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, psbT, psbZ 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, rps12_copy3, 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 None Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor infA Conserved open reading frames ycf1, ycf1_copy2, ycf2, ycf2_copy2 Other genes clpP1, 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 None 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) [14320:14463](-) [13150:13560](-) ndhA (2/2) [130309:130859](-) [128677:129217](-) ndhB (2/2) [99905:100681](-) [98474:99229](-) ndhB_copy2 (2/2) [150911:151687](+) [152363:153118](+) petB (2/2) [79109:79114](+) [79887:80528](+) petD (2/2) [80756:80763](+) [81522:81996](+) rpl16 (2/2) [86685:86693](-) [85430:85828](-) rpl2 (2/2) [89341:89733](-) [88244:88678](-) rpl2_copy2 (2/2) [161859:162251](+) [162914:163348](+) rpoC1 (2/2) [24348:24777](-) [21953:23565](-) rps12 (3/3) [73832:73945](-) [102093:102323](-) [101539:101565](-) rps12_copy2 (3/3) [73832:73945](-) [102092:102323](-) [101539:101564](-) rps12_copy3 (3/3) [73832:73945](-) [149269:149499](+) [150027:150053](+) rps16 (2/2) [6413:6452](-) [5328:5542](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: pafI 3 [47512:47639](-) [46558:46784](-) [45657:45811](-)] clpP1 3 [76176:76246](-) [74983:75274](-) [74081:74350](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon rps19 GTG ndhD ACG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 131 genes (112 unique genes). Including: 87 protein-coding genes (79 are unique) 36 tRNA genes (29 are unique) 8 rRNA genes (4 are unique) Details are as follows: 87 protein-coding genes (79 are unique) Genes Length Location accD 1407 [60465:61871](+) atpA 1518 [11559:13076](-) atpB 1497 [56209:57705](-) atpE 402 [55811:56212](-) atpF 555 [14320:14463](-) [13150:13560](-) atpH 246 [14884:15129](-) atpI 744 [15795:16538](-) ccsA 966 [123343:124308](+) cemA 690 [64565:65254](+) clpP1 633 [76176:76246](-) [74983:75274](-) [74081:74350](-) infA 234 [84040:84273](-) matK 1527 [2087:3613](-) ndhA 1092 [130309:130859](-) [128677:129217](-) ndhB 1533 [99905:100681](-) [98474:99229](-) ndhB_copy2 1533 [150911:151687](+) [152363:153118](+) ndhC 363 [53729:54091](-) ndhD 1503 [124503:126005](-) ndhE 306 [126641:126946](-) ndhF 2250 [119080:121329](-) ndhG 531 [127174:127704](-) ndhH 1182 [130861:132042](-) ndhI 513 [128045:128557](-) ndhJ 477 [52419:52895](-) ndhK 678 [52992:53669](-) pafI 510 [47512:47639](-) [46558:46784](-) [45657:45811](-) pafII 555 [63156:63710](+) pbf1 132 [78542:78673](-) petA 963 [65467:66429](+) petB 648 [79109:79114](+) [79887:80528](+) petD 483 [80756:80763](+) [81522:81996](+) petG 114 [69706:69819](+) petL 96 [69405:69500](+) petN 90 [30104:30193](+) psaA 2253 [42611:44863](-) psaB 2205 [40381:42585](-) psaC 246 [126137:126382](-) psaI 111 [62593:62703](+) psaJ 135 [70792:70926](+) psbA 1062 [480:1541](-) psbB 1527 [76687:78213](+) psbC 1422 [36907:38328](+) psbD 1062 [35898:36959](+) psbE 252 [67938:68189](-) psbF 120 [67810:67929](-) psbH 222 [78774:78995](+) psbI 111 [8903:9013](+) psbJ 123 [67396:67518](-) psbK 186 [8293:8478](+) psbL 117 [67666:67782](-) psbM 105 [31366:31470](-) psbT 102 [78369:78470](+) psbZ 189 [39057:39245](+) rbcL 1428 [58527:59954](+) rpl14 369 [84944:85312](-) rpl16 408 [86685:86693](-) [85430:85828](-) rpl2 828 [89341:89733](-) [88244:88678](-) rpl20 393 [72681:73073](-) rpl22 399 [87444:87842](-) rpl23 15 [89872:89886](-) rpl23_copy2 15 [161706:161720](+) rpl2_copy2 828 [161859:162251](+) [162914:163348](+) rpl32 174 [122257:122430](+) rpl33 201 [71490:71690](+) rpl36 114 [83827:83940](-) rpoA 1014 [82183:83196](-) rpoB 3213 [24804:28016](-) rpoC1 2043 [24348:24777](-) [21953:23565](-) rpoC2 4071 [17708:21778](-) rps11 417 [83273:83689](-) rps12 372 [73832:73945](-) [102093:102323](-) [101539:101565](-) rps12_copy2 372 [73832:73945](-) [102092:102323](-) [101539:101564](-) rps12_copy3 372 [73832:73945](-) [149269:149499](+) [150027:150053](+) rps14 303 [39955:40257](-) rps15 264 [132140:132403](-) rps16 255 [6413:6452](-) [5328:5542](-) rps18 315 [72186:72500](+) rps19 279 [87906:88184](-) rps2 711 [16737:17447](-) rps3 657 [86803:87459](-) rps4 597 [48893:49489](-) rps7 468 [101018:101485](-) rps7_copy2 468 [150107:150574](+) rps8 405 [84392:84796](-) ycf1 5757 [113132:118888](+) ycf1_copy2 5757 [132704:138460](-) ycf2 6282 [90644:96925](+) ycf2_copy2 6282 [154667:160948](-) 36 tRNA genes (29 are unique) Genes Location trnH-GUG [70:144](-) trnK-UUU [4321:4357](-) [1788:1822](-) trnQ-UUG [7886:7957](-) trnS-GCU [9134:9221](-) trnR-UCU [11283:11354](+) trnC-GCA [29360:29432](+) trnD-GUC [32700:32773](-) trnY-GUA [33169:33252](-) trnE-UUC [33324:33396](-) trnT-GGU [34239:34310](+) trnS-UGA [38622:38709](-) trnG-UCC [39528:39597](+) trnfM-CAU [39735:39807](-) trnS-GGA [48475:48561](+) trnT-UGU [50072:50144](-) trnL-UAA [50669:50705](+) [51254:51303](+) trnF-GAA [51671:51743](+) trnV-UAC [55254:55291](-) [54633:54669](-) trnM-CAU [55462:55534](+) trnW-CCA [69928:70001](-) trnP-UGG [70317:70390](-) trnI-CAU [90196:90269](-) trnL-CAA [97830:97910](-) trnV-GAC [103972:104043](+) trnI-GAU [106058:106099](+) [107044:107078](+) trnA-UGC [107145:107182](+) [107983:108017](+) trnR-ACG [111831:111904](+) trnN-GUU [112507:112578](-) trnL-UAG [123117:123196](+) trnN-GUU_copy2 [139014:139085](+) trnR-ACG_copy2 [139688:139761](-) trnA-UGC_copy2 [144410:144447](-) [143575:143609](-) trnI-GAU_copy2 [145493:145534](-) [144514:144548](-) trnV-GAC_copy2 [147549:147620](-) trnL-CAA_copy2 [153682:153762](+) trnI-CAU_copy2 [161323:161396](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [104271:105761](+) rrn23 [108174:110986](+) rrn4.5 [111085:111187](+) rrn5 [111444:111564](+) rrn5_copy2 [140028:140148](-) rrn4.5_copy2 [140405:140507](-) rrn23_copy2 [140606:143418](-) rrn16_copy2 [145831:147321](-) This genome has 23 genes with intron(s). Details are as follows: 18 gene(s) have 1 intron(s) Genes Exons rps16 [6413:6452](-) [5328:5542](-) atpF [14320:14463](-) [13150:13560](-) rpoC1 [24348:24777](-) [21953:23565](-) petB [79109:79114](+) [79887:80528](+) petD [80756:80763](+) [81522:81996](+) rpl16 [86685:86693](-) [85430:85828](-) rpl2 [89341:89733](-) [88244:88678](-) ndhB [99905:100681](-) [98474:99229](-) ndhA [130309:130859](-) [128677:129217](-) ndhB_copy2 [150911:151687](+) [152363:153118](+) rpl2_copy2 [161859:162251](+) [162914:163348](+) trnK-UUU [4321:4357](-) [1788:1822](-) trnL-UAA [50669:50705](+) [51254:51303](+) trnV-UAC [55254:55291](-) [54633:54669](-) trnI-GAU [106058:106099](+) [107044:107078](+) trnA-UGC [107145:107182](+) [107983:108017](+) trnA-UGC_copy2 [144410:144447](-) [143575:143609](-) trnI-GAU_copy2 [145493:145534](-) [144514:144548](-) 5 gene(s) have 2 intron(s) Genes Exons rps12 [73832:73945](-) [102093:102323](-) [101539:101565](-) rps12_copy2 [73832:73945](-) [102092:102323](-) [101539:101564](-) pafI [47512:47639](-) [46558:46784](-) [45657:45811](-) rps12_copy3 [73832:73945](-) [149269:149499](+) [150027:150053](+) clpP1 [76176:76246](-) [74983:75274](-) [74081:74350](-)