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, psbD_copy2, psbE, psbF, psbH, psbI, psbJ, psbK, psbM, psbT, psbZ, ycf3 Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, rpl22, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36 Small subunit of ribosome 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 None Subunit of Acetyl-CoA-carboxylase None Translational initiation factor infA Conserved open reading frames ycf1, ycf15, ycf15_copy2, ycf1_copy2, ycf4 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 psbL, psbN Large subunit of ribosome None Small subunit of ribosome rps11 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 ycf2 Other genes None 2. Multicopy genes with different lengths: Genes Length Location psbD 1062 [33810:34872](+) psbD_copy2 195 [79030:79225](-) ycf1 759 [108319:109078](+) ycf1_copy2 5202 [122461:127663](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [12904:13048](-) [11797:12206](-) ndhA (2/2) [119998:120550](-) [118418:118959](-) ndhB (2/2) [95448:96222](-) [94011:94768](-) ndhB_copy2 (2/2) [139761:140535](+) [141215:141972](+) petB (2/2) [74668:74673](+) [75474:76115](+) petD (2/2) [76317:76325](+) [77077:77550](+) rpl16 (2/2) [82448:82456](-) [81031:81429](-) rpl2 (2/2) [85216:85606](-) [84120:84553](-) rpl2_copy2 (2/2) [150377:150767](+) [151430:151863](+) rpoC1 (2/2) [23357:23788](-) [21003:22613](-) rps12 (3/3) [70861:70974](-) [97600:97831](-) [97034:97059](-) rps12_copy2 (3/3) [70861:70974](-) [138152:138383](+) [138924:138949](+) rps16 (2/2) [5908:5947](-) [4827:5035](-) ycf3 (3/3) [45227:45350](-) [44265:44494](-) [43364:43516](-) ### 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 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 127 genes (108 unique genes). Including: 82 protein-coding genes (74 are unique) 37 tRNA genes (30 are unique) 8 rRNA genes (4 are unique) Details are as follows: 82 protein-coding genes (74 are unique) Genes Length Location atpA 1524 [10219:11742](-) atpB 1497 [55607:57103](+) atpE 405 [57100:57504](+) atpF 555 [12904:13048](-) [11797:12206](-) atpH 246 [13426:13671](-) atpI 744 [14829:15572](-) ccsA 966 [113121:114086](+) cemA 690 [62255:62944](+) infA 240 [79581:79820](-) matK 1272 [1879:3150](-) ndhA 1095 [119998:120550](-) [118418:118959](-) ndhB 1533 [95448:96222](-) [94011:94768](-) ndhB_copy2 1533 [139761:140535](+) [141215:141972](+) ndhC 363 [50968:51330](-) ndhD 1521 [114316:115836](-) ndhE 306 [116438:116743](-) ndhF 2283 [109015:111297](-) ndhG 531 [116957:117487](-) ndhH 1182 [120552:121733](-) ndhI 504 [117835:118338](-) ndhJ 477 [49662:50138](-) ndhK 678 [50235:50912](-) petA 963 [63157:64119](+) petB 648 [74668:74673](+) [75474:76115](+) petD 483 [76317:76325](+) [77077:77550](+) petG 114 [67210:67323](+) petL 96 [66951:67046](+) petN 90 [29273:29362](+) psaA 2253 [40469:42721](-) psaB 2205 [38239:40443](-) psaC 246 [115940:116185](-) psaI 111 [60248:60358](+) psaJ 135 [68162:68296](+) psbA 1062 [355:1416](-) psbB 1527 [72194:73720](+) psbC 1422 [34820:36241](+) psbD 1062 [33811:34872](+) psbD_copy2 195 [79031:79225](-) psbE 252 [65478:65729](-) psbF 120 [65349:65468](-) psbH 222 [74323:74544](+) psbI 111 [7994:8104](+) psbJ 123 [64953:65075](-) psbK 180 [7463:7642](+) psbM 105 [30457:30561](-) psbT 102 [73923:74024](+) psbZ 189 [36904:37092](+) rbcL 1449 [53374:54822](-) rpl14 369 [80533:80901](-) rpl16 408 [82448:82456](-) [81031:81429](-) rpl2 825 [85216:85606](-) [84120:84553](-) rpl20 387 [69676:70062](-) rpl22 468 [83248:83715](-) rpl23 99 [85625:85723](-) rpl23_copy2 99 [150260:150358](+) rpl2_copy2 825 [150377:150767](+) [151430:151863](+) rpl32 162 [112034:112195](+) rpl33 201 [68743:68943](+) rpl36 114 [79352:79465](-) rpoA 1020 [77752:78771](-) rpoB 3213 [23815:27027](-) rpoC1 2043 [23357:23788](-) [21003:22613](-) rpoC2 4140 [16698:20837](-) rps12 372 [70861:70974](-) [97600:97831](-) [97034:97059](-) rps12_copy2 372 [70861:70974](-) [138152:138383](+) [138924:138949](+) rps14 309 [37804:38112](-) rps15 273 [121836:122108](-) rps16 249 [5908:5947](-) [4827:5035](-) rps18 210 [69219:69428](+) rps19 279 [83778:84056](-) rps2 711 [15793:16503](-) rps3 504 [82586:83089](-) rps4 606 [46332:46937](-) rps7 468 [96513:96980](-) rps7_copy2 468 [139003:139470](+) rps8 405 [79947:80351](-) ycf1 759 [108320:109078](+) ycf15 192 [98782:98973](-) ycf15_copy2 192 [137010:137201](+) ycf1_copy2 5202 [122462:127663](-) ycf3 507 [45227:45350](-) [44265:44494](-) [43364:43516](-) ycf4 549 [60788:61336](+) 37 tRNA genes (30 are unique) Genes Location trnH-GUG [2:74](-) trnK-UUU [4131:4167](-) [1632:1666](-) trnQ-UUG [7082:7153](-) trnS-GCU [8230:8317](-) trnG-UCC [9080:9102](+) [9789:9836](+) trnR-UCU [10035:10106](+) trnC-GCA [28309:28379](+) trnD-GUC [31263:31336](-) trnY-GUA [31449:31532](-) trnE-UUC [31592:31664](-) trnT-GGU [32394:32465](+) trnS-UGA [36473:36564](-) trnG-GCC [37368:37438](+) trnfM-CAU [37586:37659](-) trnS-GGA [45974:46060](+) trnT-UGU [47267:47339](-) trnL-UAA [47981:48015](+) [48507:48556](+) trnF-GAA [48917:48989](+) trnV-UAC [53089:53126](-) [52468:52502](-) trnM-CAU [57728:57799](-) trnW-CCA [67450:67523](-) trnP-UGG [67693:67766](-) trnI-CAU [86113:86186](-) trnL-CAA [93382:93462](-) trnV-GAC [99439:99510](+) trnI-GAU [101513:101549](+) [102497:102531](+) trnA-UGC [102596:102633](+) [103433:103467](+) trnR-ACG [107245:107318](+) trnN-GUU [107920:107991](-) trnL-UAG [112939:113018](+) trnN-GUU_copy2 [127992:128063](+) trnR-ACG_copy2 [128665:128738](-) trnA-UGC_copy2 [133350:133387](-) [132516:132550](-) trnI-GAU_copy2 [134434:134470](-) [133452:133486](-) trnV-GAC_copy2 [136473:136544](-) trnL-CAA_copy2 [142521:142601](+) trnI-CAU_copy2 [149797:149870](+) 8 rRNA genes (4 are unique) Genes Location rrn16S [99729:101219](+) rrn23S [103624:106235](+) rrn4.5S [106533:106635](+) rrn5S [106892:107011](+) rrn5S_copy2 [128972:129091](-) rrn4.5S_copy2 [129348:129450](-) rrn23S_copy2 [129748:132359](-) rrn16S_copy2 [134764:136254](-) This genome has 22 genes with intron(s). Details are as follows: 19 gene(s) have 1 intron(s) Genes Exons rps16 [5908:5947](-) [4827:5035](-) atpF [12904:13048](-) [11797:12206](-) rpoC1 [23357:23788](-) [21003:22613](-) petB [74668:74673](+) [75474:76115](+) petD [76317:76325](+) [77077:77550](+) rpl16 [82448:82456](-) [81031:81429](-) rpl2 [85216:85606](-) [84120:84553](-) ndhB [95448:96222](-) [94011:94768](-) ndhA [119998:120550](-) [118418:118959](-) ndhB_copy2 [139761:140535](+) [141215:141972](+) rpl2_copy2 [150377:150767](+) [151430:151863](+) trnK-UUU [4131:4167](-) [1632:1666](-) trnG-UCC [9080:9102](+) [9789:9836](+) trnL-UAA [47981:48015](+) [48507:48556](+) trnV-UAC [53089:53126](-) [52468:52502](-) trnI-GAU [101513:101549](+) [102497:102531](+) trnA-UGC [102596:102633](+) [103433:103467](+) trnA-UGC_copy2 [133350:133387](-) [132516:132550](-) trnI-GAU_copy2 [134434:134470](-) [133452:133486](-) 3 gene(s) have 2 intron(s) Genes Exons rps12 [70861:70974](-) [97600:97831](-) [97034:97059](-) ycf3 [45227:45350](-) [44265:44494](-) [43364:43516](-) rps12_copy2 [70861:70974](-) [138152:138383](+) [138924:138949](+)