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, rpl14_copy2, rpl16, rpl16_copy2, rpl2, rpl20, rpl22, rpl22_copy2, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps12_copy2, rps14, rps15, rps16, rps18, rps19, rps19_copy2, rps2, rps3, rps3_copy2, rps4, rps7, rps7_copy2, rps8, rps8_copy2 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, 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 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) [16583:16727](-) [15433:15842](-) clpP (3/3) [71607:71677](-) [70522:70810](-) [69580:69825](-) ndhA (2/2) [121995:122547](-) [120446:120984](-) ndhB (2/2) [95549:96325](-) [94091:94846](-) ndhB_copy2 (2/2) [142535:143311](+) [144014:144769](+) petB (2/2) [74572:74577](+) [75361:76002](+) petD (2/2) [76207:76214](+) [76947:77442](+) rpl16 (2/2) [82141:82149](-) [80765:81163](-) rpl16_copy2 (2/2) [156711:156719](+) [157697:158095](+) rpl2 (2/2) [84978:85368](-) [83893:84326](-) rpl2_copy2 (2/2) [153492:153882](+) [154534:154967](+) rpoC1 (2/2) [27098:27527](-) [24717:26329](-) rps12 (3/3) [69308:69421](-) [97737:97968](-) [97170:97195](-) rps12_copy2 (3/3) [69308:69421](-) [140892:141123](+) [141665:141690](+) rps16 (2/2) [1194:1233](+) [2122:2342](+) ycf3 (3/3) [49067:49190](-) [48111:48340](-) [47211:47363](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: rps4 2 [159532:159534](+) [1:630](+)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon rps19 GTG rpl2 ACG ndhD ACG rpl2_copy2 ACG rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 135 genes (112 unique genes). Including: 91 protein-coding genes (79 are unique) 36 tRNA genes (29 are unique) 8 rRNA genes (4 are unique) Details are as follows: 91 protein-coding genes (79 are unique) Genes Length Location accD 1443 [57403:58845](+) atpA 1524 [13843:15366](-) atpB 1503 [52869:54371](-) atpE 402 [52471:52872](-) atpF 555 [16583:16727](-) [15433:15842](-) atpH 246 [17163:17408](-) atpI 744 [18519:19262](-) ccsA 966 [114852:115817](+) cemA 690 [61104:61793](+) clpP 606 [71607:71677](-) [70522:70810](-) [69580:69825](-) infA 171 [79348:79518](-) matK 1530 [3792:5321](+) ndhA 1092 [121995:122547](-) [120446:120984](-) ndhB 1533 [95549:96325](-) [94091:94846](-) ndhB_copy2 1533 [142535:143311](+) [144014:144769](+) ndhC 363 [12037:12399](-) ndhD 1503 [116075:117577](-) ndhE 306 [118229:118534](-) ndhF 2235 [110362:112596](-) ndhG 534 [118817:119350](-) ndhH 1182 [122549:123730](-) ndhI 543 [119830:120372](-) ndhJ 477 [10684:11160](-) ndhK 678 [11296:11973](-) petA 969 [62001:62969](+) petB 648 [74572:74577](+) [75361:76002](+) petD 504 [76207:76214](+) [76947:77442](+) petG 114 [65797:65910](+) petL 96 [65517:65612](+) petN 90 [32362:32451](+) psaA 2253 [44219:46471](-) psaB 2205 [41989:44193](-) psaC 246 [117740:117985](-) psaI 111 [59383:59493](+) psaJ 135 [66692:66826](+) psbA 1062 [5893:6954](+) psbB 1527 [72087:73613](+) psbC 1422 [38551:39972](+) psbD 1062 [37542:38603](+) psbE 252 [63892:64143](-) psbF 120 [63763:63882](-) psbH 222 [74231:74452](+) psbI 111 [8484:8594](+) psbJ 123 [63382:63504](-) psbK 186 [7894:8079](+) psbL 117 [63624:63740](-) psbM 105 [33247:33351](-) psbN 132 [73997:74128](-) psbT 108 [73803:73910](+) psbZ 189 [40553:40741](+) rbcL 1428 [55240:56667](+) rpl14 369 [80254:80622](-) rpl14_copy2 369 [158238:158606](+) rpl16 408 [82141:82149](-) [80765:81163](-) rpl16_copy2 408 [156711:156719](+) [157697:158095](+) rpl2 825 [84978:85368](-) [83893:84326](-) rpl20 354 [68163:68516](-) rpl22 540 [82955:83494](-) rpl22_copy2 540 [155366:155905](+) rpl23 282 [85387:85668](-) rpl23_copy2 282 [153192:153473](+) rpl2_copy2 825 [153492:153882](+) [154534:154967](+) rpl32 222 [113656:113877](+) rpl33 201 [67218:67418](+) rpl36 114 [79215:79328](-) rpoA 1020 [77588:78607](-) rpoB 3213 [27554:30766](-) rpoC1 2043 [27098:27527](-) [24717:26329](-) rpoC2 4152 [20398:24549](-) rps11 417 [78680:79096](-) rps12 372 [69308:69421](-) [97737:97968](-) [97170:97195](-) rps12_copy2 372 [69308:69421](-) [140892:141123](+) [141665:141690](+) rps14 303 [41555:41857](-) rps15 273 [123878:124150](-) rps16 261 [1194:1233](+) [2122:2342](+) rps18 306 [67607:67912](+) rps19 279 [83554:83832](-) rps19_copy2 279 [155028:155306](+) rps2 711 [19482:20192](-) rps3 657 [82314:82970](-) rps3_copy2 657 [155890:156546](+) rps4 633 [159532:159534](+) [1:630](+) rps7 468 [96649:97116](-) rps7_copy2 468 [141744:142211](+) rps8 399 [79638:80036](-) rps8_copy2 399 [158824:159222](+) ycf1 5637 [124554:130190](-) ycf2 6834 [85976:92809](+) ycf2_copy2 6834 [146051:152884](-) ycf3 507 [49067:49190](-) [48111:48340](-) [47211:47363](-) ycf4 555 [59942:60496](+) 36 tRNA genes (29 are unique) Genes Location trnK-UUU [2995:3031](+) [5578:5612](+) trnH-GUG [7285:7358](+) trnQ-UUG [7486:7557](-) trnS-GCU [8681:8768](-) trnL-UAA [9344:9378](+) [9872:9921](+) trnF-GAA [10071:10143](+) trnG-UCC [12701:12723](+) [13435:13482](+) trnR-UCU [13642:13713](+) trnC-GCA [31848:31918](+) trnD-GUC [34505:34578](-) trnY-GUA [34956:35039](-) trnE-UUC [35099:35171](-) trnT-GGU [35893:35964](+) trnS-UGA [40135:40227](-) trnG-GCC [41070:41140](+) trnfM-CAU [41319:41392](-) trnS-GGA [50110:50196](+) trnV-UAC [51926:51963](-) [51307:51341](-) trnM-CAU [52143:52215](+) trnW-CCA [66056:66129](-) trnP-UGG [66293:66366](-) trnI-CAU [85834:85907](-) trnL-CAA [93450:93530](-) trnV-GAC [99795:99866](+) trnI-GAU [101876:101912](+) [102860:102894](+) trnA-UGC [102959:102996](+) [103810:103844](+) trnR-ACG [107586:107659](+) trnN-GUU [108275:108346](-) trnL-UAG [114657:114736](+) trnN-GUU_copy2 [130514:130585](+) trnR-ACG_copy2 [131201:131274](-) trnA-UGC_copy2 [135864:135901](-) [135016:135050](-) trnI-GAU_copy2 [136948:136984](-) [135966:136000](-) trnV-GAC_copy2 [138994:139065](-) trnL-CAA_copy2 [145330:145410](+) trnI-CAU_copy2 [152953:153026](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [100095:101585](+) rrn23 [103997:106805](+) rrn4.5 [106905:107007](+) rrn5 [107232:107352](+) rrn5_copy2 [131508:131628](-) rrn4.5_copy2 [131853:131955](-) rrn23_copy2 [132053:134863](-) rrn16_copy2 [137275:138765](-) This genome has 25 genes with intron(s). Details are as follows: 21 gene(s) have 1 intron(s) Genes Exons rps4 [159532:159534](+) [1:630](+) rps16 [1194:1233](+) [2122:2342](+) atpF [16583:16727](-) [15433:15842](-) rpoC1 [27098:27527](-) [24717:26329](-) petB [74572:74577](+) [75361:76002](+) petD [76207:76214](+) [76947:77442](+) rpl16 [82141:82149](-) [80765:81163](-) rpl2 [84978:85368](-) [83893:84326](-) ndhB [95549:96325](-) [94091:94846](-) ndhA [121995:122547](-) [120446:120984](-) ndhB_copy2 [142535:143311](+) [144014:144769](+) rpl2_copy2 [153492:153882](+) [154534:154967](+) rpl16_copy2 [156711:156719](+) [157697:158095](+) trnK-UUU [2995:3031](+) [5578:5612](+) trnL-UAA [9344:9378](+) [9872:9921](+) trnG-UCC [12701:12723](+) [13435:13482](+) trnV-UAC [51926:51963](-) [51307:51341](-) trnI-GAU [101876:101912](+) [102860:102894](+) trnA-UGC [102959:102996](+) [103810:103844](+) trnA-UGC_copy2 [135864:135901](-) [135016:135050](-) trnI-GAU_copy2 [136948:136984](-) [135966:136000](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [69308:69421](-) [97737:97968](-) [97170:97195](-) ycf3 [49067:49190](-) [48111:48340](-) [47211:47363](-) rps12_copy2 [69308:69421](-) [140892:141123](+) [141665:141690](+) clpP [71607:71677](-) [70522:70810](-) [69580:69825](-)