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 ndhE, ndhJ 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, rps12_copy2, 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 Other genes orf42, orf42_copy2 Possible missing protein coding genes: Group of genes Name of genes Subunits of ATP synthase None Subunits of NADH-dehydrogenase ndhA, ndhB, ndhC, ndhD, ndhF, ndhG, ndhH, ndhI, ndhK 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) [13297:13440](-) [11940:12350](-) clpP (3/3) [73274:73342](-) [72087:72377](-) [71166:71417](-) petB (2/2) [76573:76578](+) [77312:77953](+) petD (2/2) [78139:78146](+) [78992:79505](+) rpl16 (2/2) [84595:84603](-) [83043:83441](-) rpl2 (2/2) [87677:88063](-) [86584:87015](-) rpl2_copy2 (2/2) [154774:155160](+) [155822:156253](+) rpoC1 (2/2) [23196:23630](-) [20792:22420](-) rps12 (3/3) [70904:71032](-) [100697:100925](-) [100123:100148](-) rps12_copy2 (3/3) [70904:71032](-) [141912:142140](+) [142689:142714](+) rps16 (2/2) [5991:6030](-) [4752:5011](-) ycf3 (3/3) [45566:45689](-) [44614:44843](-) [43682:43834](-) ### 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 ATA orf42 ATC ycf1 TTG orf42_copy2 ATC rpl2_copy2 ATA rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 123 genes (104 unique genes). Including: 78 protein-coding genes (71 are unique) 37 tRNA genes (29 are unique) 8 rRNA genes (4 are unique) Details are as follows: 78 protein-coding genes (71 are unique) Genes Length Location accD 1458 [58558:60015](+) atpA 1575 [10291:11865](-) atpB 1497 [53720:55216](-) atpE 405 [53319:53723](-) atpF 555 [13297:13440](-) [11940:12350](-) atpH 246 [13604:13849](-) atpI 720 [14518:15237](-) ccsA 966 [116324:117289](+) cemA 696 [62290:62985](+) clpP 612 [73274:73342](-) [72087:72377](-) [71166:71417](-) infA 234 [81567:81800](-) matK 1599 [1705:3303](-) ndhE 306 [120054:120359](-) ndhJ 477 [50031:50507](-) orf42 174 [105943:106116](-) orf42_copy2 174 [136721:136894](+) petA 963 [63228:64190](+) petB 648 [76573:76578](+) [77312:77953](+) petD 522 [78139:78146](+) [78992:79505](+) petG 114 [67171:67284](+) petL 96 [66886:66981](+) petN 90 [30257:30346](-) psaA 2253 [40787:43039](-) psaB 2205 [38557:40761](-) psaC 246 [119230:119475](-) psaI 111 [60466:60576](+) psaJ 135 [68088:68222](+) psbA 1062 [132:1193](-) psbB 1527 [73998:75524](+) psbC 1422 [35265:36686](+) psbD 1062 [34256:35317](+) psbE 252 [65737:65988](-) psbF 120 [65607:65726](-) psbH 222 [76167:76388](+) psbI 111 [8133:8243](+) psbJ 123 [65225:65347](-) psbK 186 [7464:7649](+) psbL 117 [65468:65584](-) psbM 105 [29346:29450](+) psbN 132 [75923:76054](-) psbT 102 [75752:75853](+) psbZ 189 [37148:37336](+) rbcL 1464 [56274:57737](+) rpl14 369 [82537:82905](-) rpl16 408 [84595:84603](-) [83043:83441](-) rpl2 819 [87677:88063](-) [86584:87015](-) rpl20 357 [69799:70155](-) rpl22 357 [85507:85863](-) rpl23 282 [88088:88369](-) rpl23_copy2 282 [154468:154749](+) rpl2_copy2 819 [154774:155160](+) [155822:156253](+) rpl32 174 [115225:115398](+) rpl33 201 [68821:69021](+) rpl36 114 [81339:81452](-) rpoA 999 [79669:80667](-) rpoB 3213 [23657:26869](-) rpoC1 2064 [23196:23630](-) [20792:22420](-) rpoC2 4155 [16470:20624](-) rps11 417 [80751:81167](-) rps12 384 [70904:71032](-) [100697:100925](-) [100123:100148](-) rps12_copy2 384 [70904:71032](-) [141912:142140](+) [142689:142714](+) rps14 303 [38118:38420](-) rps15 273 [125309:125581](-) rps16 300 [5991:6030](-) [4752:5011](-) rps18 306 [69209:69514](+) rps19 282 [86062:86343](-) rps19_copy2 282 [156494:156775](+) rps2 711 [15528:16238](-) rps3 657 [84773:85429](-) rps4 606 [46635:47240](-) rps7 468 [99597:100064](-) rps7_copy2 468 [142773:143240](+) rps8 396 [81914:82309](-) ycf1 4419 [125870:130288](-) ycf2 6939 [88677:95615](+) ycf2_copy2 6939 [147222:154160](-) ycf3 507 [45566:45689](-) [44614:44843](-) [43682:43834](-) ycf4 555 [60980:61534](+) 37 tRNA genes (29 are unique) Genes Location trnK-UUU [4219:4257](-) [1445:1470](-) trnQ-UUG [7044:7115](-) trnS-GCU [8398:8485](-) trnG-GCC [9180:9203](+) [9902:9948](+) trnR-UCU [10107:10178](+) trnC-GCA [28252:28334](+) trnD-GUC [31399:31472](-) trnY-GUA [31785:31868](-) trnE-UUC [31928:32000](-) trnT-GGU [33245:33316](+) trnS-UGA [36824:36915](-) trnG-UCC [37634:37704](+) trnfM-CAU [37881:37954](-) trnS-GGA [46241:46327](+) trnT-UGU [47578:47650](-) trnL-UAA [48257:48291](+) [49091:49140](+) trnF-GAA [49496:49568](+) trnV-UAC [52841:52879](-) [52230:52264](-) trnM-CAU [53056:53127](+) trnP-UGG [67650:67724](-) trnH-GUG [86466:86540](+) trnI-CAU [88535:88608](-) trnL-CAA [96601:96681](-) trnV-GAC [102639:102710](+) trnI-GAU [104732:104773](+) [105720:105754](+) trnA-UGC [105819:105856](+) [106658:106692](+) trnR-ACG [110413:110486](+) trnN-GUU [111043:111114](-) trnL-UAG [116055:116134](+) trnN-GUU_copy2 [131723:131794](+) trnR-ACG_copy2 [132351:132424](-) trnA-UGC_copy2 [136981:137018](-) [136145:136179](-) trnI-GAU_copy2 [138064:138105](-) [137083:137117](-) trnV-GAC_copy2 [140127:140198](-) trnL-CAA_copy2 [146156:146236](+) trnI-CAU_copy2 [154229:154302](+) trnH-GUG_copy2 [156297:156371](-) 8 rRNA genes (4 are unique) Genes Location rrn16 [102940:104429](+) rrn23 [106838:109644](+) rrn4.5 [109743:109845](+) rrn5 [110058:110178](+) rrn5_copy2 [132659:132779](-) rrn4.5_copy2 [132992:133094](-) rrn23_copy2 [133193:135999](-) rrn16_copy2 [138408:139897](-) This genome has 20 genes with intron(s). Details are as follows: 16 gene(s) have 1 intron(s) Genes Exons rps16 [5991:6030](-) [4752:5011](-) atpF [13297:13440](-) [11940:12350](-) rpoC1 [23196:23630](-) [20792:22420](-) petB [76573:76578](+) [77312:77953](+) petD [78139:78146](+) [78992:79505](+) rpl16 [84595:84603](-) [83043:83441](-) rpl2 [87677:88063](-) [86584:87015](-) rpl2_copy2 [154774:155160](+) [155822:156253](+) trnK-UUU [4219:4257](-) [1445:1470](-) trnG-GCC [9180:9203](+) [9902:9948](+) trnL-UAA [48257:48291](+) [49091:49140](+) trnV-UAC [52841:52879](-) [52230:52264](-) trnI-GAU [104732:104773](+) [105720:105754](+) trnA-UGC [105819:105856](+) [106658:106692](+) trnA-UGC_copy2 [136981:137018](-) [136145:136179](-) trnI-GAU_copy2 [138064:138105](-) [137083:137117](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [70904:71032](-) [100697:100925](-) [100123:100148](-) ycf3 [45566:45689](-) [44614:44843](-) [43682:43834](-) rps12_copy2 [70904:71032](-) [141912:142140](+) [142689:142714](+) clpP [73274:73342](-) [72087:72377](-) [71166:71417](-)