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, rpl16, rpl2, rpl20, rpl22, 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, 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 infA 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) [12981:13125](-) [11857:11927](-) clpP (3/3) [74142:74527](-) [73237:73527](-) [72317:72581](-) ndhA (2/2) [125262:125817](-) [123707:124245](-) ndhB (2/2) [99471:100247](-) [98012:98770](-) ndhB_copy2 (2/2) [145105:145881](+) [146582:147340](+) petB (2/2) [77437:77442](+) [78204:78845](+) petD (2/2) [79065:79072](+) [79822:80317](+) rpl16 (2/2) [85304:85312](-) [83712:84143](-) rpl2 (2/2) [88214:88604](-) [87108:87541](-) rpl2_copy2 (2/2) [156748:157138](+) [157811:158244](+) rpoC1 (2/2) [23518:23949](-) [21176:22777](-) rps12 (3/3) [71022:71135](-) [101596:101827](-) [101034:101059](-) rps12_copy2 (3/3) [71022:71135](-) [143525:143756](+) [144293:144318](+) rps16 (2/2) [6924:6963](-) [5858:6120](-) ycf3 (3/3) [45572:45695](-) [44615:44844](-) [43700:43852](-) ### 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 psbC GTG rps14 GTG rps19 GTG rpl2 ACG ndhD ACG rpl2_copy2 ACG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 129 genes (112 unique genes). Including: 84 protein-coding genes (78 are unique) 37 tRNA genes (30 are unique) 8 rRNA genes (4 are unique) Details are as follows: 84 protein-coding genes (78 are unique) Genes Length Location accD 1530 [59862:61391](+) atpA 1524 [10267:11790](-) atpB 1497 [55535:57031](-) atpE 402 [55137:55538](-) atpF 216 [12981:13125](-) [11857:11927](-) atpH 246 [13628:13873](-) atpI 744 [14991:15734](-) ccsA 966 [118356:119321](+) cemA 690 [63259:63948](+) clpP 942 [74142:74527](-) [73237:73527](-) [72317:72581](-) matK 1533 [2086:3618](-) ndhA 1095 [125262:125817](-) [123707:124245](-) ndhB 1536 [99471:100247](-) [98012:98770](-) ndhB_copy2 1536 [145105:145881](+) [146582:147340](+) ndhC 363 [51930:52292](-) ndhD 1503 [119524:121026](-) ndhE 306 [121648:121953](-) ndhF 2226 [114383:116608](-) ndhG 531 [122161:122691](-) ndhH 1182 [125819:127000](-) ndhI 537 [123067:123603](-) ndhJ 477 [50618:51094](-) ndhK 672 [51203:51874](-) petA 969 [64171:65139](+) petB 648 [77437:77442](+) [78204:78845](+) petD 504 [79065:79072](+) [79822:80317](+) petG 114 [67506:67619](+) petL 96 [67247:67342](+) petN 90 [28874:28963](+) psaA 2253 [40681:42933](-) psaB 2205 [38451:40655](-) psaC 246 [121162:121407](-) psaI 111 [62246:62356](+) psaJ 135 [68416:68550](+) psbA 1062 [512:1573](-) psbB 1527 [74959:76485](+) psbC 1386 [34869:36254](+) psbD 1062 [33824:34885](+) psbE 252 [66294:66545](-) psbF 120 [66165:66284](-) psbH 228 [77086:77313](+) psbI 111 [8299:8409](+) psbJ 123 [65783:65905](-) psbK 186 [7718:7903](+) psbL 117 [66021:66137](-) psbM 105 [30055:30159](-) psbN 132 [76852:76983](-) psbT 108 [76669:76776](+) psbZ 189 [36927:37115](+) rbcL 1428 [57745:59172](+) rpl14 369 [83258:83626](-) rpl16 441 [85304:85312](-) [83712:84143](-) rpl2 825 [88214:88604](-) [87108:87541](-) rpl20 354 [69879:70232](-) rpl22 519 [86159:86677](-) rpl23 309 [88606:88914](-) rpl23_copy2 309 [156438:156746](+) rpl2_copy2 825 [156748:157138](+) [157811:158244](+) rpl32 147 [117271:117417](+) rpl33 201 [68926:69126](+) rpl36 114 [82128:82241](-) rpoA 999 [80528:81526](-) rpoB 3216 [23976:27191](-) rpoC1 2034 [23518:23949](-) [21176:22777](-) rpoC2 4137 [16864:21000](-) rps11 423 [81592:82014](-) rps12 372 [71022:71135](-) [101596:101827](-) [101034:101059](-) rps12_copy2 372 [71022:71135](-) [143525:143756](+) [144293:144318](+) rps14 303 [38017:38319](-) rps15 282 [127048:127329](-) rps16 303 [6924:6963](-) [5858:6120](-) rps18 333 [69298:69630](+) rps19 279 [86731:87009](-) rps2 711 [15940:16650](-) rps3 666 [85509:86174](-) rps4 624 [46922:47545](-) rps7 324 [100652:100975](-) rps7_copy2 324 [144377:144700](+) rps8 399 [82674:83072](-) ycf1 5733 [127736:133468](-) ycf2 7125 [89324:96448](+) ycf2_copy2 7125 [148904:156028](-) ycf3 507 [45572:45695](-) [44615:44844](-) [43700:43852](-) ycf4 555 [62544:63098](+) 37 tRNA genes (30 are unique) Genes Location trnH-GUG [5:79](-) trnK-UUU [4370:4406](-) [1795:1829](-) trnQ-UUG [7277:7348](-) trnS-GCU [8576:8663](-) trnG-UCC [9108:9130](+) [9829:9876](+) trnR-UCU [10052:10123](+) trnC-GCA [28345:28415](+) trnD-GUC [31319:31392](-) trnY-GUA [31694:31777](-) trnE-UUC [31837:31909](-) trnT-GGU [32591:32662](-) trnS-UGA [36483:36570](-) trnG-GCC [37557:37627](+) trnfM-CAU [37792:37865](-) trnS-GGA [46558:46644](-) trnT-UGU [47914:47986](-) trnL-UAA [48838:48872](+) [49298:49347](+) trnF-GAA [49703:49775](+) trnV-UAC [54610:54648](-) [53993:54027](-) trnM-CAU [54835:54906](-) trnW-CCA [67751:67825](-) trnP-UGG [67986:68059](-) trnI-CAU [89088:89161](-) trnL-CAA [97380:97460](-) trnV-GAC [103161:103232](+) trnI-GAU [105253:105289](+) [106243:106277](+) trnA-UGC [106342:106379](+) [107180:107214](+) trnR-ACG [110991:111064](+) trnN-GUU [111665:111736](-) trnL-UAG [118198:118277](+) trnN-GUU_copy2 [133616:133687](+) trnR-ACG_copy2 [134288:134361](-) trnA-UGC_copy2 [138973:139010](-) [138138:138172](-) trnI-GAU_copy2 [140063:140099](-) [139075:139109](-) trnV-GAC_copy2 [142120:142191](-) trnL-CAA_copy2 [147892:147972](+) trnI-CAU_copy2 [156191:156264](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [103464:104954](+) rrn23 [107373:110177](+) rrn4.5 [110276:110378](+) rrn5 [110604:110724](+) rrn5_copy2 [134628:134748](-) rrn4.5_copy2 [134974:135076](-) rrn23_copy2 [135175:137979](-) rrn16_copy2 [140398:141888](-) This genome has 23 genes with intron(s). Details are as follows: 19 gene(s) have 1 intron(s) Genes Exons rps16 [6924:6963](-) [5858:6120](-) atpF [12981:13125](-) [11857:11927](-) rpoC1 [23518:23949](-) [21176:22777](-) petB [77437:77442](+) [78204:78845](+) petD [79065:79072](+) [79822:80317](+) rpl16 [85304:85312](-) [83712:84143](-) rpl2 [88214:88604](-) [87108:87541](-) ndhB [99471:100247](-) [98012:98770](-) ndhA [125262:125817](-) [123707:124245](-) ndhB_copy2 [145105:145881](+) [146582:147340](+) rpl2_copy2 [156748:157138](+) [157811:158244](+) trnK-UUU [4370:4406](-) [1795:1829](-) trnG-UCC [9108:9130](+) [9829:9876](+) trnL-UAA [48838:48872](+) [49298:49347](+) trnV-UAC [54610:54648](-) [53993:54027](-) trnI-GAU [105253:105289](+) [106243:106277](+) trnA-UGC [106342:106379](+) [107180:107214](+) trnA-UGC_copy2 [138973:139010](-) [138138:138172](-) trnI-GAU_copy2 [140063:140099](-) [139075:139109](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [71022:71135](-) [101596:101827](-) [101034:101059](-) ycf3 [45572:45695](-) [44615:44844](-) [43700:43852](-) rps12_copy2 [71022:71135](-) [143525:143756](+) [144293:144318](+) clpP [74142:74527](-) [73237:73527](-) [72317:72581](-)