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, ycf3 Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36 Small subunit of ribosome rps11, rps12, 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, ycf2, ycf2_copy2, ycf4 Other genes lhbA 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 psbZ 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 None Conserved open reading frames ycf15 Other genes None 2. Multicopy genes with different lengths: Genes Length Location rpl2 816 join{[88287:88675](-), [87193:87621](-)} rpl2_copy2 819 join{[154255:154643](+), [155306:155737](+)} 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [13255:13398](-) [12136:12546](-) clpP (3/3) [74883:74953](-) [73796:74087](-) [72927:73172](-) ndhA (2/2) [122575:123126](-) [120953:121492](-) ndhB (2/2) [99262:100038](-) [97806:98561](-) ndhB_copy2 (2/2) [142893:143669](+) [144370:145125](+) petB (2/2) [77844:77849](+) [78654:79295](+) petD (2/2) [79495:79502](+) [80208:80727](+) rpl16 (2/2) [85545:85553](-) [84152:84550](-) rpl2 (2/2) [88288:88675](-) [87194:87621](-) rpl2_copy2 (2/2) [154256:154643](+) [155307:155737](+) rpoC1 (2/2) [23728:24157](-) [21373:22994](-) rps12 (3/3) [72663:72776](-) [101460:101690](-) [100897:100923](-) rps16 (2/2) [6085:6124](-) [5175:5239](-) ycf3 (3/3) [46171:46296](-) [45200:45428](-) [44323:44474](-) ### 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 cemA GTG psbL TAT rpl2 GCG ndhD TAT rpl2_copy2 GCG 6. Genes with nonstandard stop codon: Genes Stop codon ndhD TTA 7. Conclusion This genome has 126 genes (111 unique genes). Including: 83 protein-coding genes (78 are unique) 35 tRNA genes (29 are unique) 8 rRNA genes (4 are unique) Details are as follows: 83 protein-coding genes (78 are unique) Genes Length Location accD 1491 [60073:61563](+) atpA 1524 [10538:12061](-) atpB 1497 [55751:57247](-) atpE 405 [55350:55754](-) atpF 555 [13255:13398](-) [12136:12546](-) atpH 246 [13888:14133](-) atpI 744 [15189:15932](-) ccsA 966 [115532:116497](+) cemA 690 [63856:64545](+) clpP 609 [74883:74953](-) [73796:74087](-) [72927:73172](-) infA 234 [82726:82959](-) lhbA 189 [37802:37990](+) matK 1539 [1902:3440](-) ndhA 1092 [122575:123126](-) [120953:121492](-) ndhB 1533 [99262:100038](-) [97806:98561](-) ndhB_copy2 1533 [142893:143669](+) [144370:145125](+) ndhC 363 [52022:52384](-) ndhD 1493 [116725:118217](-) ndhE 306 [118882:119187](-) ndhF 2226 [111168:113393](-) ndhG 531 [119457:119987](-) ndhH 1182 [123128:124309](-) ndhI 543 [120332:120874](-) ndhJ 477 [50713:51189](-) ndhK 186 [51957:52142](-) petA 963 [64768:65730](+) petB 648 [77844:77849](+) [78654:79295](+) petD 528 [79495:79502](+) [80208:80727](+) petG 114 [69172:69285](+) petL 96 [68898:68993](+) petN 90 [29814:29903](+) psaA 2253 [41415:43667](-) psaB 2205 [39185:41389](-) psaC 246 [118361:118606](-) psaI 111 [62197:62307](+) psaJ 135 [70071:70205](+) psbA 1062 [382:1443](-) psbB 1527 [75390:76916](+) psbC 1422 [35692:37113](+) psbD 1062 [34683:35744](+) psbE 252 [67450:67701](-) psbF 120 [67321:67440](-) psbH 222 [77500:77721](+) psbI 111 [8111:8221](+) psbJ 123 [66934:67056](-) psbK 195 [7499:7693](+) psbL 126 [67182:67307](-) psbM 105 [30780:30884](-) psbN 132 [77261:77392](-) psbT 108 [77094:77201](+) rbcL 1428 [57986:59413](+) rpl14 369 [83659:84027](-) rpl16 408 [85545:85553](-) [84152:84550](-) rpl2 816 [88288:88675](-) [87194:87621](-) rpl20 354 [71540:71893](-) rpl23 282 [88697:88978](-) rpl23_copy2 282 [153953:154234](+) rpl2_copy2 819 [154256:154643](+) [155307:155737](+) rpl32 168 [113782:113949](+) rpl33 201 [70629:70829](+) rpl36 114 [82496:82609](-) rpoA 1020 [80864:81883](-) rpoB 3189 [24184:27372](-) rpoC1 2052 [23728:24157](-) [21373:22994](-) rpoC2 4134 [17072:21205](-) rps11 396 [81957:82352](-) rps12 372 [72663:72776](-) [101460:101690](-) [100897:100923](-) rps14 303 [38748:39050](-) rps15 273 [124420:124692](-) rps16 105 [6085:6124](-) [5175:5239](-) rps18 306 [70961:71266](+) rps19 279 [86866:87144](-) rps2 711 [16134:16844](-) rps3 657 [85696:86352](-) rps4 606 [47099:47704](-) rps7 468 [100371:100838](-) rps7_copy2 468 [142093:142560](+) rps8 399 [83080:83478](-) ycf1 4038 [124980:129017](-) ycf2 6864 [89286:96149](+) ycf2_copy2 6864 [146782:153645](-) ycf3 507 [46171:46296](-) [45200:45428](-) [44323:44474](-) ycf4 555 [62756:63310](+) 35 tRNA genes (29 are unique) Genes Location trnH-GUG [4:78](-) trnK-UUU [4152:4188](-) [1610:1644](-) trnQ-UUG [7091:7163](-) trnS-GCU [8361:8448](-) trnG-UCC [9343:9366](+) [10143:10191](+) trnR-UCU [10350:10421](+) trnC-GCA [28660:28741](+) trnD-GUC [31877:31950](-) trnY-GUA [32340:32423](-) trnE-UUC [32487:32559](-) trnT-GGU [33151:33222](+) trnS-UGA [37369:37461](-) trnG-UCC_copy2 [38269:38339](+) trnfM-CAU [38502:38575](-) trnS-GGA [46730:46816](+) trnT-UGU [48051:48122](-) trnL-UAA [49005:49039](+) [49542:49591](+) trnF-GAA [49955:50027](+) trnV-UAC [54896:54934](-) [54284:54320](-) trnM-CAU [55084:55155](+) trnW-CCA [69406:69479](-) trnP-UGG [69644:69717](-) trnI-CAU [89144:89217](-) trnL-CAA [97162:97242](-) trnV-GAC [103550:103621](+) trnI-GAU [105625:105665](+) [106605:106639](+) trnA-UGC [106704:106741](+) [107541:107575](+) trnL-UAG [115362:115441](+) trnN-GUU [130810:130881](+) trnR-ACG [131529:131602](-) trnA-UGC_copy2 [136188:136225](-) [135353:135387](-) trnI-GAU_copy2 [137266:137306](-) [136287:136321](-) trnV-GAC_copy2 [139310:139381](-) trnL-CAA_copy2 [145689:145769](+) trnI-CAU_copy2 [153714:153787](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [103849:105339](+) rrn23 [107728:110534](+) rrn4.5 [110639:110741](+) rrn5 [110966:111085](+) rrn5_copy2 [131846:131965](-) rrn4.5_copy2 [132190:132292](-) rrn23_copy2 [132397:135203](-) rrn16_copy2 [137592:139082](-) This genome has 22 genes with intron(s). Details are as follows: 19 gene(s) have 1 intron(s) Genes Exons rps16 [6085:6124](-) [5175:5239](-) atpF [13255:13398](-) [12136:12546](-) rpoC1 [23728:24157](-) [21373:22994](-) petB [77844:77849](+) [78654:79295](+) petD [79495:79502](+) [80208:80727](+) rpl16 [85545:85553](-) [84152:84550](-) rpl2 [88288:88675](-) [87194:87621](-) ndhB [99262:100038](-) [97806:98561](-) ndhA [122575:123126](-) [120953:121492](-) ndhB_copy2 [142893:143669](+) [144370:145125](+) rpl2_copy2 [154256:154643](+) [155307:155737](+) trnK-UUU [4152:4188](-) [1610:1644](-) trnG-UCC [9343:9366](+) [10143:10191](+) trnL-UAA [49005:49039](+) [49542:49591](+) trnV-UAC [54896:54934](-) [54284:54320](-) trnI-GAU [105625:105665](+) [106605:106639](+) trnA-UGC [106704:106741](+) [107541:107575](+) trnA-UGC_copy2 [136188:136225](-) [135353:135387](-) trnI-GAU_copy2 [137266:137306](-) [136287:136321](-) 3 gene(s) have 2 intron(s) Genes Exons rps12 [72663:72776](-) [101460:101690](-) [100897:100923](-) ycf3 [46171:46296](-) [45200:45428](-) [44323:44474](-) clpP [74883:74953](-) [73796:74087](-) [72927:73172](-)