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, ndhD, ndhE, ndhF, 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, rpl23, rpl23_copy2, rpl2_copy2, rpl32, 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 None c-type cytochrom synthesis gene ccsA Envelop membrane protein cemA Maturase matK Protease clpP Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor None Conserved open reading frames ycf1, ycf15, ycf15_copy2, ycf1_copy2, ycf2, ycf2_copy2, ycf4, ycf68, ycf68_copy2 Other genes rbcl 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 rpl22 Small subunit of ribosome None DNA dependent RNA polymerase None Subunit of rubisco rbcL c-type cytochrom synthesis gene None Envelop membrane protein None Maturase None Protease None Subunit of Acetyl-CoA-carboxylase None Translational initiation factor infA Conserved open reading frames None Other genes None 2. Multicopy genes with different lengths: Genes Length Location ycf1 1068 [113437:114505](+) ycf1_copy2 5676 [129748:135424](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [13729:13887](-) [12577:12987](-) clpP (3/3) [76286:76354](-) [75198:75488](-) [74283:74510](-) ndhA (2/2) [127211:127762](-) [125593:126126](-) ndhB (2/2) [100397:101173](-) [98956:99711](-) ndhB_copy2 (2/2) [147689:148465](+) [149151:149906](+) petB (2/2) [79297:79302](+) [80080:80733](+) petD (2/2) [80935:80943](+) [81688:82164](+) rpl16 (2/2) [86916:86924](-) [85456:85854](-) rpl2 (2/2) [89805:90194](-) [88685:89119](-) rpl2_copy2 (2/2) [158668:159057](+) [159743:160177](+) rpoC1 (2/2) [24565:24999](-) [22127:23761](-) rps12 (2/3) [74017:74130](-) [102563:102805](-) rps12_copy2 (2/3) [74017:74130](-) [146057:146299](+) rps16 (2/2) [6394:6441](-) [5527:5751](-) ycf3 (3/3) [47305:47430](-) [46254:46481](-) [45339:45491](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: ycf68 2 [106785:106827](+) [106856:107037](+)] ycf68_copy2 2 [142035:142077](-) [141825:142006](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon rps16 ATT petN ATT psbL ACG psbT ATC rps19 ATT ycf68 GTG ndhD GTG ycf68_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 132 genes (111 unique genes). Including: 88 protein-coding genes (79 are unique) 36 tRNA genes (28 are unique) 8 rRNA genes (4 are unique) Details are as follows: 88 protein-coding genes (79 are unique) Genes Length Location accD 1494 [61022:62515](+) atpA 1524 [10992:12515](-) atpB 1503 [56628:58130](-) atpE 402 [56230:56631](-) atpF 570 [13729:13887](-) [12577:12987](-) atpH 246 [14355:14600](-) atpI 744 [15897:16640](-) ccsA 972 [120129:121100](+) cemA 696 [65104:65799](+) clpP 588 [76286:76354](-) [75198:75488](-) [74283:74510](-) matK 1524 [2069:3592](-) ndhA 1086 [127211:127762](-) [125593:126126](-) ndhB 1533 [100397:101173](-) [98956:99711](-) ndhB_copy2 1533 [147689:148465](+) [149151:149906](+) ndhC 363 [54178:54540](-) ndhD 1530 [121358:122887](-) ndhE 306 [123548:123853](-) ndhF 2295 [114433:116727](-) ndhG 531 [124104:124634](-) ndhH 1182 [127764:128945](-) ndhI 504 [125009:125512](-) ndhJ 477 [52791:53267](-) ndhK 684 [53446:54129](-) petA 963 [66009:66971](+) petB 660 [79297:79302](+) [80080:80733](+) petD 486 [80935:80943](+) [81688:82164](+) petG 114 [70311:70424](+) petL 96 [70045:70140](+) petN 96 [30511:30606](+) psaA 2253 [42332:44584](-) psaB 2205 [40102:42306](-) psaC 246 [123006:123251](-) psaI 114 [63085:63198](+) psaJ 135 [71303:71437](+) psbA 1062 [436:1497](-) psbB 1527 [76833:78359](+) psbC 1422 [36340:37761](+) psbD 1062 [35331:36392](+) psbE 252 [68558:68809](-) psbF 120 [68429:68548](-) psbH 222 [78954:79175](+) psbI 111 [8594:8704](+) psbJ 123 [68030:68152](-) psbK 186 [7948:8133](+) psbL 117 [68290:68406](-) psbM 105 [31856:31960](-) psbN 132 [78718:78849](-) psbT 117 [78533:78649](+) psbZ 189 [38417:38605](+) rbcl 1428 [58842:60269](+) rpl14 369 [84948:85316](-) rpl16 408 [86916:86924](-) [85456:85854](-) rpl2 825 [89805:90194](-) [88685:89119](-) rpl20 354 [72809:73162](-) rpl23 282 [90213:90494](-) rpl23_copy2 282 [158368:158649](+) rpl2_copy2 825 [158668:159057](+) [159743:160177](+) rpl32 159 [117949:118107](+) rpl33 201 [71917:72117](+) rpl36 114 [83954:84067](-) rpoA 975 [82351:83325](-) rpoB 3213 [25026:28238](-) rpoC1 2070 [24565:24999](-) [22127:23761](-) rpoC2 4155 [17833:21987](-) rps11 417 [83391:83807](-) rps12 357 [74017:74130](-) [102563:102805](-) rps12_copy2 357 [74017:74130](-) [146057:146299](+) rps14 303 [39669:39971](-) rps15 273 [129075:129347](-) rps16 273 [6394:6441](-) [5527:5751](-) rps18 306 [72301:72606](+) rps19 282 [88343:88624](-) rps2 702 [16896:17597](-) rps3 648 [87091:87738](-) rps4 606 [48737:49342](-) rps7 468 [101491:101958](-) rps7_copy2 468 [146904:147371](+) rps8 411 [84337:84747](-) ycf1 1068 [113438:114505](+) ycf15 192 [103658:103849](-) ycf15_copy2 192 [145013:145204](+) ycf1_copy2 5676 [129749:135424](-) ycf2 6885 [90823:97707](+) ycf2_copy2 6885 [151155:158039](-) ycf3 507 [47305:47430](-) [46254:46481](-) [45339:45491](-) ycf4 555 [63623:64177](+) ycf68 225 [106785:106827](+) [106856:107037](+) ycf68_copy2 225 [142035:142077](-) [141825:142006](-) 36 tRNA genes (28 are unique) Genes Location trnH-GUG [3:77](-) trnK-UUU [4384:4420](-) [1769:1807](-) trnQ-UUG [7510:7581](-) trnS-GCU [8885:8972](-) trnR-UCU [10783:10854](+) trnC-GCA [29420:29490](+) trnD-GUC [32482:32555](-) trnY-GUA [32970:33053](-) trnE-UUC [33112:33184](-) trnT-GGU [33872:33943](+) trnS-UGA [38029:38121](-) trnG-GCC [39175:39245](+) trnM-CAU [39430:39503](-) trnS-GGA [48341:48427](+) trnT-UGU [49813:49885](-) trnL-UAA [51087:51123](+) [51638:51687](+) trnF-GAA [52067:52139](+) trnV-UAC [55646:55684](-) [54996:55030](-) trnM-CAU_copy2 [55881:55953](+) trnW-CCA [70541:70614](-) trnP-UGG [70772:70845](-) trnM-CAU_copy3 [90655:90728](-) trnL-CAA [98280:98360](-) trnV-GAC [104557:104628](+) trnI-GAU [106644:106685](+) [107629:107663](+) trnA-UGC [107728:107765](+) [108588:108622](+) trnR-ACG [112386:112459](+) trnN-GUU [113043:113114](-) trnL-UAG [119939:120018](+) trnN-GUU_copy2 [135748:135819](+) trnR-ACG_copy2 [136403:136476](-) trnA-UGC_copy2 [141097:141134](-) [140240:140274](-) trnI-GAU_copy2 [142177:142218](-) [141199:141233](-) trnV-GAC_copy2 [144234:144305](-) trnL-CAA_copy2 [150502:150582](+) trnI-CAU [158134:158207](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [104857:106347](+) rrn23 [108782:111590](+) rrn4.5 [111690:111792](+) rrn5 [112017:112137](+) rrn5_copy2 [136725:136845](-) rrn4.5_copy2 [137070:137172](-) rrn23_copy2 [137277:140080](-) rrn16_copy2 [142515:144005](-) This genome has 24 genes with intron(s). Details are as follows: 22 gene(s) have 1 intron(s) Genes Exons rps12 [74017:74130](-) [102563:102805](-) rps16 [6394:6441](-) [5527:5751](-) atpF [13729:13887](-) [12577:12987](-) rpoC1 [24565:24999](-) [22127:23761](-) rps12_copy2 [74017:74130](-) [146057:146299](+) petB [79297:79302](+) [80080:80733](+) petD [80935:80943](+) [81688:82164](+) rpl16 [86916:86924](-) [85456:85854](-) rpl2 [89805:90194](-) [88685:89119](-) ndhB [100397:101173](-) [98956:99711](-) ycf68 [106785:106827](+) [106856:107037](+) ndhA [127211:127762](-) [125593:126126](-) ycf68_copy2 [142035:142077](-) [141825:142006](-) ndhB_copy2 [147689:148465](+) [149151:149906](+) rpl2_copy2 [158668:159057](+) [159743:160177](+) trnK-UUU [4384:4420](-) [1769:1807](-) trnL-UAA [51087:51123](+) [51638:51687](+) trnV-UAC [55646:55684](-) [54996:55030](-) trnI-GAU [106644:106685](+) [107629:107663](+) trnA-UGC [107728:107765](+) [108588:108622](+) trnA-UGC_copy2 [141097:141134](-) [140240:140274](-) trnI-GAU_copy2 [142177:142218](-) [141199:141233](-) 2 gene(s) have 2 intron(s) Genes Exons ycf3 [47305:47430](-) [46254:46481](-) [45339:45491](-) clpP [76286:76354](-) [75198:75488](-) [74283:74510](-)