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, ndhC, ndhD, ndhD_copy2, ndhE, ndhE_copy2, ndhF, ndhG, ndhG_copy2, ndhH, ndhH_copy2, ndhI, ndhI_copy2, ndhJ, ndhK Subunits of cytochrome b/f complex petA, petB, petD, petD_copy2, 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, psbT, psbZ, ycf3 Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, rpl22, rpl23, rpl23_copy2, rpl23_copy3, rpl32, rpl32_copy2, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps14, rps14_copy2, rps14_copy3, rps15, rps15_copy2, rps16, rps16_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 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 ycf4 Other genes 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 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 ycf1, ycf15, ycf2 Other genes None 2. Multicopy genes with different lengths: Genes Length Location rpl23 288 [10622:10910](+) rpl23_copy2 384 [109278:109662](+) rpl23_copy3 384 [174281:174665](-) petD 483 join{[63689:63697](-), [62412:62887](-)} petD_copy2 27 [149932:149959](+) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [41102:41245](+) [41962:42372](+) ndhA (2/2) [130100:130651](+) [131744:132283](+) ndhA_copy2 (2/2) [153293:153844](-) [151661:152200](-) ndhB (2/2) [3239:4015](+) [4701:5456](+) petB (2/2) [65274:65279](-) [63888:64529](-) petD (2/2) [63690:63697](-) [62413:62887](-) petD_copy2 (1/2) [149933:149959](+) rpl16 (2/2) [14936:14944](+) [15967:16392](+) rpl2 (1/2) [10917:11723](+) rpoC1 (2/2) [30309:30740](+) [31433:33043](+) rps12 (3/3) [77094:77207](-) [1593:1824](+) [2362:2387](+) rps16 (2/2) [110213:110256](+) [111129:111354](+) rps16_copy2 (2/2) [173688:173731](-) [172590:172815](-) ycf3 (3/3) [101314:101441](+) [102154:102381](+) [103125:103278](+) ### 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 rps2 GTG ndhD GTG ndhD_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 138 genes (109 unique genes). Including: 91 protein-coding genes (75 are unique) 39 tRNA genes (30 are unique) 8 rRNA genes (4 are unique) Details are as follows: 91 protein-coding genes (75 are unique) Genes Length Location atpA 1524 [42439:43962](+) atpB 1497 [90595:92091](-) atpE 414 [90185:90598](-) atpF 555 [41102:41245](+) [41962:42372](+) atpH 246 [40453:40698](+) atpI 744 [38549:39292](+) ccsA 963 [137661:138623](-) ccsA_copy2 963 [145321:146283](+) cemA 690 [85606:86295](-) infA 597 [17593:18189](+) matK 1521 [105485:107005](+) ndhA 1092 [130100:130651](+) [131744:132283](+) ndhA_copy2 1092 [153293:153844](-) [151661:152200](-) ndhB 1533 [3239:4015](+) [4701:5456](+) ndhC 363 [95642:96004](+) ndhD 1521 [135895:137415](+) ndhD_copy2 1521 [146529:148049](-) ndhE 306 [134983:135288](+) ndhE_copy2 306 [148656:148961](-) ndhF 2238 [141430:143667](+) ndhG 534 [134229:134762](+) ndhG_copy2 534 [149182:149715](-) ndhH 1182 [128917:130098](+) ndhH_copy2 1182 [153846:155027](-) ndhI 534 [132384:132917](+) ndhI_copy2 534 [151027:151560](-) ndhJ 477 [96846:97322](+) ndhK 678 [96063:96740](+) pbf1 132 [65738:65869](+) petA 963 [84423:85385](-) petB 648 [65274:65279](-) [63888:64529](-) petD 483 [63690:63697](-) [62413:62887](-) petD_copy2 27 [149933:149959](+) petG 114 [73432:73545](+) petL 96 [73159:73254](+) petN 90 [79650:79739](+) psaA 2253 [49108:51360](+) psaB 2205 [51386:53590](+) psaC 246 [135540:135785](+) psaC_copy2 246 [148159:148404](-) psaI 111 [87486:87596](-) psaJ 135 [74393:74527](+) psbA 1062 [107512:108573](+) psbB 1527 [66140:67666](-) psbC 1422 [55524:56945](-) psbD 1062 [56893:57954](-) psbE 252 [71615:71866](-) psbF 120 [71486:71605](-) psbH 222 [65409:65630](-) psbI 111 [46038:46148](-) psbJ 123 [71089:71211](-) psbK 192 [46541:46732](-) psbL 117 [71347:71463](-) psbM 105 [80909:81013](-) psbT 108 [65930:66037](-) psbZ 189 [54668:54856](-) rbcL 1428 [92892:94319](+) rpl14 396 [16491:16886](+) rpl16 435 [14936:14944](+) [15967:16392](+) rpl2 807 [10917:11723](+) rpl20 354 [75960:76313](-) rpl22 465 [12101:12565](+) rpl23 288 [10623:10910](+) rpl23_copy2 384 [109279:109662](+) rpl23_copy3 384 [174282:174665](-) rpl32 204 [139311:139514](-) rpl32_copy2 204 [144430:144633](+) rpl33 207 [74984:75190](+) rpl36 114 [18298:18411](+) rpoA 831 [19045:19875](+) rpoB 3207 [26399:29605](+) rpoC1 2043 [30309:30740](+) [31433:33043](+) rpoC2 4116 [33255:37370](+) rps11 420 [18525:18944](+) rps12 372 [77094:77207](-) [1593:1824](+) [2362:2387](+) rps14 303 [53736:54038](+) rps14_copy2 303 [112082:112384](+) rps14_copy3 303 [171560:171862](-) rps15 279 [128552:128830](+) rps15_copy2 279 [155114:155392](-) rps16 270 [110213:110256](+) [111129:111354](+) rps16_copy2 270 [173688:173731](-) [172590:172815](-) rps18 324 [75357:75680](+) rps19 279 [11777:12055](+) rps2 699 [37620:38318](+) rps3 666 [12550:13215](+) rps4 630 [99976:100605](+) rps7 399 [2513:2911](+) rps8 399 [17086:17484](+) ycf3 510 [101314:101441](+) [102154:102381](+) [103125:103278](+) ycf4 555 [86519:87073](-) 39 tRNA genes (30 are unique) Genes Location trnV-GAC [56:127](-) trnL-CAA [6035:6115](+) trnI-CAU [9857:9930](+) trnfM-CAU [39712:39778](+) trnR-UCU [44076:44147](-) trnS-CGA [45083:45113](-) [44361:44420](-) trnS-GCU [45810:45896](+) trnQ-UUG [47076:47147](+) trnfM-CAU_copy2 [54210:54276](+) trnG-UCC [54335:54405](-) trnS-UGA [55195:55287](+) trnT-GGU [59422:59493](-) trnW-CCA [73682:73753](-) trnP-GGG [73909:73979](-) trnC-GCA [78844:78924](+) trnD-GUC [82555:82628](-) trnY-GUA [82738:82821](-) trnE-UUC [82874:82946](-) trnM-CAU [89908:89979](+) trnV-UAC [94535:94573](+) [95161:95197](+) trnF-GAA [97852:97921](-) trnL-UAA [98823:98859](-) [98286:98335](-) trnT-UGU [99541:99613](+) trnS-GGA [100897:100983](-) trnK-UUU [104737:104773](+) [107289:107323](+) trnH-GUG [108924:108997](+) trnfM-CAU_copy3 [112553:112626](+) trnI-GAU [118629:118670](+) [119609:119643](+) trnA-UGC [119714:119751](+) [120559:120593](+) trnR-ACG [124405:124478](+) trnN-GUU [125000:125071](-) trnL-UAG [138726:138805](-) trnL-UAG_copy2 [145139:145218](+) trnN-GUU_copy2 [158873:158945](+) trnR-ACG_copy2 [159466:159539](-) trnA-UGC_copy2 [164193:164230](-) [163351:163385](-) trnI-GAU_copy2 [165274:165315](-) [164301:164335](-) trnfM-CAU_copy4 [171318:171391](-) trnH-GUG_copy2 [174947:175021](-) 8 rRNA genes (4 are unique) Genes Location rrn16 [116839:118327](+) rrn23 [120746:123555](+) rrn4.5 [123681:123781](+) rrn5 [124041:124158](+) rrn5_copy2 [159786:159903](-) rrn4.5_copy2 [160163:160263](-) rrn23_copy2 [160389:163198](-) rrn16_copy2 [165617:167105](-) This genome has 20 genes with intron(s). Details are as follows: 18 gene(s) have 1 intron(s) Genes Exons ndhB [3239:4015](+) [4701:5456](+) rpl16 [14936:14944](+) [15967:16392](+) rpoC1 [30309:30740](+) [31433:33043](+) atpF [41102:41245](+) [41962:42372](+) petD [63690:63697](-) [62413:62887](-) petB [65274:65279](-) [63888:64529](-) rps16 [110213:110256](+) [111129:111354](+) ndhA [130100:130651](+) [131744:132283](+) ndhA_copy2 [153293:153844](-) [151661:152200](-) rps16_copy2 [173688:173731](-) [172590:172815](-) trnS-CGA [45083:45113](-) [44361:44420](-) trnV-UAC [94535:94573](+) [95161:95197](+) trnL-UAA [98823:98859](-) [98286:98335](-) trnK-UUU [104737:104773](+) [107289:107323](+) trnI-GAU [118629:118670](+) [119609:119643](+) trnA-UGC [119714:119751](+) [120559:120593](+) trnA-UGC_copy2 [164193:164230](-) [163351:163385](-) trnI-GAU_copy2 [165274:165315](-) [164301:164335](-) 2 gene(s) have 2 intron(s) Genes Exons rps12 [77094:77207](-) [1593:1824](+) [2362:2387](+) ycf3 [101314:101441](+) [102154:102381](+) [103125:103278](+)