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, psbD_copy2, 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 rps12, rps12_copy2, rps14, rps15, rps15_copy2, 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 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 rpl22 Small subunit of ribosome rps11 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 psbD 1062 [33470:34532](+) psbD_copy2 213 [81776:81989](-) rps15 258 [117635:117893](+) rps15_copy2 273 [130631:130904](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [13438:13582](-) [12313:12722](-) clpP (3/3) [74563:74633](-) [72979:73272](-) [72112:72343](-) ndhA (2/2) [128800:129352](-) [127158:127696](-) ndhB (2/2) [98269:99043](-) [96832:97589](-) ndhB_copy2 (2/2) [149497:150271](+) [150951:151708](+) petB (2/2) [77543:77548](+) [78264:78905](+) petD (2/2) [79101:79108](+) [79838:80312](+) rpl16 (2/2) [85144:85152](-) [83860:84258](-) rpl2 (2/2) [87941:88331](-) [86815:87248](-) rpl2_copy2 (2/2) [160209:160599](+) [161292:161725](+) rpoC1 (1/2) [21386:22456](-) rps12 (3/3) [71862:71975](-) [100401:100632](-) [99839:99864](-) rps12_copy2 (3/3) [71862:71975](-) [147908:148139](+) [148676:148701](+) rps16 (2/2) [6271:6310](-) [5180:5406](-) ycf3 (3/3) [45132:45257](-) [44176:44403](-) [43297:43449](-) ### 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 rps19 GTG ndhD CTG rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 132 genes (111 unique genes). Including: 87 protein-coding genes (77 are unique) 37 tRNA genes (30 are unique) 8 rRNA genes (4 are unique) Details are as follows: 87 protein-coding genes (77 are unique) Genes Length Location accD 852 [59917:60768](+) atpA 1512 [10737:12248](-) atpB 1497 [54196:55692](-) atpE 402 [53798:54199](-) atpF 555 [13438:13582](-) [12313:12722](-) atpH 246 [13963:14208](-) atpI 744 [15138:15881](-) ccsA 972 [121811:122782](+) cemA 690 [63197:63886](+) clpP 597 [74563:74633](-) [72979:73272](-) [72112:72343](-) infA 276 [82391:82666](-) matK 1536 [1994:3529](-) ndhA 1092 [128800:129352](-) [127158:127696](-) ndhB 1533 [98269:99043](-) [96832:97589](-) ndhB_copy2 1533 [149497:150271](+) [150951:151708](+) ndhC 363 [51177:51539](-) ndhD 1530 [123026:124555](-) ndhE 306 [125159:125464](-) ndhF 2238 [117937:120174](-) ndhG 531 [125681:126211](-) ndhH 1182 [129354:130535](-) ndhI 507 [126572:127078](-) ndhJ 477 [49867:50343](-) ndhK 678 [50445:51122](-) petA 963 [64103:65065](+) petB 648 [77543:77548](+) [78264:78905](+) petD 483 [79101:79108](+) [79838:80312](+) petG 114 [68031:68144](+) petL 96 [67758:67853](+) petN 90 [29611:29700](+) psaA 2253 [40152:42404](-) psaB 2205 [37922:40126](-) psaC 246 [124652:124897](-) psaI 111 [61328:61438](+) psaJ 135 [68970:69104](+) psbA 1059 [423:1481](-) psbB 1527 [75078:76604](+) psbC 1422 [34480:35901](+) psbD 1062 [33471:34532](+) psbD_copy2 213 [81777:81989](-) psbE 252 [66621:66872](-) psbF 120 [66487:66606](-) psbH 222 [77197:77418](+) psbI 111 [8543:8653](+) psbJ 123 [66085:66207](-) psbK 180 [7974:8153](+) psbL 117 [66347:66463](-) psbM 105 [30721:30825](-) psbN 132 [76960:77091](-) psbT 102 [76793:76894](+) psbZ 189 [36546:36734](+) rbcL 1458 [56501:57958](+) rpl14 369 [83365:83733](-) rpl16 408 [85144:85152](-) [83860:84258](-) rpl2 825 [87941:88331](-) [86815:87248](-) rpl20 378 [70679:71056](-) rpl23 282 [88350:88631](-) rpl23_copy2 282 [159909:160190](+) rpl2_copy2 825 [160209:160599](+) [161292:161725](+) rpl32 162 [120616:120777](+) rpl33 201 [69575:69775](+) rpl36 114 [82182:82295](-) rpoA 750 [80504:81253](-) rpoB 3213 [24243:27455](-) rpoC1 1071 [21386:22456](-) rpoC2 4173 [17051:21223](-) rps12 372 [71862:71975](-) [100401:100632](-) [99839:99864](-) rps12_copy2 372 [71862:71975](-) [147908:148139](+) [148676:148701](+) rps14 303 [37497:37799](-) rps15 258 [117636:117893](+) rps15_copy2 273 [130632:130904](-) rps16 267 [6271:6310](-) [5180:5406](-) rps18 495 [69942:70436](+) rps19 279 [86463:86741](-) rps19_copy2 279 [161799:162077](+) rps2 711 [16107:16817](-) rps3 663 [85290:85952](-) rps4 600 [46315:46914](-) rps7 468 [99318:99785](-) rps7_copy2 468 [148755:149222](+) rps8 405 [82785:83189](-) ycf1 5433 [111773:117205](+) ycf1_copy2 5433 [131335:136767](-) ycf2 6333 [89179:95511](+) ycf2_copy2 6333 [153029:159361](-) ycf3 507 [45132:45257](-) [44176:44403](-) [43297:43449](-) ycf4 555 [61892:62446](+) 37 tRNA genes (30 are unique) Genes Location trnH-GUG [19:92](-) trnK-UUU [4244:4280](-) [1714:1748](-) trnQ-UUG [7566:7637](-) trnS-GCU [8778:8864](-) trnG-UCC [9601:9623](+) [10306:10353](+) trnR-UCU [10555:10626](+) trnC-GCA [28688:28758](+) trnD-GUC [31535:31608](-) trnY-GUA [31718:31800](-) trnE-UUC [31851:31923](-) trnT-GGU [32499:32570](+) trnS-UGA [36145:36237](-) trnG-GCC [37038:37108](+) trnfM-CAU [37279:37352](-) trnS-GGA [45916:46001](+) trnT-UGU [47393:47465](-) trnL-UAA [48180:48214](+) [48735:48784](+) trnF-GAA [49135:49206](+) trnV-UAC [52655:52688](+) [53271:53308](+) trnM-CAU [53507:53579](+) trnW-CCA [68274:68347](-) trnP-UGG [68513:68586](-) trnI-CAU [88852:88925](+) trnL-CAA [96210:96290](-) trnV-GAC [102227:102298](+) trnI-GAU [104351:104386](+) [105323:105358](+) trnA-UGC [105423:105460](+) [106273:106307](+) trnR-ACG [110107:110180](+) trnN-GUU [110550:110621](-) trnL-UAG [121647:121726](+) trnN-GUU_copy2 [137919:137990](+) trnR-ACG_copy2 [138360:138433](-) trnA-UGC_copy2 [143080:143117](-) [142233:142267](-) trnI-GAU_copy2 [144154:144189](-) [143182:143217](-) trnV-GAC_copy2 [146242:146313](-) trnL-CAA_copy2 [152250:152330](+) trnI-CAU_copy2 [159615:159688](-) 8 rRNA genes (4 are unique) Genes Location rrn16S [102523:104011](+) rrn23S [106474:109290](+) rrn4.5S [109389:109491](+) rrn5S [109743:109863](+) rrn5S_copy2 [138677:138797](-) rrn4.5S_copy2 [139049:139151](-) rrn23S_copy2 [139250:142066](-) rrn16S_copy2 [144529:146017](-) This genome has 22 genes with intron(s). Details are as follows: 18 gene(s) have 1 intron(s) Genes Exons rps16 [6271:6310](-) [5180:5406](-) atpF [13438:13582](-) [12313:12722](-) petB [77543:77548](+) [78264:78905](+) petD [79101:79108](+) [79838:80312](+) rpl16 [85144:85152](-) [83860:84258](-) rpl2 [87941:88331](-) [86815:87248](-) ndhB [98269:99043](-) [96832:97589](-) ndhA [128800:129352](-) [127158:127696](-) ndhB_copy2 [149497:150271](+) [150951:151708](+) rpl2_copy2 [160209:160599](+) [161292:161725](+) trnK-UUU [4244:4280](-) [1714:1748](-) trnG-UCC [9601:9623](+) [10306:10353](+) trnL-UAA [48180:48214](+) [48735:48784](+) trnV-UAC [52655:52688](+) [53271:53308](+) trnI-GAU [104351:104386](+) [105323:105358](+) trnA-UGC [105423:105460](+) [106273:106307](+) trnA-UGC_copy2 [143080:143117](-) [142233:142267](-) trnI-GAU_copy2 [144154:144189](-) [143182:143217](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [71862:71975](-) [100401:100632](-) [99839:99864](-) ycf3 [45132:45257](-) [44176:44403](-) [43297:43449](-) rps12_copy2 [71862:71975](-) [147908:148139](+) [148676:148701](+) clpP [74563:74633](-) [72979:73272](-) [72112:72343](-)