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 ndhC 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, rpl2, rpl22, rpl23 Small subunit of ribosome rps11, rps14, rps19, rps2, rps3, rps4, rps4_copy2, rps7, rps8 DNA dependent RNA polymerase rpoA, rpoB, rpoC1, rpoC2 Subunit of rubisco rbcL c-type cytochrom synthesis gene ccsA Envelop membrane protein None Maturase matK Protease clpP Subunit of Acetyl-CoA-carboxylase None Translational initiation factor None Conserved open reading frames ycf1, ycf12, ycf2, ycf4 Other genes chlB, chlL, chlN Possible missing protein coding genes: Group of genes Name of genes Subunits of ATP synthase None Subunits of NADH-dehydrogenase ndhA, ndhB, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK Subunits of cytochrome b/f complex None Subunits of photosystem I None Subunits of photosystem II None Large subunit of ribosome rpl16, rpl20, rpl32, rpl33, rpl36 Small subunit of ribosome rps12, rps15, rps16, rps18 DNA dependent RNA polymerase None Subunit of rubisco None c-type cytochrom synthesis gene None Envelop membrane protein cemA Maturase None Protease None Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor infA 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) [19123:19260](+) [19957:20364](+) clpP (1/3) [87988:88605](-) petB (2/2) [77591:77596](-) [76198:76839](-) petD (2/2) [75980:75987](-) [74801:75284](-) rpl2 (2/2) [66638:67027](+) [67687:68139](+) rpoC1 (2/2) [8491:8919](+) [9705:11324](+) ycf3 (3/3) [53998:54121](-) [52989:53218](-) [52010:52165](-) ### 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 rps7 ACG psbM ACG rpoB ACG rpoC1 ATT rpoC2 ACG rps2 ACG atpI ACG atpH ACG ycf12 ACG psbI ACG psbK ACG chlB ACG matK ATT ycf2 GCT psbZ ACG psaB ACG psaA ACG ycf3 ACG rps4 ACG rpl23 ACG rps19 ACG rps3 ACT rpl14 ATT rps8 ACG rps11 ATT rpoA ACG petD ACG petB ACG psbH ACG psbN ACG psbT ACG psbB ACG psbJ ACG psbL ACG psbF ACG psbE ACG petL ACG petG ACG psaJ ACG clpP ACG petA ACG ycf4 ACG rbcL ACG atpB ACG atpE ACG ndhC ATC chlL ACG ycf1 ACG ccsA GCG rps4_copy2 ACG 6. Genes with nonstandard stop codon: Genes Stop codon psbM CGA petN CGA rpoB CGA atpH CGA atpF CGA psbI CGT chlB CGA psbC CGA ycf3 CAG rpl14 CGA psbL CAA psbF CGA petL CGA psaJ CGA petA CAG chlL CGA ycf1 CAA 7. Conclusion This genome has 79 genes (73 unique genes). Including: 62 protein-coding genes (61 are unique) 9 tRNA genes (8 are unique) 8 rRNA genes (4 are unique) Details are as follows: 62 protein-coding genes (61 are unique) Genes Length Location atpA 1524 [20415:21938](+) atpB 1470 [96988:98457](+) atpE 429 [98474:98902](+) atpF 546 [19123:19260](+) [19957:20364](+) atpH 246 [18500:18745](+) atpI 753 [17131:17883](+) ccsA 942 [112365:113306](-) chlB 1542 [25572:27113](+) chlL 876 [101594:102469](+) chlN 1392 [102526:103917](+) clpP 618 [87988:88605](-) matK 1596 [28419:30014](+) ndhC 345 [100319:100663](+) petA 960 [88717:89676](-) petB 648 [77591:77596](-) [76198:76839](-) petD 492 [75980:75987](-) [74801:75284](-) petG 105 [83970:84074](+) petL 96 [83682:83777](+) petN 90 [4449:4538](-) psaA 2247 [48891:51137](-) psaB 2205 [46661:48865](-) psaC 279 [110234:110512](+) psaI 111 [92492:92602](-) psaJ 129 [85461:85589](+) psbA 1065 [30576:31640](+) psbB 1530 [78631:80160](-) psbC 1422 [43247:44668](+) psbD 1062 [42238:43299](+) psbE 252 [81698:81949](-) psbF 120 [81568:81687](-) psbH 228 [77808:78035](-) psbI 102 [23840:23941](-) psbJ 123 [81178:81300](-) psbK 162 [24672:24833](-) psbL 117 [81429:81545](-) psbM 99 [2595:2693](+) psbN 135 [78122:78256](+) psbT 102 [78336:78437](-) psbZ 189 [45257:45445](+) rbcL 1428 [94764:96191](-) rpl14 366 [71263:71628](+) rpl2 843 [66638:67027](+) [67687:68139](+) rpl22 357 [68465:68821](+) rpl23 279 [66315:66593](+) rpoA 732 [73204:73935](+) rpoB 3225 [5233:8457](+) rpoC1 2049 [8491:8919](+) [9705:11324](+) rpoC2 4389 [11507:15895](+) rps11 390 [72771:73160](+) rps14 303 [46046:46348](-) rps19 279 [68157:68435](+) rps2 690 [16115:16804](+) rps3 666 [68899:69564](+) rps4 597 [55478:56074](-) rps4_copy2 597 [116049:116645](-) rps7 477 [306:782](+) rps8 399 [72042:72440](+) ycf1 4791 [104236:109026](+) ycf12 102 [22776:22877](-) ycf2 5580 [32151:37730](+) ycf3 510 [53998:54121](-) [52989:53218](-) [52010:52165](-) ycf4 588 [91421:92008](-) 9 tRNA genes (8 are unique) Genes Location trnQ [25285:25356](+) trnH [31868:31941](+) trnD [38965:39038](-) trnY [39417:39498](-) trnE [39646:39718](-) trnM [45810:45883](-) trnN [57038:57109](+) trnW [84295:84368](-) trnN_copy2 [117609:117680](+) 8 rRNA genes (4 are unique) Genes Location rrn5 [58887:59007](-) rrn4.5 [59247:59349](-) rrn23 [59480:62295](-) rrn16 [63154:64652](-) rrn5_copy2 [119458:119578](-) rrn4.5_copy2 [119818:119920](-) rrn23_copy2 [120051:122866](-) rrn16_copy2 [123724:125223](-) This genome has 6 genes with intron(s). Details are as follows: 5 gene(s) have 1 intron(s) Genes Exons rpoC1 [8491:8919](+) [9705:11324](+) atpF [19123:19260](+) [19957:20364](+) rpl2 [66638:67027](+) [67687:68139](+) petD [75980:75987](-) [74801:75284](-) petB [77591:77596](-) [76198:76839](-) 1 gene(s) have 2 intron(s) Genes Exons ycf3 [53998:54121](-) [52989:53218](-) [52010:52165](-)