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, ndhA_copy2, ndhB, ndhB_copy2, ndhC, ndhD, ndhD_copy2, ndhE, ndhE_copy2, ndhF, ndhF_copy2, ndhG, ndhG_copy2, ndhH, ndhH_copy2, ndhI, ndhI_copy2, 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, psbN, psbT, psbZ, ycf3 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, rps15_copy2, 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, ycf1_copy2, 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 clpP Subunit of Acetyl-CoA-carboxylase accD 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) [18181:18325](-) [17055:17464](-) ndhA (2/2) [132474:133024](-) [130877:131417](-) ndhA_copy2 (2/2) [174615:175165](+) [176222:176762](+) ndhB (2/2) [115636:116412](+) [117133:117888](+) ndhB_copy2 (2/2) [191227:192003](-) [189751:190506](-) petB (2/2) [84005:84010](+) [84789:85430](+) petD (2/2) [85642:85649](+) [86371:86866](+) rpl16 (2/2) [91677:91685](-) [90335:90733](-) rpl2 (2/2) [94532:94940](-) [93429:93865](-) rpoC1 (2/2) [28816:29247](-) [26456:28057](-) rps12 (3/3) [76773:76886](-) [193401:193632](-) [192838:192863](-) rps12_copy2 (3/3) [76773:76886](-) [114007:114238](+) [114776:114801](+) rps16 (2/2) [12088:12127](-) [11048:11256](-) ycf3 (3/3) [56797:56922](-) [55816:56043](-) [54885:55043](-) ### 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 rps19 GTG rpl2 ATC ndhD ACG ndhD_copy2 ACG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 144 genes (111 unique genes). Including: 94 protein-coding genes (77 are unique) 42 tRNA genes (30 are unique) 8 rRNA genes (4 are unique) Details are as follows: 94 protein-coding genes (77 are unique) Genes Length Location atpA 1524 [15458:16981](-) atpB 1491 [7937:9427](+) atpE 423 [9430:9852](+) atpF 555 [18181:18325](-) [17055:17464](-) atpH 246 [18626:18871](-) atpI 744 [20262:21005](-) ccsA 969 [125510:126478](+) ccsA_copy2 969 [181161:182129](-) cemA 690 [67817:68506](+) infA 234 [88925:89158](-) matK 1500 [2032:3531](-) ndhA 1092 [132474:133024](-) [130877:131417](-) ndhA_copy2 1092 [174615:175165](+) [176222:176762](+) ndhB 1533 [115636:116412](+) [117133:117888](+) ndhB_copy2 1533 [191227:192003](-) [189751:190506](-) ndhC 363 [63336:63698](-) ndhD 1503 [126713:128215](-) ndhD_copy2 1503 [179424:180926](+) ndhE 303 [128834:129136](-) ndhE_copy2 303 [178503:178805](+) ndhF 2253 [120134:122386](-) ndhF_copy2 2253 [185253:187505](+) ndhG 531 [129395:129925](-) ndhG_copy2 531 [177714:178244](+) ndhH 1182 [133026:134207](-) ndhH_copy2 1182 [173432:174613](+) ndhI 498 [130292:130789](-) ndhI_copy2 498 [176850:177347](+) ndhJ 477 [62003:62479](-) ndhK 738 [62608:63345](-) petA 963 [68734:69696](+) petB 648 [84005:84010](+) [84789:85430](+) petD 504 [85642:85649](+) [86371:86866](+) petG 114 [73050:73163](+) petL 96 [72780:72875](+) petN 90 [34684:34773](+) psaA 2253 [52019:54271](-) psaB 2205 [49789:51993](-) psaC 246 [128332:128577](-) psaC_copy2 246 [179062:179307](+) psaI 111 [65811:65921](+) psaJ 141 [74046:74186](+) psbA 1062 [420:1481](-) psbB 1527 [80877:82403](+) psbC 1416 [45811:47226](+) psbD 1062 [44802:45863](+) psbE 252 [71283:71534](-) psbF 120 [71154:71273](-) psbH 222 [82985:83206](+) psbI 111 [13322:13432](+) psbJ 123 [70764:70886](-) psbK 186 [12738:12923](+) psbL 117 [71011:71127](-) psbM 105 [35179:35283](-) psbN 132 [82751:82882](-) psbT 114 [82577:82690](+) psbZ 189 [47887:48075](+) rbcL 1428 [6002:7429](-) rpl14 369 [89837:90205](-) rpl16 408 [91677:91685](-) [90335:90733](-) rpl2 846 [94532:94940](-) [93429:93865](-) rpl20 378 [75632:76009](-) rpl22 402 [92624:93025](-) rpl23 303 [94928:95230](-) rpl23_copy2 303 [212409:212711](+) rpl32 180 [124392:124571](+) rpl32_copy2 180 [183068:183247](-) rpl33 201 [74613:74813](+) rpl36 114 [88705:88818](-) rpoA 1029 [87041:88069](-) rpoB 3207 [29274:32480](-) rpoC1 2034 [28816:29247](-) [26456:28057](-) rpoC2 4104 [22170:26273](-) rps11 450 [88136:88585](-) rps12 372 [76773:76886](-) [193401:193632](-) [192838:192863](-) rps12_copy2 372 [76773:76886](-) [114007:114238](+) [114776:114801](+) rps14 303 [49337:49639](-) rps15 264 [134336:134599](-) rps15_copy2 264 [173040:173303](+) rps16 249 [12088:12127](-) [11048:11256](-) rps18 459 [74949:75407](+) rps19 279 [93084:93362](-) rps2 711 [21226:21936](-) rps3 687 [91850:92536](-) rps4 609 [58658:59266](-) rps7 468 [114855:115322](+) rps7_copy2 468 [192317:192784](-) rps8 402 [89272:89673](-) ycf1 5823 [138631:144453](-) ycf1_copy2 5823 [163186:169008](+) ycf2 6936 [95674:102609](+) ycf2_copy2 6936 [205030:211965](-) ycf3 513 [56797:56922](-) [55816:56043](-) [54885:55043](-) ycf4 555 [66360:66914](+) 42 tRNA genes (30 are unique) Genes Location trnH-GUG [92:166](-) trnK-UUU [4252:4288](-) [1763:1797](-) trnM-CAU [10037:10109](-) trnV-UAC [10291:10329](+) [10909:10943](+) trnQ-UUG [12332:12403](-) trnS-GCU [13564:13651](-) trnG-UCC [14319:14341](+) [15037:15084](+) trnR-UCU [15247:15318](+) trnC-GCA [33745:33815](+) trnD-GUC [42588:42661](-) trnY-GUA [43055:43138](-) trnE-UUC [43208:43280](-) trnT-GGU [43837:43908](+) trnS-UGA [47451:47543](-) trnG-GCC [48390:48460](+) trnfM-CAU [48622:48696](-) trnfM-CAU_copy2 [48744:48817](-) trnfM-CAU_copy3 [48865:48939](-) trnfM-CAU_copy4 [48988:49061](+) trnfM-CAU_copy5 [49109:49182](+) trnS-GGA [58288:58374](+) trnT-UGU [59621:59693](-) trnL-UAA [60347:60381](+) [60859:60908](+) trnF-GAA [61286:61358](+) trnW-CCA [73292:73365](-) trnP-UGG [73523:73596](-) trnI-CAU [95550:95623](-) trnL-CAA [103663:103743](-) trnR-ACG [104375:104448](-) trnA-UGC [109024:109061](-) [108186:108220](-) trnI-GAU [110112:110148](-) [109126:109160](-) trnV-GAC [112157:112228](-) trnN-GUU [118355:118426](-) trnL-UAG [125320:125399](+) trnL-UAG_copy2 [182240:182319](-) trnN-GUU_copy2 [189213:189284](+) trnV-GAC_copy2 [195411:195482](+) trnI-GAU_copy2 [197491:197527](+) [198479:198513](+) trnA-UGC_copy2 [198578:198615](+) [199419:199453](+) trnR-ACG_copy2 [203191:203264](+) trnL-CAA_copy2 [203896:203976](+) trnI-CAU_copy2 [212016:212089](+) 8 rRNA genes (4 are unique) Genes Location rrn5 [104689:104809](-) rrn4.5 [105029:105131](-) rrn23 [105222:108026](-) rrn16 [110440:111929](-) rrn16_copy2 [195710:197199](+) rrn23_copy2 [199613:202417](+) rrn4.5_copy2 [202508:202610](+) rrn5_copy2 [202830:202950](+) This genome has 22 genes with intron(s). Details are as follows: 19 gene(s) have 1 intron(s) Genes Exons rps16 [12088:12127](-) [11048:11256](-) atpF [18181:18325](-) [17055:17464](-) rpoC1 [28816:29247](-) [26456:28057](-) petB [84005:84010](+) [84789:85430](+) petD [85642:85649](+) [86371:86866](+) rpl16 [91677:91685](-) [90335:90733](-) rpl2 [94532:94940](-) [93429:93865](-) ndhB [115636:116412](+) [117133:117888](+) ndhA [132474:133024](-) [130877:131417](-) ndhA_copy2 [174615:175165](+) [176222:176762](+) ndhB_copy2 [191227:192003](-) [189751:190506](-) trnK-UUU [4252:4288](-) [1763:1797](-) trnV-UAC [10291:10329](+) [10909:10943](+) trnG-UCC [14319:14341](+) [15037:15084](+) trnL-UAA [60347:60381](+) [60859:60908](+) trnA-UGC [109024:109061](-) [108186:108220](-) trnI-GAU [110112:110148](-) [109126:109160](-) trnI-GAU_copy2 [197491:197527](+) [198479:198513](+) trnA-UGC_copy2 [198578:198615](+) [199419:199453](+) 3 gene(s) have 2 intron(s) Genes Exons rps12 [76773:76886](-) [193401:193632](-) [192838:192863](-) ycf3 [56797:56922](-) [55816:56043](-) [54885:55043](-) rps12_copy2 [76773:76886](-) [114007:114238](+) [114776:114801](+)