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, psbT, psbZ Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, rpl22, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps12_copy2, rps14, rps15, rps16, rps18, rps19, rps19_copy2, 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 Envelop membrane protein cemA Maturase matK Protease None Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor None Conserved open reading frames ycf1, ycf1_copy2, ycf2, ycf2_copy2 Other genes clpP1, pafI, pafII, pbf1 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 psbN, ycf3 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 None Translational initiation factor infA Conserved open reading frames ycf15, ycf4 Other genes None 2. Multicopy genes with different lengths: Genes Length Location ycf1 897 [108942:109839](+) ycf1_copy2 5340 [123825:129165](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [12912:13055](-) [11720:12130](-) ndhA (2/2) [121407:121963](-) [119785:120325](-) ndhB (2/2) [95998:96774](-) [94548:95303](-) ndhB_copy2 (2/2) [141334:142110](+) [142805:143560](+) petB (2/2) [74488:74493](+) [75246:75887](+) petD (2/2) [76105:76112](+) [76859:77363](+) rpl16 (2/2) [82244:82252](-) [80824:81222](-) rpl2 (2/2) [85171:85561](-) [84076:84506](-) rpl2_copy2 (2/2) [152547:152937](+) [153602:154032](+) rpoC1 (2/2) [22570:23001](-) [20216:21832](-) rps12 (3/3) [69270:69383](-) [98135:98366](-) [97567:97592](-) rps12_copy2 (3/3) [69270:69383](-) [139742:139973](+) [140516:140541](+) rps16 (2/2) [5774:5819](-) [4688:4896](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: pafI 3 [43578:43701](-) [42597:42826](-) [41706:41858](-)] clpP1 3 [71522:71592](-) [70420:70711](-) [69515:69766](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon rps19 GTG rpl2 ACG ndhD ATC rpl2_copy2 ACG rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 132 genes (112 unique genes). Including: 86 protein-coding genes (78 are unique) 38 tRNA genes (30 are unique) 8 rRNA genes (4 are unique) Details are as follows: 86 protein-coding genes (78 are unique) Genes Length Location accD 1491 [57336:58826](+) atpA 1524 [10122:11645](-) atpB 1488 [52942:54429](-) atpE 405 [52541:52945](-) atpF 555 [12912:13055](-) [11720:12130](-) atpH 246 [13269:13514](-) atpI 744 [14014:14757](-) ccsA 972 [114286:115257](+) cemA 699 [60655:61353](+) clpP1 615 [71522:71592](-) [70420:70711](-) [69515:69766](-) matK 1563 [1675:3237](-) ndhA 1098 [121407:121963](-) [119785:120325](-) ndhB 1533 [95998:96774](-) [94548:95303](-) ndhB_copy2 1533 [141334:142110](+) [142805:143560](+) ndhC 363 [49514:49876](-) ndhD 1506 [115480:116985](-) ndhE 306 [117752:118057](-) ndhF 2211 [109804:112014](-) ndhG 531 [118236:118766](-) ndhH 1182 [121965:123146](-) ndhI 543 [119145:119687](-) ndhJ 477 [48201:48677](-) ndhK 771 [48753:49523](-) pafI 507 [43578:43701](-) [42597:42826](-) [41706:41858](-) pafII 555 [59528:60082](+) pbf1 132 [73905:74036](-) petA 969 [61572:62540](+) petB 648 [74488:74493](+) [75246:75887](+) petD 513 [76105:76112](+) [76859:77363](+) petG 114 [65614:65727](+) petL 96 [65337:65432](+) petN 90 [28445:28534](+) psaA 2253 [38816:41068](-) psaB 2205 [36586:38790](-) psaC 246 [117103:117348](-) psaI 111 [59069:59179](+) psaJ 129 [66520:66648](+) psbA 1062 [92:1153](-) psbB 1527 [72021:73547](+) psbC 1422 [33165:34586](+) psbD 1062 [32156:33217](+) psbE 252 [64124:64375](-) psbF 120 [63994:64113](-) psbH 222 [74148:74369](+) psbI 111 [7420:7530](+) psbJ 123 [63607:63729](-) psbK 186 [6778:6963](+) psbL 117 [63855:63971](-) psbM 105 [29403:29507](-) psbT 102 [73734:73835](+) psbZ 189 [35163:35351](+) rbcL 1440 [55215:56654](+) rpl14 369 [80319:80687](-) rpl16 408 [82244:82252](-) [80824:81222](-) rpl2 822 [85171:85561](-) [84076:84506](-) rpl20 354 [68157:68510](-) rpl22 366 [83129:83494](-) rpl23 282 [85580:85861](-) rpl23_copy2 282 [152247:152528](+) rpl2_copy2 822 [152547:152937](+) [153602:154032](+) rpl32 174 [113004:113177](+) rpl33 201 [67198:67398](+) rpl36 114 [79177:79290](-) rpoA 1029 [77514:78542](-) rpoB 3222 [23028:26249](-) rpoC1 2049 [22570:23001](-) [20216:21832](-) rpoC2 4146 [15894:20039](-) rps11 417 [78612:79028](-) rps12 372 [69270:69383](-) [98135:98366](-) [97567:97592](-) rps12_copy2 372 [69270:69383](-) [139742:139973](+) [140516:140541](+) rps14 303 [36146:36448](-) rps15 270 [123259:123528](-) rps16 255 [5774:5819](-) [4688:4896](-) rps18 306 [67583:67888](+) rps19 279 [83542:83820](-) rps19_copy2 279 [154288:154566](+) rps2 711 [14995:15705](-) rps3 663 [82417:83079](-) rps4 606 [44609:45214](-) rps7 468 [97041:97508](-) rps7_copy2 468 [140600:141067](+) rps8 399 [79751:80149](-) ycf1 897 [108943:109839](+) ycf1_copy2 5340 [123826:129165](-) ycf2 6711 [86192:92902](+) ycf2_copy2 6711 [145206:151916](-) 38 tRNA genes (30 are unique) Genes Location trnK-UUU [4015:4051](-) [1398:1432](-) trnQ-UUG [6361:6432](-) trnS-GCU [7651:7738](-) trnG-UCC [9027:9049](+) [9751:9798](+) trnR-UCU [9932:10003](+) trnC-GCA [27495:27565](+) trnD-GUC [30238:30311](-) trnY-GUA [30621:30704](-) trnE-UUC [30764:30836](-) trnT-GGU [31333:31404](+) trnS-UGA [34734:34821](-) trnG-GCC [35661:35731](+) trnfM-CAU [35916:35989](-) trnS-GGA [44276:44363](+) trnT-UGU [45547:45619](-) trnL-UAA [46433:46467](+) [47001:47050](+) trnF-GAA [47407:47479](+) trnV-UAC [52127:52165](-) [51496:51530](-) trnM-CAU [52324:52396](+) trnW-CCA [65849:65922](-) trnP-UGG [66101:66174](-) trnH-GUG [83959:84032](+) trnI-CAU [86027:86100](-) trnL-CAA [93920:94000](-) trnV-GAC [100171:100242](+) trnI-GAU [102249:102285](+) [103227:103261](+) trnA-UGC [103326:103363](+) [104188:104222](+) trnR-ACG [107983:108056](+) trnN-GUU [108563:108634](-) trnL-UAG [114128:114207](+) trnN-GUU_copy2 [129474:129545](+) trnR-ACG_copy2 [130052:130125](-) trnA-UGC_copy2 [134745:134782](-) [133886:133920](-) trnI-GAU_copy2 [135823:135859](-) [134847:134881](-) trnV-GAC_copy2 [137866:137937](-) trnL-CAA_copy2 [144108:144188](+) trnI-CAU_copy2 [152008:152081](+) trnH-GUG_copy2 [154076:154149](-) 8 rRNA genes (4 are unique) Genes Location rrn16 [100468:101958](+) rrn23 [104368:107179](+) rrn4.5 [107281:107383](+) rrn5 [107606:107726](+) rrn5_copy2 [130382:130502](-) rrn4.5_copy2 [130725:130827](-) rrn23_copy2 [130929:133740](-) rrn16_copy2 [136150:137640](-) This genome has 23 genes with intron(s). Details are as follows: 19 gene(s) have 1 intron(s) Genes Exons rps16 [5774:5819](-) [4688:4896](-) atpF [12912:13055](-) [11720:12130](-) rpoC1 [22570:23001](-) [20216:21832](-) petB [74488:74493](+) [75246:75887](+) petD [76105:76112](+) [76859:77363](+) rpl16 [82244:82252](-) [80824:81222](-) rpl2 [85171:85561](-) [84076:84506](-) ndhB [95998:96774](-) [94548:95303](-) ndhA [121407:121963](-) [119785:120325](-) ndhB_copy2 [141334:142110](+) [142805:143560](+) rpl2_copy2 [152547:152937](+) [153602:154032](+) trnK-UUU [4015:4051](-) [1398:1432](-) trnG-UCC [9027:9049](+) [9751:9798](+) trnL-UAA [46433:46467](+) [47001:47050](+) trnV-UAC [52127:52165](-) [51496:51530](-) trnI-GAU [102249:102285](+) [103227:103261](+) trnA-UGC [103326:103363](+) [104188:104222](+) trnA-UGC_copy2 [134745:134782](-) [133886:133920](-) trnI-GAU_copy2 [135823:135859](-) [134847:134881](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [69270:69383](-) [98135:98366](-) [97567:97592](-) pafI [43578:43701](-) [42597:42826](-) [41706:41858](-) rps12_copy2 [69270:69383](-) [139742:139973](+) [140516:140541](+) clpP1 [71522:71592](-) [70420:70711](-) [69515:69766](-)