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, 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, psbA_copy2, 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, 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 rbcL c-type cytochrom synthesis gene ccsA Envelop membrane protein cemA Maturase matK Protease clpP Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor infA Conserved open reading frames ycf1, ycf12, ycf2, ycf2_copy2, ycf4 Other genes chlB, chlL, chlN, rpl21 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 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 None Subunit of Acetyl-CoA-carboxylase None 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) [11511:11655](-) [10368:10783](-) clpP (3/3) [70453:70523](-) [69451:69742](-) [68658:68897](-) ndhA (2/2) [123398:123955](-) [121923:122480](-) ndhB (3/2) [1:38](-) [159866:160568](-) [158254:159024](-) petB (2/2) [73566:73571](+) [74390:75028](+) petD (2/2) [75239:75246](+) [75898:76369](+) rpl16 (2/2) [81163:81171](-) [80004:80408](-) rpl2 (2/2) [83903:84299](-) [82753:83189](-) rpoC1 (2/2) [21602:22033](-) [19220:20869](-) rps12 (3/3) [68277:68390](-) [144381:144612](-) [143767:143792](-) rps12_copy2 (3/3) [68277:68390](-) [100886:101117](+) [101706:101731](+) rps16 (2/2) [3298:3345](-) [2379:2612](-) ycf3 (3/3) [41689:41813](-) [40707:40935](-) [39898:40059](-) ### The exon column shows the number of (actual exons/expected exons). ### 4. Genes with internal stop codon: ['matK', 'rps16', 'chlB', 'atpI', 'rps2', 'rpoC2', 'rpoC1', 'rpoB', 'ycf3', 'rps4', 'petA', 'rps11', 'infA', 'rps3', 'rpl22', 'rpl2', 'rps7', 'ycf2', 'ndhF', 'rpl21', 'rpl32', 'ndhI', 'ycf2_copy2', 'rps7_copy2'] 5. Genes with nonstandard start codon: Genes Start codon ndhB ACG matK GCG atpH ACG psbM ACG petN ACG psbC ACG psaB ACG atpB ACG accD ACG ycf4 ACG rps18 ACG psbB ACG petD ACG rpl36 ACG rps8 ACG rps7 GTG ndhF ACG rps15 ACG ycf1 ACG chlL ACG rps7_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon petB TCA 7. Conclusion This genome has 130 genes (116 unique genes). Including: 88 protein-coding genes (84 are unique) 34 tRNA genes (28 are unique) 8 rRNA genes (4 are unique) Details are as follows: 88 protein-coding genes (84 are unique) Genes Length Location accD 933 [52814:53746](+) atpA 1524 [8758:10281](-) atpB 1482 [48732:50213](-) atpE 399 [48328:48726](-) atpF 561 [11511:11655](-) [10368:10783](-) atpH 246 [12009:12254](-) atpI 747 [13001:13747](-) ccsA 906 [116604:117509](+) cemA 1497 [55330:56826](+) chlB 1545 [3483:5027](-) chlL 882 [132758:133639](-) chlN 1395 [131292:132686](-) clpP 603 [70453:70523](-) [69451:69742](-) [68658:68897](-) infA 243 [78422:78664](-) matK 1506 [227:1732](-) ndhA 1116 [123398:123955](-) [121923:122480](-) ndhB 1512 [1:38](-) [159866:160568](-) [158254:159024](-) ndhC 399 [46380:46778](-) ndhD 1506 [117938:119443](-) ndhE 303 [120151:120453](-) ndhF 2229 [111873:114101](-) ndhG 594 [120527:121120](-) ndhH 1179 [123957:125135](-) ndhI 495 [121292:121786](-) ndhJ 513 [45098:45610](-) ndhK 738 [45682:46419](-) petA 972 [57032:58003](+) petB 645 [73566:73571](+) [74390:75028](+) petD 480 [75239:75246](+) [75898:76369](+) petG 117 [64842:64958](+) petL 96 [64586:64681](+) petN 90 [27765:27854](-) psaA 2253 [37289:39541](-) psaB 2205 [35059:37263](-) psaC 246 [119593:119838](-) psaI 111 [54089:54199](+) psaJ 129 [65860:65988](+) psbA 1062 [102739:103800](+) psbA_copy2 1062 [141698:142759](-) psbB 1527 [70987:72513](+) psbC 1422 [29975:31396](-) psbD 1062 [31344:32405](-) psbE 252 [63564:63815](-) psbF 120 [63429:63548](-) psbH 225 [73210:73434](+) psbI 111 [6337:6447](+) psbJ 126 [63053:63178](-) psbK 177 [5657:5833](+) psbL 117 [63291:63407](-) psbM 105 [26728:26832](+) psbN 132 [72984:73115](-) psbT 105 [72752:72856](+) psbZ 189 [29214:29402](-) rbcL 1428 [50858:52285](+) rpl14 369 [79399:79767](-) rpl16 414 [81163:81171](-) [80004:80408](-) rpl2 834 [83903:84299](-) [82753:83189](-) rpl20 357 [66975:67331](-) rpl21 357 [114420:114776](+) rpl22 378 [82046:82423](-) rpl23 264 [84368:84631](-) rpl32 219 [114967:115185](+) rpl33 201 [66214:66414](+) rpl36 114 [78186:78299](-) rpoA 1017 [76673:77689](-) rpoB 3216 [22084:25299](-) rpoC1 2082 [21602:22033](-) [19220:20869](-) rpoC2 4284 [14770:19053](-) rps11 393 [77726:78118](-) rps12 372 [68277:68390](-) [144381:144612](-) [143767:143792](-) rps12_copy2 372 [68277:68390](-) [100886:101117](+) [101706:101731](+) rps14 303 [34540:34842](-) rps15 270 [125241:125510](-) rps16 282 [3298:3345](-) [2379:2612](-) rps18 228 [66502:66729](+) rps19 279 [82441:82719](-) rps2 708 [13940:14647](-) rps3 657 [81284:81940](-) rps4 621 [42631:43251](-) rps7 474 [101797:102270](+) rps7_copy2 474 [143228:143701](-) rps8 402 [78801:79202](-) ycf1 5115 [125815:130929](-) ycf12 102 [7166:7267](+) ycf2 6261 [104553:110813](+) ycf2_copy2 6261 [134685:140945](-) ycf3 516 [41689:41813](-) [40707:40935](-) [39898:40059](-) ycf4 555 [54604:55158](+) 34 tRNA genes (28 are unique) Genes Location trnQ-UUG [5258:5329](-) trnS-GCU [6523:6609](-) trnG-UCC [7445:7467](+) [8357:8404](+) trnR-UCU [8584:8654](+) trnD-GUC [25989:26062](+) trnY-GUA [26115:26196](-) trnE-UUC [26213:26285](-) trnC-GCA [28309:28380](-) trnG-GCC [28879:28949](-) trnS-UGA [29611:29699](+) trnT-GGU [33792:33863](-) trnfM-CAU [34332:34405](-) trnS-GGA [42091:42177](+) trnL-UAA [43874:43907](+) [44496:44546](+) trnF-GAA [44803:44875](+) trnM-CAU [48063:48135](+) trnR-UCG [52408:52488](+) trnW-CCA [65153:65226](-) trnP-UGG [65428:65501](-) trnI-CAU [84798:84871](-) trnT-UGU [87439:87471](+) [87998:88037](+) trnR-ACG [88768:88842](-) trnA-UGC [93539:93575](-) [92684:92719](-) trnI-GAU [94650:94685](-) [93663:93698](-) trnH-GUG [104222:104295](+) trnN-GUU [111331:111402](-) trnP-GGG [115781:115854](-) trnL-UAG [116140:116218](+) trnN-GUU_copy2 [134096:134167](+) trnH-GUG_copy2 [141203:141276](-) trnI-GAU_copy2 [150813:150848](+) [151800:151835](+) trnA-UGC_copy2 [151923:151959](+) [152779:152814](+) trnR-ACG_copy2 [156656:156730](+) trnT-UGU_copy2 [158027:158059](-) [157461:157500](-) 8 rRNA genes (4 are unique) Genes Location rrn5 [89087:89209](-) rrn4.5 [89458:89560](-) rrn23 [89677:92494](-) rrn16 [94998:96497](-) rrn16_copy2 [149001:150500](+) rrn23_copy2 [153004:155821](+) rrn4.5_copy2 [155938:156040](+) rrn5_copy2 [156289:156411](+) This genome has 21 genes with intron(s). Details are as follows: 16 gene(s) have 1 intron(s) Genes Exons rps16 [3298:3345](-) [2379:2612](-) atpF [11511:11655](-) [10368:10783](-) rpoC1 [21602:22033](-) [19220:20869](-) petB [73566:73571](+) [74390:75028](+) petD [75239:75246](+) [75898:76369](+) rpl16 [81163:81171](-) [80004:80408](-) rpl2 [83903:84299](-) [82753:83189](-) ndhA [123398:123955](-) [121923:122480](-) trnG-UCC [7445:7467](+) [8357:8404](+) trnL-UAA [43874:43907](+) [44496:44546](+) trnT-UGU [87439:87471](+) [87998:88037](+) trnA-UGC [93539:93575](-) [92684:92719](-) trnI-GAU [94650:94685](-) [93663:93698](-) trnI-GAU_copy2 [150813:150848](+) [151800:151835](+) trnA-UGC_copy2 [151923:151959](+) [152779:152814](+) trnT-UGU_copy2 [158027:158059](-) [157461:157500](-) 5 gene(s) have 2 intron(s) Genes Exons rps12 [68277:68390](-) [144381:144612](-) [143767:143792](-) ndhB [1:38](-) [159866:160568](-) [158254:159024](-) ycf3 [41689:41813](-) [40707:40935](-) [39898:40059](-) rps12_copy2 [68277:68390](-) [100886:101117](+) [101706:101731](+) clpP [70453:70523](-) [69451:69742](-) [68658:68897](-)