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, 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, psbA_copy2, 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, rpl32, rpl33, rpl36 Small subunit of ribosome rps11, rps12, 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 clpP Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor infA Conserved open reading frames ycf1, ycf12, ycf2, ycf2_copy2, ycf4 Other genes chlB, chlL, chlN, rpl21 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 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 None None None 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [12469:12613](-) [11349:11758](-) clpP (3/3) [67225:67295](-) [66202:66493](-) [65309:65548](-) ndhA (2/2) [116940:117497](-) [115529:116086](-) ndhB (2/2) [440:1165](-) [149410:150180](-) petB (2/2) [70468:70473](+) [71179:71820](+) petD (2/2) [72028:72035](+) [72677:73148](+) rpl16 (2/2) [78269:78274](-) [77181:77588](-) rpl2 (2/2) [81143:81530](-) [79966:80399](-) rpoC1 (2/2) [22577:23008](-) [20190:21854](-) rps12 (2/3) [64968:65081](-) [138049:138345](-) rps16 (2/2) [4242:4283](-) [3621:3815](-) ycf3 (3/3) [42484:42608](-) [41524:41752](-) [40703:40900](-) ### The exon column shows the number of (actual exons/expected exons). ### 4. Genes with internal stop codon: ['chlB', 'atpA', 'atpI', 'rps2', 'rpoC2', 'rpoC1', 'rpoB', 'accD', 'petA', 'infA', 'rps3', 'rpl2', 'rps7', 'ycf2', 'ndhF', 'rpl21', 'ndhA', 'ndhH', 'chlL', 'ycf2_copy2', 'rps7_copy2'] 5. Genes with nonstandard start codon: Genes Start codon ndhB ACG matK ATT chlB TAT atpF ACG psbM ACG petN ATT psbC GTG ndhJ CTA accD ATT psbL ACG psbF ACG rpl20 ACG psbB ACG rpl36 ACG rps8 ACG rps19 ACG rpl23 ACG rps7 ATT ndhF GTG rpl21 ATT ccsA ACG ndhD ATT ndhE ATC ndhG ACG ndhH CAG ycf1 ATC chlL AAC rps7_copy2 ATT 6. Genes with nonstandard stop codon: Genes Stop codon petD CAG chlL CGA 7. Conclusion This genome has 130 genes (108 unique genes). Including: 87 protein-coding genes (84 are unique) 35 tRNA genes (20 are unique) 8 rRNA genes (4 are unique) Details are as follows: 87 protein-coding genes (84 are unique) Genes Length Location accD 933 [53836:54768](+) atpA 1524 [9744:11267](-) atpB 1482 [49783:51264](-) atpE 399 [49379:49777](-) atpF 555 [12469:12613](-) [11349:11758](-) atpH 246 [12947:13192](-) atpI 747 [14002:14748](-) ccsA 951 [110129:111079](+) cemA 1395 [56428:57822](+) chlB 1630 [4441:6070](-) chlL 883 [126266:127148](-) chlN 1383 [124805:126187](-) clpP 603 [67225:67295](-) [66202:66493](-) [65309:65548](-) infA 243 [75281:75523](-) matK 1440 [1379:2818](-) ndhA 1116 [116940:117497](-) [115529:116086](-) ndhB 1497 [440:1165](-) [149410:150180](-) ndhC 363 [47327:47689](-) ndhD 1491 [111496:112986](-) ndhE 303 [113708:114010](-) ndhF 2190 [105718:107907](-) ndhG 594 [114113:114706](-) ndhH 1222 [117499:118720](-) ndhI 504 [114892:115395](-) ndhJ 483 [46014:46496](-) ndhK 672 [46584:47255](-) petA 966 [58032:58997](+) petB 648 [70468:70473](+) [71179:71820](+) petD 480 [72028:72035](+) [72677:73148](+) petG 117 [61506:61622](+) petL 210 [61243:61452](+) petN 93 [29157:29249](-) psaA 2253 [38150:40402](-) psaB 2205 [35920:38124](-) psaC 246 [113125:113370](-) psaI 111 [55027:55137](+) psaJ 129 [62530:62658](+) psbA 1062 [96368:97429](+) psbA_copy2 1062 [135422:136483](-) psbB 1527 [67792:69318](+) psbC 1386 [31365:32750](-) psbD 1062 [32734:33795](-) psbE 252 [60251:60502](-) psbF 120 [60122:60241](-) psbH 225 [70021:70245](+) psbI 111 [7014:7124](+) psbJ 123 [59741:59863](-) psbK 177 [6600:6776](+) psbL 117 [59984:60100](-) psbM 108 [28136:28243](+) psbN 138 [69805:69942](-) psbT 105 [69569:69673](+) psbZ 189 [30407:30595](-) rbcL 1428 [51894:53321](+) rpl14 369 [76367:76735](-) rpl16 414 [78269:78274](-) [77181:77588](-) rpl2 822 [81143:81530](-) [79966:80399](-) rpl20 357 [63660:64016](-) rpl21 357 [108215:108571](+) rpl22 369 [79254:79622](-) rpl23 282 [81626:81907](-) rpl32 177 [108762:108938](+) rpl33 201 [62889:63089](+) rpl36 114 [75034:75147](-) rpoA 1038 [73494:74531](-) rpoB 3216 [23054:26269](-) rpoC1 2097 [22577:23008](-) [20190:21854](-) rpoC2 4263 [15784:20046](-) rps11 393 [74574:74966](-) rps12 411 [64968:65081](-) [138049:138345](-) rps14 303 [35484:35786](-) rps15 276 [118806:119081](-) rps16 237 [4242:4283](-) [3621:3815](-) rps18 228 [63171:63398](+) rps19 279 [79653:79931](-) rps2 708 [14955:15662](-) rps3 654 [78507:79160](-) rps4 594 [43446:44039](-) rps7 444 [95426:95869](+) rps7_copy2 444 [136982:137425](-) rps8 399 [75639:76037](-) ycf1 5091 [119372:124462](-) ycf12 102 [8066:8167](+) ycf2 6315 [98198:104512](+) ycf2_copy2 6315 [128339:134653](-) ycf3 552 [42484:42608](-) [41524:41752](-) [40703:40900](-) ycf4 555 [55540:56094](+) 35 tRNA genes (20 are unique) Genes Location trnG [6164:6235](-) trnS [7203:7290](-) trnG_copy2 [8361:8383](+) [9321:9368](+) trnR [9578:9649](+) trnD [27214:27287](+) trnY [27402:27483](-) trnE [27645:27717](-) trnC [29694:29765](-) trnG_copy3 [30076:30146](-) trnS_copy2 [30979:31067](+) trnT [34945:35016](-) trnfM [35201:35274](-) trnS_copy3 [42897:42983](+) trnL [44775:44808](+) [45389:45435](+) trnF [45736:45808](+) trnV [48808:48841](-) [48138:48177](-) trnM [49115:49187](+) trnSeC [53449:53522](+) trnW [61864:61937](-) trnP [62124:62197](-) trnI [82161:82234](-) trnT_copy2 [83676:83709](+) [84218:84260](+) trnR_copy2 [85173:85246](-) trnA [89952:89988](-) [89112:89147](-) trnI_copy2 [91088:91123](-) [90056:90091](-) trnH [97859:97932](+) trnN [105171:105232](-) trnP_copy2 [109600:109673](-) trnL_copy2 [109898:109977](+) trnN_copy2 [127619:127681](+) trnH_copy2 [134919:134992](-) trnI_copy3 [141728:141763](+) [142760:142795](+) trnA_copy2 [142863:142899](+) [143704:143739](+) trnR_copy3 [147605:147678](+) trnT_copy3 [149142:149175](-) [148591:148633](-) 8 rRNA genes (4 are unique) Genes Location rrn5 [85502:85624](-) rrn4.5 [85917:86019](-) rrn23 [86121:88931](-) rrn16 [91406:92905](-) rrn16_copy2 [139946:141445](+) rrn23_copy2 [143920:146730](+) rrn4.5_copy2 [146832:146934](+) rrn5_copy2 [147227:147349](+) This genome has 21 genes with intron(s). Details are as follows: 19 gene(s) have 1 intron(s) Genes Exons rps12 [64968:65081](-) [138049:138345](-) ndhB [440:1165](-) [149410:150180](-) rps16 [4242:4283](-) [3621:3815](-) atpF [12469:12613](-) [11349:11758](-) rpoC1 [22577:23008](-) [20190:21854](-) petB [70468:70473](+) [71179:71820](+) petD [72028:72035](+) [72677:73148](+) rpl16 [78269:78274](-) [77181:77588](-) rpl2 [81143:81530](-) [79966:80399](-) ndhA [116940:117497](-) [115529:116086](-) trnG_copy2 [8361:8383](+) [9321:9368](+) trnL [44775:44808](+) [45389:45435](+) trnV [48808:48841](-) [48138:48177](-) trnT_copy2 [83676:83709](+) [84218:84260](+) trnA [89952:89988](-) [89112:89147](-) trnI_copy2 [91088:91123](-) [90056:90091](-) trnI_copy3 [141728:141763](+) [142760:142795](+) trnA_copy2 [142863:142899](+) [143704:143739](+) trnT_copy3 [149142:149175](-) [148591:148633](-) 2 gene(s) have 2 intron(s) Genes Exons ycf3 [42484:42608](-) [41524:41752](-) [40703:40900](-) clpP [67225:67295](-) [66202:66493](-) [65309:65548](-)