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, 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 infA Conserved open reading frames ycf1, ycf12, ycf4 Other genes chlB, chlL, chlN, psaM, 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, ycf2 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) [13259:13403](-) [12153:12562](-) clpP (3/3) [70856:70926](-) [69749:70040](-) [68930:69169](-) ndhA (2/2) [126680:127237](-) [125187:125744](-) ndhB (2/2) [557:1282](-) [164976:165746](-) petB (2/2) [73903:73908](+) [74700:75347](+) petD (2/2) [75546:75553](+) [76200:76674](+) rpl16 (2/2) [81795:81803](-) [80609:81013](-) rpl2 (2/2) [84548:84944](-) [83383:83891](-) rpoC1 (2/2) [23313:23744](-) [20935:22566](-) rps12 (3/3) [68405:68518](-) [147882:148113](-) [147292:147317](-) rps12_copy2 (3/3) [68405:68518](-) [103580:103811](+) [104376:104401](+) rps16 (2/2) [5117:5158](-) [4129:4341](-) ycf3 (3/3) [45268:45391](-) [44309:44538](-) [43505:43663](-) ### The exon column shows the number of (actual exons/expected exons). ### 4. Genes with internal stop codon: ['matK', 'chlB', 'atpA', 'atpI', 'rps2', 'rpoC2', 'rpoC1', 'rpoB', 'ycf3', 'rps4', 'accD', 'petA', 'psbE', 'rpl20', 'rpoA', 'rps11', 'infA', 'rps8', 'rps3', 'rpl2', 'rpl23', 'rps7', 'ndhF', 'rpl21', 'ndhA', 'ycf1', 'chlN', 'chlL', 'rps7_copy2'] 5. Genes with nonstandard start codon: Genes Start codon rps12 GTG ndhB ACG matK ACG atpA ACG atpH ACG atpI ACG rpoC1 ACG psbM ACG petN ACG psbC GTG psaB ACG rps4 ACG accD ACG rps18 ACG rps12_copy2 GTG psbN ACG petB ACG petD ACG rpl36 ACG rps19 ACG ndhE ACG ndhG ACG ndhA ACG ndhH ACG ycf1 ACG chlL ACG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 128 genes (116 unique genes). Including: 87 protein-coding genes (84 are unique) 33 tRNA genes (28 are unique) 8 rRNA genes (4 are unique) Details are as follows: 87 protein-coding genes (84 are unique) Genes Length Location accD 933 [56878:57810](+) atpA 1524 [10561:12084](-) atpB 1482 [52794:54275](-) atpE 399 [52390:52788](-) atpF 555 [13259:13403](-) [12153:12562](-) atpH 246 [13778:14023](-) atpI 747 [14771:15517](-) ccsA 951 [119759:120709](+) cemA 1479 [59660:61138](+) chlB 1542 [5321:6862](-) chlL 882 [135983:136864](-) chlN 1395 [134535:135929](-) clpP 603 [70856:70926](-) [69749:70040](-) [68930:69169](-) infA 246 [78812:79057](-) matK 1509 [1480:2988](-) ndhA 1116 [126680:127237](-) [125187:125744](-) ndhB 1497 [557:1282](-) [164976:165746](-) ndhC 435 [50393:50827](-) ndhD 1509 [121126:122634](-) ndhE 303 [123387:123689](-) ndhF 2229 [114826:117054](-) ndhG 594 [123781:124374](-) ndhH 1185 [127239:128423](-) ndhI 549 [124501:125049](-) ndhJ 522 [49156:49677](-) ndhK 756 [49719:50474](-) petA 966 [61364:62329](+) petB 654 [73903:73908](+) [74700:75347](+) petD 483 [75546:75553](+) [76200:76674](+) petG 117 [65129:65245](+) petL 96 [64885:64980](+) petN 90 [30650:30739](-) psaA 2253 [40914:43166](-) psaB 2205 [38684:40888](-) psaC 246 [122782:123027](-) psaI 111 [58405:58515](+) psaJ 129 [66026:66154](+) psaM 99 [8732:8830](-) psbA 1062 [105590:106651](+) psbA_copy2 1062 [145042:146103](-) psbB 1527 [71410:72936](+) psbC 1386 [33462:34847](-) psbD 1062 [34831:35892](-) psbE 252 [63555:63806](-) psbF 120 [63426:63545](-) psbH 225 [73542:73766](+) psbI 111 [8149:8259](+) psbJ 123 [63045:63167](-) psbK 177 [7463:7639](+) psbL 117 [63287:63403](-) psbM 105 [29099:29203](+) psbN 132 [73326:73457](-) psbT 105 [73116:73220](+) psbZ 192 [32054:32245](-) rbcL 1428 [54913:56340](+) rpl14 372 [79847:80218](-) rpl16 414 [81795:81803](-) [80609:81013](-) rpl2 906 [84548:84944](-) [83383:83891](-) rpl20 357 [67014:67370](-) rpl21 357 [117307:117663](+) rpl22 381 [82672:83052](-) rpl23 285 [85002:85286](-) rpl32 177 [117856:118032](+) rpl33 201 [66264:66464](+) rpl36 114 [78548:78661](-) rpoA 1017 [77023:78039](-) rpoB 3249 [23798:27046](-) rpoC1 2064 [23313:23744](-) [20935:22566](-) rpoC2 4263 [16551:20813](-) rps11 393 [78084:78476](-) rps12 372 [68405:68518](-) [147882:148113](-) [147292:147317](-) rps12_copy2 372 [68405:68518](-) [103580:103811](+) [104376:104401](+) rps14 303 [38161:38463](-) rps15 270 [128533:128802](-) rps16 255 [5117:5158](-) [4129:4341](-) rps18 228 [66532:66759](+) rps19 279 [83070:83348](-) rps2 753 [15673:16425](-) rps3 657 [81928:82584](-) rps4 624 [46547:47170](-) rps7 474 [104467:104940](+) rps7_copy2 474 [146753:147226](-) rps8 399 [79194:79592](-) ycf1 5040 [129127:134166](-) ycf12 102 [9061:9162](+) ycf3 513 [45268:45391](-) [44309:44538](-) [43505:43663](-) ycf4 558 [58948:59505](+) 33 tRNA genes (28 are unique) Genes Location trnQ-UUG [7075:7146](-) trnS-GCU [8324:8411](-) trnG-UCC [9312:9334](+) [10194:10241](+) trnR-UCU [10379:10450](+) trnD-GUC [28178:28251](+) trnY-GUA [28343:28424](-) trnE-UUC [28579:28651](-) trnC-GCA [31144:31215](-) trnG-GCC [31798:31868](-) trnS-UGA [32608:32696](+) trnT-GGU [37463:37534](-) trnfM-CAU [37974:38048](-) trnS-GGA [45969:46055](+) trnL-CAA [47849:47882](+) [48442:48493](+) trnF-GAA [48862:48934](+) trnV-UAC [51861:51897](-) [51218:51252](-) trnM-CAU [52099:52171](+) trnR-UCG [56453:56526](+) trnW-CCA [65555:65628](-) trnP-UGG [65672:65745](-) trnI-CAU [85523:85596](-) trnR-ACG [88555:88628](-) trnA-UGC [93289:93326](-) [92475:92509](-) trnI-GAU [94381:94422](-) [93394:93428](-) trnH-GUG [107052:107126](+) trnN-GUU [114297:114367](-) trnP-GGG [119185:119258](-) trnL-UAG [119440:119519](+) trnN-GUU_copy2 [137326:137396](+) trnH-GUG_copy2 [144567:144641](-) trnI-GAU_copy2 [157271:157312](+) [158265:158299](+) trnA-UGC_copy2 [158367:158404](+) [159184:159218](+) trnR-ACG_copy2 [163065:163138](+) 8 rRNA genes (4 are unique) Genes Location rrn5 [88887:89009](-) rrn4.5 [89286:89388](-) rrn23 [89499:92315](-) rrn16 [94700:96199](-) rrn16_copy2 [155494:156993](+) rrn23_copy2 [159378:162194](+) rrn4.5_copy2 [162305:162407](+) rrn5_copy2 [162684:162806](+) This genome has 20 genes with intron(s). Details are as follows: 16 gene(s) have 1 intron(s) Genes Exons ndhB [557:1282](-) [164976:165746](-) rps16 [5117:5158](-) [4129:4341](-) atpF [13259:13403](-) [12153:12562](-) rpoC1 [23313:23744](-) [20935:22566](-) petB [73903:73908](+) [74700:75347](+) petD [75546:75553](+) [76200:76674](+) rpl16 [81795:81803](-) [80609:81013](-) rpl2 [84548:84944](-) [83383:83891](-) ndhA [126680:127237](-) [125187:125744](-) trnG-UCC [9312:9334](+) [10194:10241](+) trnL-CAA [47849:47882](+) [48442:48493](+) trnV-UAC [51861:51897](-) [51218:51252](-) trnA-UGC [93289:93326](-) [92475:92509](-) trnI-GAU [94381:94422](-) [93394:93428](-) trnI-GAU_copy2 [157271:157312](+) [158265:158299](+) trnA-UGC_copy2 [158367:158404](+) [159184:159218](+) 4 gene(s) have 2 intron(s) Genes Exons rps12 [68405:68518](-) [147882:148113](-) [147292:147317](-) ycf3 [45268:45391](-) [44309:44538](-) [43505:43663](-) rps12_copy2 [68405:68518](-) [103580:103811](+) [104376:104401](+) clpP [70856:70926](-) [69749:70040](-) [68930:69169](-)