1. Annotated protein coding genes: Group of genes Name of genes Subunits of ATP synthase atpA, atpB, atpE, atpH, atpI Subunits of NADH-dehydrogenase ndhA, ndhA_copy2, ndhB, ndhC, ndhD, ndhD_copy2, ndhE, ndhE_copy2, ndhF, ndhH, ndhH_copy2, ndhI, ndhI_copy2, ndhJ 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, ycf3 Large subunit of ribosome rpl14, rpl16, rpl2, rpl22, rpl23, rpl32, rpl32_copy2, rpl33, rpl36 Small subunit of ribosome rps11, rps14, rps15, rps15_copy2, rps18, rps19, rps2, rps3, rps4, rps7, rps8 DNA dependent RNA polymerase rpoA, rpoB, rpoC1, rpoC2 Subunit of rubisco rbcL c-type cytochrom synthesis gene None Envelop membrane protein cemA Maturase matK Protease None Subunit of Acetyl-CoA-carboxylase None Translational initiation factor None Conserved open reading frames ycf4 Other genes lhbA Possible missing protein coding genes: Group of genes Name of genes Subunits of ATP synthase atpF Subunits of NADH-dehydrogenase ndhG, ndhK Subunits of cytochrome b/f complex None Subunits of photosystem I None Subunits of photosystem II psbZ Large subunit of ribosome rpl20 Small subunit of ribosome rps12, rps16 DNA dependent RNA polymerase None Subunit of rubisco None c-type cytochrom synthesis gene ccsA Envelop membrane protein None Maturase None Protease clpP Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor infA Conserved open reading frames ycf1, ycf15, ycf2 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 ndhA (2/2) [124724:125287](+) [126379:126918](+) ndhA_copy2 (2/2) [155311:155874](-) [153680:154219](-) ndhB (2/2) [100427:101203](-) [98992:99747](-) petB (1/2) [42497:43177](+) petD (1/2) [44105:44629](+) rpl16 (1/2) [88617:89054](-) rpl2 (1/2) [93383:94186](-) rpoC1 (2/2) [76175:76606](-) [73813:75450](-) ycf3 (3/3) [6290:6418](-) [5351:5578](-) [4467:4619](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: psbA 2 [1:236](-) [175220:176045](-)] rpoA 2 [85383:86186](-) [85285:85371](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon atpB ATA petN ATT psbT ATC petB ATA rps2 GTG rpoC2 GTG rpl16 ATC rps19 GTG rps7 ATT ndhD GTG ndhD_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 119 genes (100 unique genes). Including: 75 protein-coding genes (67 are unique) 36 tRNA genes (29 are unique) 8 rRNA genes (4 are unique) Details are as follows: 75 protein-coding genes (67 are unique) Genes Length Location atpA 1524 [62966:64489](-) atpB 1491 [15604:17094](+) atpE 414 [17091:17504](+) atpH 246 [66214:66459](-) atpI 744 [67600:68343](-) cemA 690 [21398:22087](+) lhbA 189 [52109:52297](+) matK 1521 [731:2251](-) ndhA 1104 [124724:125287](+) [126379:126918](+) ndhA_copy2 1104 [155311:155874](-) [153680:154219](-) ndhB 1533 [100427:101203](-) [98992:99747](-) ndhC 363 [11814:12176](-) ndhD 1521 [134573:136093](+) ndhD_copy2 1521 [144505:146025](-) ndhE 306 [133668:133973](+) ndhE_copy2 306 [146625:146930](-) ndhF 2244 [139474:141717](+) ndhH 1182 [123541:124722](+) ndhH_copy2 1182 [155876:157057](-) ndhI 534 [127019:127552](+) ndhI_copy2 534 [153046:153579](-) ndhJ 477 [10497:10973](-) petA 963 [22318:23280](+) petB 681 [42497:43177](+) petD 525 [44105:44629](+) petG 114 [34064:34177](-) petL 96 [34357:34452](-) petN 96 [27938:28033](-) psaA 2253 [55591:57843](-) psaB 2205 [53361:55565](-) psaC 246 [134218:134463](+) psaC_copy2 246 [146135:146380](-) psaI 111 [20070:20180](+) psaJ 135 [33086:33220](-) psbA 1062 [1:236](-) [175220:176045](-) psbB 1527 [39399:40925](+) psbC 1464 [49993:51456](+) psbD 1062 [49026:50087](+) psbE 252 [35757:36008](+) psbF 120 [36018:36137](+) psbH 222 [41435:41656](+) psbI 111 [60794:60904](+) psbJ 123 [36407:36529](+) psbK 186 [60213:60398](+) psbL 117 [36160:36276](+) psbM 105 [26707:26811](+) psbN 132 [41196:41327](-) psbT 117 [41019:41135](+) rbcL 1428 [13478:14905](-) rpl14 396 [88126:88521](-) rpl16 438 [88617:89054](-) rpl2 804 [93383:94186](-) rpl22 468 [92538:93005](-) rpl23 288 [94193:94480](-) rpl32 204 [137976:138179](-) rpl32_copy2 204 [142419:142622](+) rpl33 207 [32427:32633](-) rpl36 114 [86819:86932](-) rpoA 891 [85383:86186](-) [85285:85371](-) rpoB 3207 [77310:80516](-) rpoC1 2070 [76175:76606](-) [73813:75450](-) rpoC2 4080 [69530:73609](-) rps11 420 [86286:86705](-) rps14 303 [52918:53220](-) rps15 279 [123176:123454](+) rps15_copy2 279 [157144:157422](-) rps18 321 [31993:32313](-) rps19 279 [93051:93329](-) rps2 714 [68554:69267](-) rps3 687 [91867:92553](-) rps4 636 [7118:7753](-) rps7 498 [101531:102028](-) rps8 399 [87540:87938](-) ycf3 510 [6290:6418](-) [5351:5578](-) [4467:4619](-) ycf4 555 [20619:21173](+) 36 tRNA genes (29 are unique) Genes Location trnS-GGA [6747:6833](+) trnT-UGU [8127:8199](-) trnL-UAA [8931:8967](+) [9457:9506](+) trnF-GAA [9900:9969](+) trnV-UAC [13231:13269](-) [12608:12644](-) trnM-CAU [17705:17776](-) trnE-UUC [24789:24861](+) trnY-GUA [24921:25004](+) trnD-GUC [25119:25192](+) trnC-GCA [28749:28829](-) trnP-UGG [33645:33718](+) trnP-GGG [33646:33716](+) trnW-CCA [33867:33938](+) trnT-GGU [47490:47561](+) trnS-UGA [51669:51761](-) trnG-UCC [52552:52622](+) trnfM-CAU [52681:52747](-) trnQ-UUG [59802:59873](-) trnS-GCU [61046:61132](-) trnR-UCU [62780:62851](+) trnfM-CAU_copy2 [67132:67198](-) trnI-CAU [95178:95251](-) trnL-CAA [98339:98419](-) trnV-GAC [104421:104492](+) trnH-GUG [105718:105792](+) trnI-GAU [111434:111475](+) [112417:112451](+) trnA-UGC [112516:112553](+) [113361:113395](+) trnR-ACG [117206:117279](+) trnN-GUU [117792:117864](-) trnL-UAG [137399:137478](-) trnL-UAG_copy2 [143120:143199](+) trnN-GUU_copy2 [162734:162806](+) trnR-ACG_copy2 [163319:163392](-) trnA-UGC_copy2 [168045:168082](-) [167203:167237](-) trnI-GAU_copy2 [169123:169164](-) [168147:168181](-) trnH-GUG_copy2 [174806:174880](-) 8 rRNA genes (4 are unique) Genes Location rrn16 [109643:111131](+) rrn23 [113553:116356](+) rrn4.5 [116482:116582](+) rrn5 [116842:116959](+) rrn5_copy2 [163639:163756](-) rrn4.5_copy2 [163999:164099](-) rrn23_copy2 [164220:167023](-) rrn16_copy2 [169455:170943](-) This genome has 13 genes with intron(s). Details are as follows: 12 gene(s) have 1 intron(s) Genes Exons psbA [1:236](-) [175220:176045](-) rpoC1 [76175:76606](-) [73813:75450](-) rpoA [85383:86186](-) [85285:85371](-) ndhB [100427:101203](-) [98992:99747](-) ndhA [124724:125287](+) [126379:126918](+) ndhA_copy2 [155311:155874](-) [153680:154219](-) trnL-UAA [8931:8967](+) [9457:9506](+) trnV-UAC [13231:13269](-) [12608:12644](-) trnI-GAU [111434:111475](+) [112417:112451](+) trnA-UGC [112516:112553](+) [113361:113395](+) trnA-UGC_copy2 [168045:168082](-) [167203:167237](-) trnI-GAU_copy2 [169123:169164](-) [168147:168181](-) 1 gene(s) have 2 intron(s) Genes Exons ycf3 [6290:6418](-) [5351:5578](-) [4467:4619](-)