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 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, 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, 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 clpP Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor None 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 ndhK Subunits of cytochrome b/f complex None Subunits of photosystem I None Subunits of photosystem II psbJ 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 ycf15 Other genes None 2. Multicopy genes with different lengths: Genes Length Location ycf1 5394 [108440:113834](+) ycf1_copy2 504 [127060:127564](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [49243:49386](+) [50114:50524](+) clpP (3/3) [71464:71534](-) [70470:70761](-) [69477:69704](-) ndhA (2/2) [115786:116349](+) [117649:118104](+) ndhB (2/2) [95941:96663](-) [94493:95248](-) ndhB_copy2 (2/2) [139342:140064](+) [140757:141512](+) petB (2/2) [74444:74449](+) [75265:75906](+) petD (2/2) [76107:76114](+) [76846:77320](+) rpl16 (2/2) [82297:82305](-) [80806:81216](-) rpl2 (2/2) [85046:85435](-) [83935:84369](-) rpl2_copy2 (2/2) [150570:150959](+) [151636:152070](+) rpoC1 (2/2) [37918:38379](+) [39159:40817](+) rps12 (2/3) [69268:69396](+) [138164:138457](+) rps12_copy2 (2/3) [69268:69396](+) [97548:97841](-) rps16 (2/2) [55856:55895](+) [56775:57004](+) ycf3 (3/3) [15888:16013](+) [16703:16930](+) [17674:17826](+) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: rpoC2 2 [40992:45098](+) [45112:45159](+)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon atpE ATT psbC GTG petN ATT rpoC1 ATT accD ATT psbL TTG rps12 CTG rps12_copy2 CTG psbB ATA rpoA ATT rps3 ATT rps19 GTG ndhI ATA ndhD ATT 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 125 genes (107 unique genes). Including: 82 protein-coding genes (75 are unique) 35 tRNA genes (28 are unique) 8 rRNA genes (4 are unique) Details are as follows: 82 protein-coding genes (75 are unique) Genes Length Location accD 1392 [57616:59007](+) atpA 1533 [50606:52138](+) atpB 1497 [7114:8610](+) atpE 411 [8598:9008](+) atpF 555 [49243:49386](+) [50114:50524](+) atpH 246 [48467:48712](+) atpI 744 [46372:47115](+) ccsA 978 [122519:123496](-) cemA 690 [60702:61391](+) clpP 591 [71464:71534](-) [70470:70761](-) [69477:69704](-) matK 1530 [2058:3587](-) ndhA 1020 [115786:116349](+) [117649:118104](+) ndhB 1479 [95941:96663](-) [94493:95248](-) ndhB_copy2 1479 [139342:140064](+) [140757:141512](+) ndhC 363 [10295:10657](+) ndhD 1509 [120709:122217](+) ndhE 306 [119724:120029](+) ndhF 2256 [124809:127064](+) ndhG 531 [118967:119497](+) ndhH 1182 [114603:115784](+) ndhI 519 [118159:118677](+) ndhJ 477 [11502:11978](+) petA 963 [61582:62544](+) petB 648 [74444:74449](+) [75265:75906](+) petD 483 [76107:76114](+) [76846:77320](+) petG 114 [65644:65757](+) petL 96 [65406:65501](+) petN 96 [32304:32399](-) psaA 2253 [18673:20925](+) psaB 2205 [20951:23155](+) psaC 246 [120331:120576](+) psaI 105 [59319:59423](+) psaJ 135 [66475:66609](+) psbA 1062 [386:1447](-) psbB 1542 [71962:73503](+) psbC 1452 [25612:27063](-) psbD 1062 [26981:28042](-) psbE 252 [63825:64076](-) psbF 120 [63696:63815](-) psbH 222 [74086:74307](+) psbI 111 [54113:54223](-) psbK 186 [54686:54871](-) psbL 132 [63557:63688](-) psbM 105 [31458:31562](+) psbN 132 [73841:73972](-) psbT 108 [73675:73782](+) psbZ 189 [24795:24983](-) rbcL 1449 [4903:6351](-) rpl14 369 [80316:80684](-) rpl16 420 [82297:82305](-) [80806:81216](-) rpl2 825 [85046:85435](-) [83935:84369](-) rpl20 393 [68080:68472](-) rpl23 282 [85457:85738](-) rpl23_copy2 282 [150267:150548](+) rpl2_copy2 825 [150570:150959](+) [151636:152070](+) rpl32 162 [124134:124295](-) rpl33 201 [67115:67315](+) rpl36 114 [79088:79201](-) rpoA 1011 [77543:78553](-) rpoB 3213 [34706:37918](+) rpoC1 2121 [37918:38379](+) [39159:40817](+) rpoC2 4155 [40992:45098](+) [45112:45159](+) rps11 417 [78630:79046](-) rps12 423 [69268:69396](+) [138164:138457](+) rps12_copy2 423 [69268:69396](+) [97548:97841](-) rps14 303 [23273:23575](+) rps15 273 [114234:114506](+) rps16 270 [55856:55895](+) [56775:57004](+) rps18 312 [67542:67853](+) rps19 279 [83598:83876](-) rps2 711 [45414:46124](+) rps3 660 [82458:83117](-) rps4 606 [14727:15332](+) rps7 468 [97024:97491](-) rps7_copy2 468 [138514:138981](+) rps8 405 [79632:80036](-) ycf1 5394 [108441:113834](+) ycf1_copy2 504 [127061:127564](-) ycf2 6882 [86348:93229](+) ycf2_copy2 6882 [142776:149657](-) ycf3 507 [15888:16013](+) [16703:16930](+) [17674:17826](+) ycf4 585 [59627:60211](+) 35 tRNA genes (28 are unique) Genes Location trnH-GUG [17:91](+) trnK-UUU [4321:4357](-) [1711:1745](-) trnV-UAC [9419:9457](+) [10041:10075](+) trnF-GAA [12617:12690](-) trnL-UAA [13100:13151](-) trnT-UGU [14375:14449](+) trnS-GGA [15557:15644](-) trnG-GCC [23922:23990](-) trnS-UGA [25334:25426](+) trnT-GGU [29416:29489](-) trnE-UUC [30301:30375](+) trnY-GUA [30440:30525](+) trnD-GUC [30961:31036](+) trnC-GCA [33477:33547](-) trnR-UCU [52332:52403](-) trnG-UCC [53402:53423](-) [52646:52696](-) trnS-GCU [53862:53948](+) trnQ-UUG [55324:55395](+) trnW-CCA [65915:65988](-) trnP-UGG [66169:66242](-) trnM-CAU [86185:86259](-) trnL-CAA [93812:93894](-) trnV-GAC [99461:99532](+) trnI-GAU [101538:101579](+) [102531:102565](+) trnA-UGC [102636:102673](+) [103495:103529](+) trnR-ACG [107294:107368](+) trnN-GUU [108014:108087](-) trnL-UAG [123590:123669](-) trnN-GUU_copy2 [127918:127991](+) trnR-ACG_copy2 [128637:128711](-) trnA-UGC_copy2 [133332:133369](-) [132476:132510](-) trnI-GAU_copy2 [134426:134467](-) [133440:133474](-) trnV-GAC_copy2 [136473:136544](-) trnL-CAA_copy2 [142111:142193](+) trnM-CAU_copy2 [149746:149820](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [99754:101244](+) rrn23 [103681:106493](+) rrn4.5 [106594:106697](+) rrn5 [106926:107046](+) rrn5_copy2 [128959:129079](-) rrn4.5_copy2 [129308:129411](-) rrn23_copy2 [129512:132324](-) rrn16_copy2 [134761:136251](-) This genome has 23 genes with intron(s). Details are as follows: 21 gene(s) have 1 intron(s) Genes Exons rpoC1 [37918:38379](+) [39159:40817](+) rpoC2 [40992:45098](+) [45112:45159](+) atpF [49243:49386](+) [50114:50524](+) rps16 [55856:55895](+) [56775:57004](+) rps12 [69268:69396](+) [138164:138457](+) rps12_copy2 [69268:69396](+) [97548:97841](-) petB [74444:74449](+) [75265:75906](+) petD [76107:76114](+) [76846:77320](+) rpl16 [82297:82305](-) [80806:81216](-) rpl2 [85046:85435](-) [83935:84369](-) ndhB [95941:96663](-) [94493:95248](-) ndhA [115786:116349](+) [117649:118104](+) ndhB_copy2 [139342:140064](+) [140757:141512](+) rpl2_copy2 [150570:150959](+) [151636:152070](+) trnK-UUU [4321:4357](-) [1711:1745](-) trnV-UAC [9419:9457](+) [10041:10075](+) trnG-UCC [53402:53423](-) [52646:52696](-) trnI-GAU [101538:101579](+) [102531:102565](+) trnA-UGC [102636:102673](+) [103495:103529](+) trnA-UGC_copy2 [133332:133369](-) [132476:132510](-) trnI-GAU_copy2 [134426:134467](-) [133440:133474](-) 2 gene(s) have 2 intron(s) Genes Exons ycf3 [15888:16013](+) [16703:16930](+) [17674:17826](+) clpP [71464:71534](-) [70470:70761](-) [69477:69704](-)