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, ndhE, ndhF, 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, 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, rpl22_copy2, rpl2_copy2, rpl32, rpl32_copy2, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps12_copy2, rps14, rps15, rps15_copy2, rps16, rps19, rps19_copy2, rps2, rps4, rps7, rps7_copy2, rps8 DNA dependent RNA polymerase rpoB, rpoC1, rpoC2 Subunit of rubisco rbcL c-type cytochrom synthesis gene ccsA Envelop membrane protein cemA Maturase matK Protease None Subunit of Acetyl-CoA-carboxylase None Translational initiation factor None Conserved open reading frames ycf4, ycf68, ycf68_copy2 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 rpl23 Small subunit of ribosome rps18, rps3 DNA dependent RNA polymerase rpoA 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 infA Conserved open reading frames ycf1, ycf15, ycf2 Other genes None 2. Multicopy genes with different lengths: Genes Length Location ndhB 1479 join{[34283:35006](-), [32823:33579](-)} ndhB_copy2 1503 join{[161405:162152](+), [162856:163612](+)} 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [61940:62099](-) [60704:61110](-) ndhA (2/2) [13467:14015](-) [11881:12420](-) ndhA_copy2 (2/2) [182421:182968](+) [184015:184555](+) ndhB (2/2) [34284:35006](-) [32824:33579](-) ndhB_copy2 (2/2) [161406:162152](+) [162857:163612](+) petB (1/2) [126002:126691](+) petD (1/2) [127704:128180](+) rpl16 (1/2) [148149:148559](-) rpl2 (2/2) [42673:43065](+) [43707:44138](+) rpl2_copy2 (2/2) [153371:153763](-) [152298:152729](-) rpoC1 (2/2) [74388:74822](-) [72080:73720](-) rps12 (3/3) [120893:121006](-) [36478:36705](-) [35894:35932](-) rps12_copy2 (3/3) [144380:144493](-) [159731:159958](+) [160504:160542](+) rps16 (2/2) [54827:54870](-) [53763:53970](-) ycf3 (3/3) [57224:57355](-) [56235:56460](-) [55326:55486](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: ycf68 2 [26632:26673](-) [26370:26600](-)] ycf68_copy2 2 [169763:169804](+) [169836:170066](+)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon ndhE ATC rpl2 ACG rpoC2 TTG petB ATA petD ATA rpl16 ATC rpl2_copy2 ACG ndhB_copy2 ATT 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 132 genes (101 unique genes). Including: 84 protein-coding genes (71 are unique) 40 tRNA genes (26 are unique) 8 rRNA genes (4 are unique) Details are as follows: 84 protein-coding genes (71 are unique) Genes Length Location atpA 1524 [59088:60611](-) atpB 1458 [92768:94225](+) atpE 402 [94240:94641](+) atpF 567 [61940:62099](-) [60704:61110](-) atpH 246 [62542:62787](-) atpI 744 [63561:64304](-) ccsA 966 [4990:5955](+) cemA 690 [111283:111972](+) matK 1548 [50465:52012](-) ndhA 1089 [13467:14015](-) [11881:12420](-) ndhA_copy2 1089 [182421:182968](+) [184015:184555](+) ndhB 1479 [34284:35006](-) [32824:33579](-) ndhB_copy2 1503 [161406:162152](+) [162857:163612](+) ndhC 363 [96201:96563](+) ndhD 1509 [7581:9089](-) ndhE 306 [9892:10197](-) ndhF 2205 [353:2557](+) ndhG 531 [10403:10933](-) ndhG_copy2 531 [185503:186033](+) ndhH 1182 [14017:15198](-) ndhH_copy2 1182 [181238:182419](+) ndhI 543 [11250:11792](-) ndhI_copy2 543 [184644:185186](+) ndhJ 492 [97425:97916](+) ndhK 726 [96533:97258](+) petA 969 [112192:113160](+) petB 690 [126002:126691](+) petD 477 [127704:128180](+) petG 114 [116759:116872](+) petL 96 [116487:116582](+) petN 90 [82372:82461](-) psaA 2253 [137985:140237](-) psaB 2205 [135755:137959](-) psaC 246 [9214:9459](-) psaI 111 [109568:109678](+) psaJ 129 [117643:117771](+) psbA 1062 [48723:49784](-) psbB 1527 [122782:124308](+) psbC 1422 [86089:87510](-) psbD 1062 [87458:88519](-) psbE 252 [114700:114951](-) psbF 120 [114570:114689](-) psbH 222 [124914:125135](+) psbI 111 [104394:104504](-) psbJ 123 [114183:114305](-) psbK 186 [104844:105029](-) psbL 117 [114431:114547](-) psbM 105 [81976:82080](+) psbN 132 [124662:124793](-) psbT 108 [124480:124587](+) psbZ 189 [85344:85532](-) rbcL 1440 [90629:92068](-) rpl14 369 [147642:148010](-) rpl16 411 [148149:148559](-) rpl2 825 [42673:43065](+) [43707:44138](+) rpl20 372 [119822:120193](-) rpl22 387 [44794:45180](+) rpl22_copy2 387 [151256:151642](-) rpl2_copy2 825 [153371:153763](-) [152298:152729](-) rpl32 192 [32346:32537](+) rpl32_copy2 192 [163899:164090](-) rpl33 201 [118295:118495](+) rpl36 114 [65666:65779](-) rpoB 3246 [74850:78095](-) rpoC1 2076 [74388:74822](-) [72080:73720](-) rpoC2 5172 [66730:71901](-) rps11 438 [131204:131641](-) rps12 381 [120893:121006](-) [36478:36705](-) [35894:35932](-) rps12_copy2 381 [144380:144493](-) [159731:159958](+) [160504:160542](+) rps14 306 [135315:135620](-) rps15 264 [15298:15561](-) rps15_copy2 264 [180875:181138](+) rps16 252 [54827:54870](-) [53763:53970](-) rps19 231 [44503:44733](+) rps19_copy2 231 [151703:151933](-) rps2 726 [141933:142658](-) rps4 615 [107849:108463](+) rps7 489 [35351:35839](-) rps7_copy2 489 [160597:161085](+) rps8 414 [147058:147471](-) ycf3 519 [57224:57355](-) [56235:56460](-) [55326:55486](-) ycf4 558 [109926:110483](+) ycf68 273 [26632:26673](-) [26370:26600](-) ycf68_copy2 273 [169763:169804](+) [169836:170066](+) 40 tRNA genes (26 are unique) Genes Location trnL-UAG [4842:4922](+) trnT-UGU [7214:7288](-) trnN-GUU [18652:18725](+) trnR-ACG [20953:21027](-) trnA-UGC [25726:25762](-) [24869:24904](-) trnI-GAU [26779:26814](-) [25822:25856](-) trnM-CAU [29101:29175](-) trnM-CAU_copy2 [29276:29349](-) trnL-CAA [30940:31022](-) trnM-CAU_copy3 [41683:41760](+) trnH-GUG [44181:44255](-) trnH-GUG_copy2 [47769:47843](-) trnK-UUU [52905:52941](-) [50169:50203](-) trnS-GGA [65371:65459](+) trnE-UUC [80005:80078](+) trnY-GUA [80199:80282](+) trnD-GUC [80830:80905](+) trnC-GCA [82988:83058](-) trnG-UCC [84975:85046](-) trnF-GAA [85650:85738](-) trnS-UGA [85864:85951](+) trnV-GAC [90264:90335](-) trnM-CAU_copy4 [94784:94858](-) trnF-GAA_copy2 [98556:98628](-) trnV-UAC [99669:99706](-) [98979:99025](-) trnR-UCU [101749:101820](-) trnG-GCC [102710:102733](-) [101945:101992](-) trnS-GCU [104185:104273](+) trnQ-UUG [106699:106771](+) trnW-CCA [116974:117047](-) trnP-UGG [117165:117240](-) trnH-GUG_copy3 [152180:152254](+) trnM-CAU_copy5 [154676:154753](-) trnL-CAA_copy2 [165414:165496](+) trnM-CAU_copy6 [167087:167160](+) trnM-CAU_copy7 [167261:167335](+) trnI-GAU_copy2 [169622:169657](+) [170580:170614](+) trnA-UGC_copy2 [170674:170711](+) [171533:171567](+) trnR-ACG_copy2 [175409:175483](+) trnN-GUU_copy2 [177711:177784](-) 8 rRNA genes (4 are unique) Genes Location rrn5 [21356:21475](-) rrn4.5 [21709:21811](-) rrn23 [21909:24704](-) rrn16 [27322:28786](-) rrn16_copy2 [167650:169150](+) rrn23_copy2 [171719:174527](+) rrn4.5_copy2 [174625:174727](+) rrn5_copy2 [174961:175080](+) This genome has 21 genes with intron(s). Details are as follows: 18 gene(s) have 1 intron(s) Genes Exons ndhA [13467:14015](-) [11881:12420](-) ycf68 [26632:26673](-) [26370:26600](-) ndhB [34284:35006](-) [32824:33579](-) rpl2 [42673:43065](+) [43707:44138](+) rps16 [54827:54870](-) [53763:53970](-) atpF [61940:62099](-) [60704:61110](-) rpoC1 [74388:74822](-) [72080:73720](-) rpl2_copy2 [153371:153763](-) [152298:152729](-) ndhB_copy2 [161406:162152](+) [162857:163612](+) ycf68_copy2 [169763:169804](+) [169836:170066](+) ndhA_copy2 [182421:182968](+) [184015:184555](+) trnA-UGC [25726:25762](-) [24869:24904](-) trnI-GAU [26779:26814](-) [25822:25856](-) trnK-UUU [52905:52941](-) [50169:50203](-) trnV-UAC [99669:99706](-) [98979:99025](-) trnG-GCC [102710:102733](-) [101945:101992](-) trnI-GAU_copy2 [169622:169657](+) [170580:170614](+) trnA-UGC_copy2 [170674:170711](+) [171533:171567](+) 3 gene(s) have 2 intron(s) Genes Exons rps12 [120893:121006](-) [36478:36705](-) [35894:35932](-) ycf3 [57224:57355](-) [56235:56460](-) [55326:55486](-) rps12_copy2 [144380:144493](-) [159731:159958](+) [160504:160542](+)