101531](+) [102481:102515](+) trnA-UGC [102579:102616](+) [103433:103467](+) trnR-ACG [107236:107309](+) trnN-GUU [107885:107956](-) trnL-UAG [113799:113878](+) trnN-GUU_copy2 [129313:129384](+) trnR-ACG_copy2 [129960:130033](-) trnA-UGC_copy2 [134653:134690](-) [133802:133836](-) trnI-GAU_copy2 [135738:135774](-) [134754:134788](-) trnV-GAC_copy2 [137799:137870](-) trnL-CAA_copy2 [143823:143903](+) trnI-CAU_copy2 [151548:151621](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [99705:101195](+) rrn23 [103626:106435](+) rrn4.5 [106534:106636](+) rrn5 [106864:106984](+) rrn5_copy2 [130285:130405](-) rrn4.5_copy2 [130633:130735](-) rrn23_copy2 [130834:133643](-) rrn16_copy2 [136074:137564](-) This genome has 23 genes with intron(s). Details are as follows: 19 gene(s) have 1 intron(s) Genes Exons rps16 [5970:6009](-) [4913:5145](-) atpF [12972:13116](-) [11870:12279](-) rpoC1 [23295:23726](-) [20929:22539](-) petB [74396:74401](+) [75189:75830](+) petD [76015:76022](+) [76761:77235](+) rpl16 [82081:82089](-) [80648:81046](-) rpl2 [84792:85182](-) [83695:84128](-) ndhB [95441:96217](-) [93993:94748](-) ndhA [120889:121438](-) [119187:119725](-) ndhB_copy2 [141052:141828](+) [142521:143276](+) rpl2_copy2 [152087:152477](+) [153141:153574](+) trnK-UUU [4112:4148](-) [1607:1641](-) trnG-UCC [9123:9145](+) [9831:9878](+) trnL-UAA [47161:47195](+) [47477:47526](+) trnV-UAC [51365:51402](-) [50736:50770](-) trnI-GAU [101495:101531](+) [102481:102515](+) trnA-UGC [102579:102616](+) [103433:103467](+) trnA-UGC_copy2 [134653:134690](-) [133802:133836](-) trnI-GAU_copy2 [135738:135774](-) [134754:134788](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [69116:69229](-) [97584:97815](-) [97030:97055](-) pafI [44550:44673](-) [43568:43797](-) [42657:42809](-) rps12_copy2 [69116:69229](-) [139454:139685](+) [140214:140239](+) clpP1 [71342:71412](-) [70225:70516](-) [69343:69570](-)