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, ndhE, ndhF, ndhF_copy2, 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, rpl32, rpl32_copy2, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps12_copy2, rps14, rps15, 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, 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 ndhD 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) [20142:20286](-) [19012:19421](-) ndhA (2/2) [135514:136064](+) [137120:137657](+) ndhB (2/2) [110210:110986](+) [111704:112459](+) ndhB_copy2 (2/2) [154652:155428](-) [153179:153934](-) petB (2/2) [79281:79286](+) [80038:80679](+) petD (2/2) [80902:80909](+) [81636:82131](+) rpl16 (1/2) [85610:86017](-) rpl2 (2/2) [88849:89242](-) [87755:88191](-) rpoC1 (2/2) [26239:26670](+) [27432:29042](+) rps12 (3/3) [70896:71009](-) [156826:157057](-) [156264:156289](-) rps12_copy2 (3/3) [70896:71009](-) [108581:108812](+) [109349:109374](+) rps16 (1/2) [13340:13645](-) ycf3 (3/3) [51162:51285](-) [50124:50353](-) [49199:49351](-) ### 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 ACG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 129 genes (109 unique genes). Including: 84 protein-coding genes (76 are unique) 37 tRNA genes (29 are unique) 8 rRNA genes (4 are unique) Details are as follows: 84 protein-coding genes (76 are unique) Genes Length Location atpA 1524 [17409:18932](-) atpB 1491 [7735:9225](+) atpE 402 [9222:9623](+) atpF 555 [20142:20286](-) [19012:19421](-) atpH 246 [20693:20938](-) atpI 744 [34528:35271](+) ccsA 963 [122637:123599](+) ccsA_copy2 963 [142039:143001](-) cemA 696 [62147:62842](+) infA 234 [84161:84394](-) matK 1503 [1998:3500](-) ndhA 1089 [135514:136064](+) [137120:137657](+) ndhB 1533 [110210:110986](+) [111704:112459](+) ndhB_copy2 1533 [154652:155428](-) [153179:153934](-) ndhC 363 [58094:58456](-) ndhE 306 [139358:139663](+) ndhF 2253 [114407:116659](-) ndhF_copy2 2253 [148979:151231](+) ndhG 531 [138598:139128](+) ndhH 1191 [134322:135512](+) ndhI 498 [137745:138242](+) ndhJ 477 [56754:57230](-) ndhK 753 [57351:58103](-) petA 963 [63062:64024](+) petB 648 [79281:79286](+) [80038:80679](+) petD 504 [80902:80909](+) [81636:82131](+) petG 114 [67342:67455](+) petL 96 [67079:67174](+) petN 90 [21256:21345](-) psaA 2253 [46337:48589](-) psaB 2205 [44107:46311](-) psaC 246 [139937:140182](+) psaI 111 [60172:60282](+) psaJ 141 [68305:68445](+) psbA 1062 [363:1424](-) psbB 1527 [76115:77641](+) psbC 1416 [40013:41428](+) psbD 1062 [39004:40065](+) psbE 252 [65604:65855](-) psbF 120 [65475:65594](-) psbH 222 [78221:78442](+) psbI 111 [14974:15084](+) psbJ 123 [65085:65207](-) psbK 186 [14376:14561](+) psbL 117 [65332:65448](-) psbM 105 [35690:35794](-) psbN 132 [77996:78127](-) psbT 114 [77822:77935](+) psbZ 189 [42074:42262](+) rbcL 1428 [5534:6961](-) rpl14 369 [85111:85479](-) rpl16 408 [85610:86017](-) rpl2 831 [88849:89242](-) [87755:88191](-) rpl20 393 [69851:70243](-) rpl22 399 [86952:87350](-) rpl23 291 [89260:89550](-) rpl23_copy2 291 [176088:176378](+) rpl32 180 [121524:121703](+) rpl32_copy2 180 [143935:144114](-) rpl33 201 [68883:69083](+) rpl36 114 [83947:84060](-) rpoA 1020 [82293:83312](-) rpoB 3207 [22999:26205](+) rpoC1 2043 [26239:26670](+) [27432:29042](+) rpoC2 4173 [29209:33381](+) rps11 450 [83379:83828](-) rps12 372 [70896:71009](-) [156826:157057](-) [156264:156289](-) rps12_copy2 372 [70896:71009](-) [108581:108812](+) [109349:109374](+) rps14 303 [43661:43963](-) rps15 264 [133924:134187](+) rps16 306 [13340:13645](-) rps18 444 [69219:69662](+) rps19 279 [87410:87688](-) rps2 711 [33605:34315](+) rps3 687 [86177:86863](-) rps4 627 [53376:54002](-) rps7 468 [109428:109895](+) rps7_copy2 468 [155743:156210](-) rps8 402 [84503:84904](-) ycf1 5634 [125837:131470](+) ycf2 6963 [89989:96951](+) ycf2_copy2 6963 [168687:175649](-) ycf3 507 [51162:51285](-) [50124:50353](-) [49199:49351](-) ycf4 555 [60718:61272](+) 37 tRNA genes (29 are unique) Genes Location trnH-GUG [39:113](-) trnK-UUU [4214:4250](-) [1705:1739](-) trnM-CAU [9820:9892](-) trnQ-UUG [13885:13956](-) trnS-GCU [15225:15312](-) trnG-UCC [16300:16322](+) [17012:17059](+) trnR-UCU [17198:17269](+) trnC-GCA [21723:21793](-) trnD-GUC [36818:36891](-) trnY-GUA [37259:37342](-) trnE-UUC [37402:37474](-) trnT-GGU [38034:38105](+) trnS-UGA [41656:41748](-) trnG-GCC [43320:43390](+) trnfM-CAU [43455:43528](-) trnS-GGA [52981:53064](+) trnT-UGU [54352:54424](-) trnL-UAA [55098:55132](+) [55618:55667](+) trnF-GAA [56050:56122](+) trnW-CCA [67581:67654](-) trnP-UGG [67808:67881](-) trnI-CAU [89857:89930](-) trnL-CAA [97994:98075](-) trnR-ACG [98682:98755](-) trnA-UGC [103584:103621](-) [102749:102783](-) trnI-GAU [104667:104703](-) [103678:103712](-) trnV-GAC [106699:106770](-) trnN-GUU [112700:112771](-) trnL-UAG [122453:122532](+) trnL-UAG_copy2 [143106:143185](-) trnN-GUU_copy2 [152867:152938](+) trnV-GAC_copy2 [158868:158939](+) trnI-GAU_copy2 [160935:160971](+) [161926:161960](+) trnA-UGC_copy2 [162017:162054](+) [162855:162889](+) trnR-ACG_copy2 [166883:166956](+) trnL-CAA_copy2 [167563:167644](+) trnI-CAU_copy2 [175708:175781](+) 8 rRNA genes (4 are unique) Genes Location rrn5 [98996:99116](-) rrn4.5 [99584:99686](-) rrn23 [99777:102596](-) rrn16 [104977:106472](-) rrn16_copy2 [159166:160661](+) rrn23_copy2 [163042:165861](+) rrn4.5_copy2 [165952:166054](+) rrn5_copy2 [166522:166642](+) This genome has 18 genes with intron(s). Details are as follows: 15 gene(s) have 1 intron(s) Genes Exons atpF [20142:20286](-) [19012:19421](-) rpoC1 [26239:26670](+) [27432:29042](+) petB [79281:79286](+) [80038:80679](+) petD [80902:80909](+) [81636:82131](+) rpl2 [88849:89242](-) [87755:88191](-) ndhB [110210:110986](+) [111704:112459](+) ndhA [135514:136064](+) [137120:137657](+) ndhB_copy2 [154652:155428](-) [153179:153934](-) trnK-UUU [4214:4250](-) [1705:1739](-) trnG-UCC [16300:16322](+) [17012:17059](+) trnL-UAA [55098:55132](+) [55618:55667](+) trnA-UGC [103584:103621](-) [102749:102783](-) trnI-GAU [104667:104703](-) [103678:103712](-) trnI-GAU_copy2 [160935:160971](+) [161926:161960](+) trnA-UGC_copy2 [162017:162054](+) [162855:162889](+) 3 gene(s) have 2 intron(s) Genes Exons rps12 [70896:71009](-) [156826:157057](-) [156264:156289](-) ycf3 [51162:51285](-) [50124:50353](-) [49199:49351](-) rps12_copy2 [70896:71009](-) [108581:108812](+) [109349:109374](+)