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, ndhA_copy2, ndhB, ndhB_copy2, ndhC, ndhD, ndhE, ndhE_copy2, ndhF, ndhG, ndhG_copy2, ndhH, ndhH_copy2, ndhI, ndhI_copy2, 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, rpl16, rpl2, rpl20, rpl22, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps12_copy2, rps14, rps15, rps15_copy2, 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 None 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 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 accD Translational initiation factor infA Conserved open reading frames ycf15 Other genes None 2. Multicopy genes with different lengths: Genes Length Location ndhE 171 [124566:124737](+) ndhE_copy2 303 [132229:132532](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [39079:39223](+) [39961:40370](+) clpP (3/3) [78756:78874](-) [77701:77999](-) [76793:77031](-) ndhA (2/2) [120732:121284](+) [122305:122843](+) ndhA_copy2 (2/2) [135818:136370](-) [134259:134797](-) ndhB (2/2) [98235:99011](-) [96807:97562](-) ndhB_copy2 (2/2) [158091:158867](+) [159540:160295](+) petB (2/2) [51356:51361](+) [52179:52820](+) petD (2/2) [53014:53021](+) [53742:54219](+) rpl16 (2/2) [84786:84794](-) [83264:83662](-) rpl2 (2/2) [87571:87961](-) [86473:86903](-) rpl2_copy2 (2/2) [169141:169531](+) [170199:170629](+) rpoC1 (1/2) [30408:32456](+) rps12 (3/3) [73708:73821](-) [100395:100626](-) [99839:99864](-) rps12_copy2 (3/3) [73708:73821](-) [156476:156707](+) [157238:157263](+) rps16 (1/2) [4770:5042](-) ycf3 (3/3) [8572:8700](+) [9396:9623](+) [10367:10519](+) ### 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 psbL ACG ndhD ACG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 136 genes (111 unique genes). Including: 90 protein-coding genes (77 are unique) 38 tRNA genes (30 are unique) 8 rRNA genes (4 are unique) Details are as follows: 90 protein-coding genes (77 are unique) Genes Length Location atpA 1503 [40437:41939](+) atpB 1497 [60441:61937](+) atpE 402 [61934:62335](+) atpF 555 [39079:39223](+) [39961:40370](+) atpH 246 [38410:38655](+) atpI 744 [74054:74797](-) ccsA 930 [128948:129877](+) cemA 693 [64785:65477](+) clpP 657 [78756:78874](-) [77701:77999](-) [76793:77031](-) matK 1530 [1947:3476](-) ndhA 1092 [120732:121284](+) [122305:122843](+) ndhA_copy2 1092 [135818:136370](-) [134259:134797](-) ndhB 1533 [98235:99011](-) [96807:97562](-) ndhB_copy2 1533 [158091:158867](+) [159540:160295](+) ndhC 363 [56180:56542](-) ndhD 1527 [130095:131621](-) ndhE 171 [124567:124737](+) ndhE_copy2 303 [132230:132532](-) ndhF 2247 [124939:127185](-) ndhG 531 [123812:124342](+) ndhG_copy2 531 [132760:133290](-) ndhH 1182 [119549:120730](+) ndhH_copy2 1182 [136372:137553](-) ndhI 504 [122926:123429](+) ndhI_copy2 504 [133673:134176](-) ndhJ 477 [54824:55300](-) ndhK 570 [55560:56129](-) petA 963 [65660:66622](+) petB 648 [51356:51361](+) [52179:52820](+) petD 486 [53014:53021](+) [53742:54219](+) petG 114 [69962:70075](+) petL 96 [69690:69785](+) petN 90 [24922:25011](-) psaA 2253 [11215:13467](+) psaB 2205 [13493:15697](+) psaC 246 [131735:131980](-) psaI 111 [62831:62941](+) psaJ 135 [70929:71063](+) psbA 1062 [333:1394](-) psbB 1527 [48950:50476](+) psbC 1422 [17613:19034](-) psbD 1062 [18982:20043](-) psbE 261 [68176:68436](-) psbF 120 [68047:68166](-) psbH 222 [51098:51319](+) psbI 111 [44023:44133](-) psbJ 123 [67646:67768](-) psbK 186 [44559:44744](-) psbL 117 [67908:68024](-) psbM 105 [24315:24419](+) psbN 132 [50864:50995](-) psbT 102 [50691:50792](+) psbZ 189 [16892:17080](-) rbcL 1428 [58307:59734](-) rpl14 369 [82767:83135](-) rpl16 408 [84786:84794](-) [83264:83662](-) rpl2 822 [87571:87961](-) [86473:86903](-) rpl20 381 [72561:72941](-) rpl22 429 [85614:86042](-) rpl23 282 [87980:88261](-) rpl23_copy2 282 [168841:169122](+) rpl2_copy2 822 [169141:169531](+) [170199:170629](+) rpl32 159 [127858:128016](+) rpl33 195 [71528:71722](+) rpl36 114 [80651:80764](-) rpoA 1011 [79049:80059](-) rpoB 3213 [27160:30372](+) rpoC1 2049 [30408:32456](+) rpoC2 4152 [32626:36777](+) rps11 405 [80140:80544](-) rps12 372 [73708:73821](-) [100395:100626](-) [99839:99864](-) rps12_copy2 372 [73708:73821](-) [156476:156707](+) [157238:157263](+) rps14 303 [15826:16128](+) rps15 330 [119125:119454](+) rps15_copy2 330 [137648:137977](-) rps16 273 [4770:5042](-) rps18 366 [71915:72280](+) rps19 330 [86086:86415](-) rps2 711 [75007:75717](-) rps3 672 [84958:85629](-) rps4 606 [6728:7333](+) rps7 468 [99318:99785](-) rps7_copy2 468 [157317:157784](+) rps8 396 [82206:82601](-) ycf1 6930 [111851:118780](+) ycf1_copy2 6930 [138322:145251](-) ycf2 6474 [89125:95598](+) ycf2_copy2 6474 [161504:167977](-) ycf3 510 [8572:8700](+) [9396:9623](+) [10367:10519](+) ycf4 555 [63274:63828](+) 38 tRNA genes (30 are unique) Genes Location trnH-GUG [4:77](-) trnK-UUU [4210:4246](-) [1620:1654](-) trnT-UGU [6358:6430](+) trnS-GGA [7644:7730](-) trnfM-CAU [16287:16360](+) trnG-GCC [16531:16601](-) trnS-UGA [17344:17430](+) trnT-GGU [21203:21274](-) trnM-CAU [21689:21760](+) trnE-UUC [22833:22905](+) trnY-GUA [22951:23034](+) trnD-GUC [23144:23217](+) trnC-GCA [25772:25842](-) trnR-UCU [42044:42115](-) trnG-UCC [43034:43056](-) [42282:42329](-) trnS-GCU [43794:43881](+) trnQ-UUG [45193:45264](+) trnF-GAA [45330:45402](-) trnV-UAC [46161:46198](-) [45557:45591](-) trnM-CAU_copy2 [48532:48603](-) trnL-UAA [57988:58022](-) [57431:57480](-) trnW-CCA [70191:70262](-) trnP-UGG [70440:70513](-) trnI-CAU [88959:89032](-) trnL-CAA [96142:96222](-) trnV-GAC [102472:102543](+) trnI-GAU [104559:104601](+) [105542:105576](+) trnA-UGC [105657:105694](+) [106511:106545](+) trnR-ACG [110312:110385](+) trnN-GUU [110660:110731](-) trnL-UAG [128746:128825](+) trnN-GUU_copy2 [146371:146442](+) trnR-ACG_copy2 [146717:146790](-) trnA-UGC_copy2 [151408:151445](-) [150557:150591](-) trnI-GAU_copy2 [152501:152543](-) [151526:151560](-) trnV-GAC_copy2 [154559:154630](-) trnL-CAA_copy2 [160880:160960](+) trnI-CAU_copy2 [168070:168143](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [102773:104264](+) rrn23 [106694:109508](+) rrn4.5 [109609:109711](+) rrn5 [109926:110046](+) rrn5_copy2 [147056:147176](-) rrn4.5_copy2 [147391:147493](-) rrn23_copy2 [147594:150408](-) rrn16_copy2 [152838:154329](-) This genome has 22 genes with intron(s). Details are as follows: 18 gene(s) have 1 intron(s) Genes Exons atpF [39079:39223](+) [39961:40370](+) petB [51356:51361](+) [52179:52820](+) petD [53014:53021](+) [53742:54219](+) rpl16 [84786:84794](-) [83264:83662](-) rpl2 [87571:87961](-) [86473:86903](-) ndhB [98235:99011](-) [96807:97562](-) ndhA [120732:121284](+) [122305:122843](+) ndhA_copy2 [135818:136370](-) [134259:134797](-) ndhB_copy2 [158091:158867](+) [159540:160295](+) rpl2_copy2 [169141:169531](+) [170199:170629](+) trnK-UUU [4210:4246](-) [1620:1654](-) trnG-UCC [43034:43056](-) [42282:42329](-) trnV-UAC [46161:46198](-) [45557:45591](-) trnL-UAA [57988:58022](-) [57431:57480](-) trnI-GAU [104559:104601](+) [105542:105576](+) trnA-UGC [105657:105694](+) [106511:106545](+) trnA-UGC_copy2 [151408:151445](-) [150557:150591](-) trnI-GAU_copy2 [152501:152543](-) [151526:151560](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [73708:73821](-) [100395:100626](-) [99839:99864](-) ycf3 [8572:8700](+) [9396:9623](+) [10367:10519](+) rps12_copy2 [73708:73821](-) [156476:156707](+) [157238:157263](+) clpP [78756:78874](-) [77701:77999](-) [76793:77031](-)