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, 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 ycf15, ycf4 Other genes None 2. Multicopy genes with different lengths: Genes Length Location ycf1 1470 [114621:116091](+) ycf1_copy2 5481 [130272:135753](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [13538:13682](-) [12375:12784](-) ndhA (2/2) [127775:128327](-) [126120:126658](-) ndhB (2/2) [101268:102044](-) [99812:100567](-) ndhB_copy2 (2/2) [148331:149107](+) [149808:150563](+) petB (2/2) [79349:79354](+) [80194:80835](+) petD (2/2) [81034:81041](+) [81799:82294](+) rpl16 (2/2) [87349:87357](-) [85853:86251](-) rpl2 (2/2) [90239:90629](-) [89143:89573](-) rpl2_copy2 (2/2) [159746:160136](+) [160802:161232](+) rpoC1 (2/2) [24302:24733](-) [21911:23530](-) rps12 (3/3) [74002:74115](-) [103454:103685](-) [102892:102917](-) rps12_copy2 (3/3) [74002:74115](-) [146690:146921](+) [147458:147483](+) rps16 (2/2) [6310:6349](-) [5252:5505](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: pafI 3 [46676:46799](-) [45622:45851](-) [44744:44896](-)] clpP1 3 [76334:76404](-) [75162:75453](-) [74277:74522](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon psbC GTG cemA GTG psbL ACG rpl2 ACG ndhD ACG rpl2_copy2 ACG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 127 genes (107 unique genes). Including: 86 protein-coding genes (79 are unique) 33 tRNA genes (24 are unique) 8 rRNA genes (4 are unique) Details are as follows: 86 protein-coding genes (79 are unique) Genes Length Location accD 1491 [60956:62446](+) atpA 1524 [10684:12207](-) atpB 1497 [56362:57858](-) atpE 402 [55964:56365](-) atpF 555 [13538:13682](-) [12375:12784](-) atpH 246 [14258:14503](-) atpI 744 [15677:16420](-) ccsA 966 [120637:121602](+) cemA 690 [65315:66004](+) clpP1 609 [76334:76404](-) [75162:75453](-) [74277:74522](-) infA 234 [84344:84577](-) matK 1539 [1989:3527](-) ndhA 1092 [127775:128327](-) [126120:126658](-) ndhB 1533 [101268:102044](-) [99812:100567](-) ndhB_copy2 1533 [148331:149107](+) [149808:150563](+) ndhC 363 [52981:53343](-) ndhD 1497 [121869:123365](-) ndhE 306 [124027:124332](-) ndhF 2226 [116059:118284](-) ndhG 531 [124591:125121](-) ndhH 1182 [128329:129510](-) ndhI 543 [125499:126041](-) ndhJ 477 [51648:52124](-) ndhK 762 [52229:52990](-) pafI 507 [46676:46799](-) [45622:45851](-) [44744:44896](-) pafII 555 [63714:64268](+) pbf1 132 [78739:78870](-) petA 963 [66234:67196](+) petB 648 [79349:79354](+) [80194:80835](+) petD 504 [81034:81041](+) [81799:82294](+) petG 114 [70383:70496](+) petL 96 [70089:70184](+) petN 90 [29795:29884](+) psaA 2253 [41846:44098](-) psaB 2205 [39616:41820](-) psaC 246 [123484:123729](-) psaI 111 [63136:63246](+) psaJ 135 [71369:71503](+) psbA 1062 [298:1359](-) psbB 1527 [76857:78383](+) psbC 1386 [36126:37511](+) psbD 1065 [35078:36142](+) psbE 252 [68570:68821](-) psbF 120 [68441:68560](-) psbH 222 [78983:79204](+) psbI 111 [8561:8671](+) psbJ 123 [68057:68179](-) psbK 180 [7977:8156](+) psbL 117 [68302:68418](-) psbM 105 [30845:30949](-) psbT 108 [78562:78669](+) psbZ 189 [38222:38410](+) rbcL 1428 [58656:60083](+) rpl14 369 [85344:85712](-) rpl16 408 [87349:87357](-) [85853:86251](-) rpl2 822 [90239:90629](-) [89143:89573](-) rpl20 387 [72822:73208](-) rpl22 432 [88241:88672](-) rpl23 282 [90648:90929](-) rpl23_copy2 282 [159446:159727](+) rpl2_copy2 822 [159746:160136](+) [160802:161232](+) rpl32 165 [119462:119626](+) rpl33 207 [71912:72118](+) rpl36 114 [84115:84228](-) rpoA 1029 [82473:83501](-) rpoB 3213 [24760:27972](-) rpoC1 2052 [24302:24733](-) [21911:23530](-) rpoC2 4125 [17617:21741](-) rps11 417 [83569:83985](-) rps12 372 [74002:74115](-) [103454:103685](-) [102892:102917](-) rps12_copy2 372 [74002:74115](-) [146690:146921](+) [147458:147483](+) rps14 303 [39175:39477](-) rps15 273 [129624:129896](-) rps16 294 [6310:6349](-) [5252:5505](-) rps18 309 [72302:72610](+) rps19 279 [88721:88999](-) rps2 711 [16659:17369](-) rps3 663 [87491:88153](-) rps4 606 [47973:48578](-) rps7 468 [102366:102833](-) rps7_copy2 468 [147542:148009](+) rps8 405 [84699:85103](-) ycf1 1470 [114622:116091](+) ycf1_copy2 5481 [130273:135753](-) ycf2 6933 [91230:98162](+) ycf2_copy2 6933 [152213:159145](-) 33 tRNA genes (24 are unique) Genes Location trnH-GUG [28:101](-) trnQ-UUG [7581:7652](-) trnS-GCU [8850:8937](-) trnR-UCU [10502:10573](+) trnC-GCA [29273:29344](+) trnD-GUC [32009:32082](-) trnY-GUA [32423:32506](-) trnE-UUC [32566:32637](-) trnT-GGU [33319:33390](+) trnS-UGA [37769:37861](-) trnG-GCC [38701:38771](+) trnM-CAU [38938:39011](-) trnS-GGA [47599:47685](+) trnT-UGU [48948:49020](-) trnF-GAA [50829:50901](+) trnM-CAU_copy2 [55668:55740](+) trnW-CCA [70619:70692](-) trnP-UGG [70877:70950](-) trnM-CAU_copy3 [91095:91168](-) trnL-CAA [99162:99242](-) trnV-GAC [105706:105777](+) trnI-GAU [107792:107827](+) [107844:107879](+) trnA-UGC [108875:108911](+) [108952:108979](+) trnR-ACG [113522:113595](+) trnN-GUU [114192:114263](-) trnL-UAG [120410:120489](+) trnN-GUU_copy2 [136112:136183](+) trnR-ACG_copy2 [136780:136853](-) trnA-UGC_copy2 [141464:141500](-) [141396:141423](-) trnI-GAU_copy2 [142548:142583](-) [142496:142531](-) trnV-GAC_copy2 [144598:144669](-) trnL-CAA_copy2 [151133:151213](+) trnM-CAU_copy4 [159207:159280](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [106005:107495](+) rrn23 [109907:112517](+) rrn4.5 [112818:112920](+) rrn5 [113150:113270](+) rrn5_copy2 [137105:137225](-) rrn4.5_copy2 [137455:137557](-) rrn23_copy2 [137858:140468](-) rrn16_copy2 [142880:144370](-) This genome has 19 genes with intron(s). Details are as follows: 15 gene(s) have 1 intron(s) Genes Exons rps16 [6310:6349](-) [5252:5505](-) atpF [13538:13682](-) [12375:12784](-) rpoC1 [24302:24733](-) [21911:23530](-) petB [79349:79354](+) [80194:80835](+) petD [81034:81041](+) [81799:82294](+) rpl16 [87349:87357](-) [85853:86251](-) rpl2 [90239:90629](-) [89143:89573](-) ndhB [101268:102044](-) [99812:100567](-) ndhA [127775:128327](-) [126120:126658](-) ndhB_copy2 [148331:149107](+) [149808:150563](+) rpl2_copy2 [159746:160136](+) [160802:161232](+) trnI-GAU [107792:107827](+) [107844:107879](+) trnA-UGC [108875:108911](+) [108952:108979](+) trnA-UGC_copy2 [141464:141500](-) [141396:141423](-) trnI-GAU_copy2 [142548:142583](-) [142496:142531](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [74002:74115](-) [103454:103685](-) [102892:102917](-) pafI [46676:46799](-) [45622:45851](-) [44744:44896](-) rps12_copy2 [74002:74115](-) [146690:146921](+) [147458:147483](+) clpP1 [76334:76404](-) [75162:75453](-) [74277:74522](-)