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, rps14, rps15, rps16, rps18, rps19, rps19_copy2, 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, ycf68, ycf68_copy2 Other genes orf1006, orf109, orf138, orf169, orf79 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 None 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) [13555:13699](-) [12345:12754](-) clpP (3/3) [75050:75120](-) [73914:74202](-) [73032:73289](-) ndhA (2/2) [120574:121129](+) [122173:122711](+) ndhB (2/2) [99956:100732](-) [98500:99255](-) ndhB_copy2 (2/2) [147868:148644](+) [149345:150100](+) petB (1/2) [78840:79538](+) petD (1/2) [80439:80963](+) rpl16 (1/2) [84474:84887](-) rpl2 (2/2) [89034:89417](-) [87940:88371](-) rpl2_copy2 (2/2) [159183:159566](+) [160229:160660](+) rpoC1 (2/2) [24292:24723](-) [21928:23550](-) rps12 (2/3) [72756:72869](-) [102118:102357](-) rps16 (2/2) [5896:5940](-) [4953:5165](-) ycf3 (3/3) [46276:46399](-) [45330:45559](-) [44387:44539](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: ycf68 2 [106566:106607](+) [106636:106950](+)] ycf68_copy2 2 [141993:142034](-) [141650:141964](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon petN ATA orf169 ATT psbT ATC petB ATT rpl36 ATA rpl16 ATC orf138 CTG rpl2 ATA ndhD ATC orf79 ATC rpl2_copy2 ATA 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 137 genes (116 unique genes). Including: 92 protein-coding genes (85 are unique) 37 tRNA genes (27 are unique) 8 rRNA genes (4 are unique) Details are as follows: 92 protein-coding genes (85 are unique) Genes Length Location accD 1533 [60534:62066](+) atpA 1524 [10757:12280](-) atpB 1488 [55953:57440](-) atpE 408 [55549:55956](-) atpF 555 [13555:13699](-) [12345:12754](-) atpH 246 [14207:14452](-) atpI 744 [15615:16358](-) ccsA 972 [127312:128283](-) cemA 711 [63962:64672](+) clpP 618 [75050:75120](-) [73914:74202](-) [73032:73289](-) infA 234 [83045:83278](-) matK 1548 [1760:3307](-) ndhA 1095 [120574:121129](+) [122173:122711](+) ndhB 1533 [99956:100732](-) [98500:99255](-) ndhB_copy2 1533 [147868:148644](+) [149345:150100](+) ndhC 363 [52489:52851](-) ndhD 1506 [125520:127025](+) ndhE 306 [124179:124484](+) ndhF 2211 [130135:132345](+) ndhG 531 [123432:123962](+) ndhH 1182 [119391:120572](+) ndhI 543 [122806:123348](+) ndhJ 480 [51164:51643](-) ndhK 753 [51746:52498](-) orf1006 3021 [132382:135402](-) orf109 330 [29375:29704](-) orf138 417 [85384:85800](+) orf169 510 [68160:68669](-) orf79 240 [146243:146482](+) petA 963 [64927:65889](+) petB 699 [78840:79538](+) petD 525 [80439:80963](+) petG 114 [69010:69123](+) petL 96 [68734:68829](+) petN 99 [30055:30153](+) psaA 2253 [41497:43749](-) psaB 2205 [39267:41471](-) psaC 246 [125150:125395](+) psaI 111 [62596:62706](+) psaJ 129 [69932:70060](+) psbA 1062 [110:1171](-) psbB 1527 [75584:77110](+) psbC 1422 [35878:37299](+) psbD 1062 [34869:35930](+) psbE 252 [67291:67542](-) psbF 120 [67161:67280](-) psbH 222 [77709:77930](+) psbI 111 [8542:8652](+) psbJ 123 [66778:66900](-) psbK 186 [7839:8024](+) psbL 117 [67022:67138](-) psbM 105 [30990:31094](-) psbN 132 [77457:77588](-) psbT 117 [77281:77397](+) psbZ 189 [37899:38087](+) rbcL 1464 [58254:59717](+) rpl14 369 [83983:84351](-) rpl16 414 [84474:84887](-) rpl2 816 [89034:89417](-) [87940:88371](-) rpl20 429 [71614:72042](-) rpl22 396 [86806:87201](-) rpl23 282 [89442:89723](-) rpl23_copy2 282 [158877:159158](+) rpl2_copy2 816 [159183:159566](+) [160229:160660](+) rpl32 174 [129334:129507](-) rpl33 201 [70671:70871](+) rpl36 123 [82821:82943](-) rpoA 1041 [81167:82207](-) rpoB 3222 [24750:27971](-) rpoC1 2055 [24292:24723](-) [21928:23550](-) rpoC2 4149 [17589:21737](-) rps11 417 [82280:82696](-) rps12 354 [72756:72869](-) [102118:102357](-) rps14 303 [38821:39123](-) rps15 258 [119011:119268](+) rps16 258 [5896:5940](-) [4953:5165](-) rps18 336 [71066:71401](+) rps19 279 [87379:87657](-) rps19_copy2 279 [160943:161221](+) rps2 711 [16635:17345](-) rps3 657 [86087:86743](-) rps4 606 [47412:48017](-) rps7 468 [101037:101504](-) rps7_copy2 468 [147096:147563](+) rps8 399 [83391:83789](-) ycf1 5382 [113198:118579](+) ycf2 6822 [90092:96913](+) ycf2_copy2 6822 [151687:158508](-) ycf3 507 [46276:46399](-) [45330:45559](-) [44387:44539](-) ycf4 555 [63052:63606](+) ycf68 357 [106566:106607](+) [106636:106950](+) ycf68_copy2 357 [141993:142034](-) [141650:141964](-) 37 tRNA genes (27 are unique) Genes Location tRNA-Lys(TTT) [4119:4155](-) [1430:1464](-) tRNA-Gln(TTG) [7352:7423](-) tRNA-Ser(GCT) [8789:8876](-) tRNA-Arg(TCT) [10575:10646](+) tRNA-Cys(GCA) [29140:29210](+) tRNA-Asp(GTC) [32171:32244](-) tRNA-Tyr(GTA) [32682:32765](-) tRNA-Glu(TTC) [32820:32892](-) tRNA-Thr(GGT) [33496:33567](+) tRNA-Ser(TGA) [37444:37535](-) tRNA-Gly(GCC) [38341:38411](+) tRNA-Met(CAT) [38586:38659](-) tRNA-Ser(GGA) [47041:47127](+) tRNA-Thr(TGT) [48468:48540](-) tRNA-Leu(TAA) [49568:49602](+) [50136:50184](+) tRNA-Phe(GAA) [50509:50581](+) tRNA-Cys(ACA) [55072:55109](-) [54433:54469](-) tRNA-Met(CAT)_copy2 [55292:55364](+) tRNA-Trp(CCA) [69244:69317](-) tRNA-Pro(TGG) [69482:69555](-) tRNA-His(GTG) [87819:87892](+) tRNA-Met(CAT)_copy3 [89889:89962](-) tRNA-Leu(CAA) [97925:98005](-) tRNA-Val(GAC) [104330:104401](+) tRNA-Ile(GAT) [106425:106466](+) [107402:107436](+) tRNA-Ala(TGC) [107500:107537](+) [108339:108373](+) tRNA-Arg(ACG) [112154:112227](+) tRNA-Asn(GTT) [112801:112872](-) tRNA-Leu(TAG) [128378:128457](-) tRNA-Asn(GTT)_copy2 [135728:135799](+) tRNA-Arg(ACG)_copy2 [136373:136446](-) tRNA-Ala(TGC)_copy2 [141063:141100](-) [140227:140261](-) tRNA-Ile(GAT)_copy2 [142134:142175](-) [141164:141198](-) tRNA-Val(GAC)_copy2 [144199:144270](-) tRNA-Leu(CAA)_copy2 [150595:150675](+) tRNA-Met(CAT)_copy4 [158638:158711](+) tRNA-His(GTG)_copy2 [160708:160781](-) 8 rRNA genes (4 are unique) Genes Location rrn16S [104629:106119](+) rrn23S [108519:111326](+) rrn4.5S [111439:111541](+) rrn5S [111770:111890](+) rrn5S_copy2 [136710:136830](-) rrn4.5S_copy2 [137059:137161](-) rrn23S_copy2 [137274:140081](-) rrn16S_copy2 [142481:143971](-) This genome has 20 genes with intron(s). Details are as follows: 18 gene(s) have 1 intron(s) Genes Exons rps12 [72756:72869](-) [102118:102357](-) rps16 [5896:5940](-) [4953:5165](-) atpF [13555:13699](-) [12345:12754](-) rpoC1 [24292:24723](-) [21928:23550](-) rpl2 [89034:89417](-) [87940:88371](-) ndhB [99956:100732](-) [98500:99255](-) ycf68 [106566:106607](+) [106636:106950](+) ndhA [120574:121129](+) [122173:122711](+) ycf68_copy2 [141993:142034](-) [141650:141964](-) ndhB_copy2 [147868:148644](+) [149345:150100](+) rpl2_copy2 [159183:159566](+) [160229:160660](+) tRNA-Lys(TTT) [4119:4155](-) [1430:1464](-) tRNA-Leu(TAA) [49568:49602](+) [50136:50184](+) tRNA-Cys(ACA) [55072:55109](-) [54433:54469](-) tRNA-Ile(GAT) [106425:106466](+) [107402:107436](+) tRNA-Ala(TGC) [107500:107537](+) [108339:108373](+) tRNA-Ala(TGC)_copy2 [141063:141100](-) [140227:140261](-) tRNA-Ile(GAT)_copy2 [142134:142175](-) [141164:141198](-) 2 gene(s) have 2 intron(s) Genes Exons ycf3 [46276:46399](-) [45330:45559](-) [44387:44539](-) clpP [75050:75120](-) [73914:74202](-) [73032:73289](-)