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, ndhD_copy2, ndhE, ndhF, ndhF_copy2, ndhG, ndhH, ndhI, ndhJ, ndhK Subunits of cytochrome b/f complex petA, petB, petD, petG, petL, petN Subunits of photosystem I psaA, psaB, psaC, psaC_copy2, psaI, psaJ Subunits of photosystem II psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbT, psbZ Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, rpl22, rpl23, rpl23_copy2, rpl32, rpl32_copy2, 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, ccsA_copy2 Envelop membrane protein cemA Maturase matK Protease None Subunit of Acetyl-CoA-carboxylase None Translational initiation factor infA Conserved open reading frames ycf1, ycf2, ycf2_copy2 Other genes pafI, pafII, pbf1 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 psbN, ycf3 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 clpP Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor None Conserved open reading frames ycf15, ycf4 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) [20314:20458](-) [19188:19597](-) ndhA (2/2) [137630:138182](-) [136030:136568](-) ndhB (2/2) [116436:117212](+) [117929:118684](+) ndhB_copy2 (2/2) [165902:166678](-) [164430:165185](-) petB (2/2) [85792:85797](+) [86561:87202](+) petD (2/2) [87416:87423](+) [88147:88642](+) rpl16 (1/2) [92101:92508](-) rpl2 (2/2) [95353:95746](-) [94254:94690](-) rpoC1 (2/2) [26940:27371](+) [28128:29738](+) rps12 (3/3) [77159:77272](-) [168070:168301](-) [167508:167533](-) rps12_copy2 (3/3) [77159:77272](-) [114813:115044](+) [115581:115606](+) rps16 (1/2) [13588:13896](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: pafI 3 [53343:53466](+) [54277:54506](+) [55279:55431](+)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon rps19 GTG rpl2 ACG ndhD ACG ndhD_copy2 ACG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 131 genes (109 unique genes). Including: 87 protein-coding genes (77 are unique) 36 tRNA genes (28 are unique) 8 rRNA genes (4 are unique) Details are as follows: 87 protein-coding genes (77 are unique) Genes Length Location atpA 1524 [17585:19108](-) atpB 1491 [7753:9243](+) atpE 402 [9240:9641](+) atpF 555 [20314:20458](-) [19188:19597](-) atpH 246 [20818:21063](-) atpI 744 [35229:35972](+) ccsA 963 [130682:131644](+) ccsA_copy2 963 [151470:152432](-) cemA 696 [65233:65928](+) infA 240 [90683:90922](-) matK 1503 [2022:3524](-) ndhA 1092 [137630:138182](-) [136030:136568](-) ndhB 1533 [116436:117212](+) [117929:118684](+) ndhB_copy2 1533 [165902:166678](-) [164430:165185](-) ndhC 363 [46481:46843](+) ndhD 1503 [131879:133381](-) ndhD_copy2 1503 [149733:151235](+) ndhE 306 [134003:134308](-) ndhF 2253 [120390:122642](-) ndhF_copy2 2253 [160472:162724](+) ndhG 531 [134557:135087](-) ndhH 1182 [138184:139365](-) ndhI 498 [135445:135942](-) ndhJ 477 [47699:48175](+) ndhK 738 [46834:47571](+) pafI 507 [53343:53466](+) [54277:54506](+) [55279:55431](+) pafII 555 [63772:64326](+) pbf1 132 [83764:83895](-) petA 963 [66148:67110](+) petB 648 [85792:85797](+) [86561:87202](+) petD 504 [87416:87423](+) [88147:88642](+) petG 114 [73512:73625](+) petL 96 [73249:73344](+) petN 90 [21898:21987](-) psaA 2253 [56051:58303](+) psaB 2205 [58329:60533](+) psaC 246 [133502:133747](-) psaC_copy2 246 [149367:149612](+) psaI 111 [63228:63338](+) psaJ 138 [74471:74608](+) psbA 1062 [373:1434](-) psbB 1527 [81871:83397](+) psbC 1416 [40743:42158](+) psbD 1062 [39734:40795](+) psbE 252 [71764:72015](-) psbF 120 [71635:71754](-) psbH 222 [83994:84215](+) psbI 111 [15110:15220](+) psbJ 123 [71245:71367](-) psbK 186 [14513:14698](+) psbL 117 [71492:71608](-) psbM 105 [36392:36496](-) psbT 114 [83590:83703](+) psbZ 189 [42814:43002](+) rbcL 1428 [5571:6998](-) rpl14 369 [91603:91971](-) rpl16 408 [92101:92508](-) rpl2 831 [95353:95746](-) [94254:94690](-) rpl20 393 [76038:76430](-) rpl22 387 [93462:93848](-) rpl23 303 [95752:96054](-) rpl23_copy2 303 [187060:187362](+) rpl32 180 [129577:129756](+) rpl32_copy2 180 [153358:153537](-) rpl33 201 [75047:75247](+) rpl36 114 [90469:90582](-) rpoA 1020 [88814:89833](-) rpoB 3207 [23701:26907](+) rpoC1 2043 [26940:27371](+) [28128:29738](+) rpoC2 4173 [29905:34077](+) rps11 450 [89900:90349](-) rps12 372 [77159:77272](-) [168070:168301](-) [167508:167533](-) rps12_copy2 372 [77159:77272](-) [114813:115044](+) [115581:115606](+) rps14 303 [60681:60983](+) rps15 264 [139505:139768](-) rps16 309 [13588:13896](-) rps18 456 [75383:75838](+) rps19 279 [93909:94187](-) rps2 711 [34295:35005](+) rps3 693 [92669:93361](-) rps4 645 [50850:51494](+) rps7 468 [115660:116127](+) rps7_copy2 468 [166987:167454](-) rps8 402 [91032:91433](-) ycf1 6114 [141716:147829](-) ycf2 6975 [96485:103459](+) ycf2_copy2 6975 [179655:186629](-) 36 tRNA genes (28 are unique) Genes Location trnH-GUG [39:113](-) trnK-UUU [4239:4275](-) [1721:1755](-) trnM-CAU [9838:9910](-) trnQ-UUG [14100:14171](-) trnS-GCU [15373:15460](-) trnG-UCC [16438:16460](+) [17137:17184](+) trnR-UCU [17374:17445](+) trnC-GCA [22406:22476](-) trnD-GUC [37513:37586](-) trnY-GUA [37983:38066](-) trnE-UUC [38126:38198](-) trnT-GGU [38757:38828](+) trnS-UGA [42388:42480](-) trnF-GAA [48809:48881](-) trnL-UAA [49796:49830](-) [49264:49313](-) trnT-UGU [50451:50523](+) trnS-GGA [52026:52109](-) trnfM-CAU [61127:61200](+) trnW-CCA [73751:73824](-) trnP-UGG [73973:74046](-) trnI-CAU [96357:96430](-) trnL-CAA [104489:104570](-) trnR-ACG [105183:105256](-) trnA-UGC [109813:109850](-) [108979:109013](-) trnI-GAU [110905:110941](-) [109915:109949](-) trnV-GAC [112939:113010](-) trnN-GUU [118925:118996](-) trnL-UAG [130504:130583](+) trnL-UAG_copy2 [152531:152610](-) trnN-GUU_copy2 [164118:164189](+) trnV-GAC_copy2 [170104:170175](+) trnI-GAU_copy2 [172173:172209](+) [173165:173199](+) trnA-UGC_copy2 [173264:173301](+) [174101:174135](+) trnR-ACG_copy2 [177858:177931](+) trnL-CAA_copy2 [178544:178625](+) trnI-CAU_copy2 [186684:186757](+) 8 rRNA genes (4 are unique) Genes Location rrn5 [105497:105617](-) rrn4.5 [105828:105930](-) rrn23 [106021:108826](-) rrn16 [111216:112711](-) rrn16_copy2 [170403:171898](+) rrn23_copy2 [174288:177093](+) rrn4.5_copy2 [177184:177286](+) rrn5_copy2 [177497:177617](+) This genome has 18 genes with intron(s). Details are as follows: 15 gene(s) have 1 intron(s) Genes Exons atpF [20314:20458](-) [19188:19597](-) rpoC1 [26940:27371](+) [28128:29738](+) petB [85792:85797](+) [86561:87202](+) petD [87416:87423](+) [88147:88642](+) rpl2 [95353:95746](-) [94254:94690](-) ndhB [116436:117212](+) [117929:118684](+) ndhA [137630:138182](-) [136030:136568](-) ndhB_copy2 [165902:166678](-) [164430:165185](-) trnK-UUU [4239:4275](-) [1721:1755](-) trnG-UCC [16438:16460](+) [17137:17184](+) trnL-UAA [49796:49830](-) [49264:49313](-) trnA-UGC [109813:109850](-) [108979:109013](-) trnI-GAU [110905:110941](-) [109915:109949](-) trnI-GAU_copy2 [172173:172209](+) [173165:173199](+) trnA-UGC_copy2 [173264:173301](+) [174101:174135](+) 3 gene(s) have 2 intron(s) Genes Exons rps12 [77159:77272](-) [168070:168301](-) [167508:167533](-) pafI [53343:53466](+) [54277:54506](+) [55279:55431](+) rps12_copy2 [77159:77272](-) [114813:115044](+) [115581:115606](+)