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, rpl16, rpl2, rpl20, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36 Small subunit of ribosome rps11, rps12, 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 None Conserved open reading frames ycf1, ycf15, ycf15_copy2, ycf1_copy2, ycf2, ycf2_copy2, ycf2_copy3 Other genes orf188, orf42, orf42_copy2, orf56, orf56_copy2, psbG 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 rpl22 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 infA Conserved open reading frames ycf4 Other genes None 2. Multicopy genes with different lengths: Genes Length Location rps19 279 [83059:83338](-) rps19_copy2 66 [152051:152117](+) ycf2 6762 [85744:92506](+) ycf2_copy2 6864 [142685:149549](-) ycf2_copy3 285 [149745:150030](-) ndhB 2220 [93596:95816](-) ndhB_copy2 777 [139380:140157](+) ycf1 5379 [108173:113552](+) ycf1_copy2 477 [126547:127024](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (1/2) [48600:49880](+) clpP (1/3) [68616:70688](-) ndhA (1/2) [117364:117903](+) ndhB (1/2) [93597:95816](-) ndhB_copy2 (1/2) [139381:140157](+) petB (1/2) [74384:75031](+) petD (1/2) [75914:76468](+) rpl16 (1/2) [80295:80696](-) rpl2 (1/2) [83398:84936](-) rpl2_copy2 (1/2) [150455:151993](+) rpoC1 (1/2) [37584:40445](+) rps12 (3/3) [68286:68398](-) [97202:97434](-) [96644:96669](-) rps16 (1/2) [56233:56436](+) ycf3 (1/3) [16525:18471](+) ### The exon column shows the number of (actual exons/expected exons). ### 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon petN ATT psbT ATC petD ATA rps19 GTG orf42 ATC orf56 TTG orf56_copy2 TTG orf42_copy2 ATC rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 137 genes (106 unique genes). Including: 92 protein-coding genes (81 are unique) 37 tRNA genes (21 are unique) 8 rRNA genes (4 are unique) Details are as follows: 92 protein-coding genes (81 are unique) Genes Length Location accD 1293 [56997:58289](+) atpA 1533 [49963:51495](+) atpB 1497 [7617:9113](+) atpE 399 [9110:9508](+) atpF 1281 [48600:49880](+) atpH 246 [47913:48158](+) atpI 744 [46066:46809](+) ccsA 978 [122284:123261](-) cemA 690 [59823:60512](+) clpP 2073 [68616:70688](-) matK 1512 [2112:3623](+) ndhA 540 [117364:117903](+) ndhB 2220 [93597:95816](-) ndhB_copy2 777 [139381:140157](+) ndhC 243 [10835:11077](+) ndhD 1485 [120522:122006](+) ndhE 306 [119543:119848](+) ndhF 2241 [124294:126534](+) ndhG 531 [118773:119303](+) ndhH 1182 [114361:115542](+) ndhI 483 [117979:118461](+) ndhJ 477 [11995:12471](+) ndhK 105 [11078:11182](+) orf188 567 [115544:116110](+) orf42 129 [102552:102680](-) orf42_copy2 129 [132518:132646](+) orf56 108 [102948:103055](-) orf56_copy2 108 [132143:132250](+) petA 963 [60699:61661](+) petB 648 [74384:75031](+) petD 555 [75914:76468](+) petG 114 [64483:64596](+) petL 96 [64229:64324](+) petN 96 [32213:32308](-) psaA 2253 [19067:21319](+) psaB 2205 [21345:23549](+) psaC 246 [120144:120389](+) psaI 99 [58535:58633](+) psaJ 135 [65372:65506](+) psbA 1062 [410:1471](-) psbB 1527 [71114:72640](+) psbC 1461 [25766:27226](-) psbD 1062 [27135:28196](-) psbE 252 [63068:63319](-) psbF 120 [62939:63058](-) psbG 705 [11188:11892](+) psbH 222 [73219:73440](+) psbI 126 [53548:53673](-) psbJ 123 [62537:62659](-) psbK 186 [54120:54305](-) psbL 117 [62800:62916](-) psbM 105 [31390:31494](+) psbN 132 [72974:73105](-) psbT 108 [72798:72905](+) psbZ 189 [24937:25125](-) rbcL 1428 [5407:6834](-) rpl14 369 [79804:80172](-) rpl16 402 [80295:80696](-) rpl2 1539 [83398:84936](-) rpl20 351 [67091:67441](-) rpl23 282 [84955:85236](-) rpl23_copy2 282 [150155:150436](+) rpl2_copy2 1539 [150455:151993](+) rpl32 150 [123736:123885](-) rpl33 201 [66064:66264](+) rpl36 114 [78517:78630](-) rpoA 996 [76685:77680](-) rpoB 3213 [34345:37557](+) rpoC1 2862 [37584:40445](+) rpoC2 4053 [40664:44716](+) rps11 417 [77755:78171](-) rps12 372 [68286:68398](-) [97202:97434](-) [96644:96669](-) rps14 303 [23667:23969](+) rps15 273 [113988:114260](+) rps16 204 [56233:56436](+) rps18 300 [66516:66815](+) rps19 279 [83060:83338](-) rps19_copy2 66 [152052:152117](+) rps2 705 [45095:45799](+) rps3 642 [82058:82699](-) rps4 606 [15367:15972](+) rps7 468 [96122:96589](-) rps7_copy2 468 [138608:139075](+) rps8 405 [79102:79506](-) ycf1 5379 [108174:113552](+) ycf15 192 [98339:98530](-) ycf15_copy2 192 [136668:136859](+) ycf1_copy2 477 [126548:127024](-) ycf2 6762 [85745:92506](+) ycf2_copy2 6864 [142686:149549](-) ycf2_copy3 285 [149746:150030](-) ycf3 1947 [16525:18471](+) 37 tRNA genes (21 are unique) Genes Location trnH [98:172](+) trnK [4345:4381](-) [1733:1767](-) trnM [9656:9727](+) trnV [9916:9954](+) [10543:10577](+) trnF [13161:13233](+) trnL [14202:14238](-) [13644:13693](-) trnT [15010:15082](+) trnS [16182:16269](-) trnfM [24144:24217](+) trnG [24336:24406](-) trnS_copy2 [25490:25582](+) trnT_copy2 [29446:29517](-) trnM_copy2 [29453:29511](-) trnE [30276:30348](+) trnY [30415:30498](+) trnD [30948:31021](+) trnC [33381:33460](-) trnR [51712:51783](-) trnS_copy3 [53309:53395](+) trnQ [54757:54828](+) trnW [64748:64821](-) trnP [65024:65097](-) trnI [85584:85657](-) trnL_copy2 [92912:92992](-) trnV_copy2 [99211:99282](+) trnI_copy2 [101296:101337](+) [102286:102320](+) trnA [102385:102422](+) [103233:103267](+) trnR_copy2 [107043:107116](+) trnN [107740:107811](-) trnL_copy3 [123347:123426](-) trnN_copy2 [127387:127458](+) trnR_copy3 [128082:128155](-) trnA_copy2 [132776:132813](-) [131931:131965](-) trnI_copy3 [133865:133902](-) [132878:132912](-) trnV_copy3 [135916:135987](-) trnL_copy4 [142205:142285](+) trnI_copy4 [149637:149710](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [99504:100994](+) rrn23 [103426:106236](+) rrn4.5 [106338:106441](+) rrn5 [106670:106790](+) rrn5_copy2 [128408:128528](-) rrn4.5_copy2 [128757:128860](-) rrn23_copy2 [128959:131769](-) rrn16_copy2 [134204:135694](-) This genome has 8 genes with intron(s). Details are as follows: 7 gene(s) have 1 intron(s) Genes Exons trnK [4345:4381](-) [1733:1767](-) trnV [9916:9954](+) [10543:10577](+) trnL [14202:14238](-) [13644:13693](-) trnI_copy2 [101296:101337](+) [102286:102320](+) trnA [102385:102422](+) [103233:103267](+) trnA_copy2 [132776:132813](-) [131931:131965](-) trnI_copy3 [133865:133902](-) [132878:132912](-) 1 gene(s) have 2 intron(s) Genes Exons rps12 [68286:68398](-) [97202:97434](-) [96644:96669](-)