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, 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, rpl14_copy2, rpl16, rpl16_copy2, rpl2, rpl20, rpl22, rpl22_copy2, rpl23, rpl23_copy2, rpl2_copy2, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps12_copy2, rps14, rps15, rps16, rps18, rps19, rps19_copy2, rps2, rps3, rps3_copy2, rps4, rps7, rps7_copy2, rps8, rps8_copy2 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 None Conserved open reading frames ycf1, ycf2, ycf2_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 psaI Subunits of photosystem II None Large subunit of ribosome rpl32 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 infA 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) [16569:16713](-) [15417:15826](-) clpP (3/3) [71606:71676](-) [70519:70809](-) [69577:69820](-) ndhA (2/2) [121968:122520](-) [120427:120965](-) ndhB (2/2) [95558:96332](-) [94098:94855](-) ndhB_copy2 (2/2) [142499:143273](+) [143976:144733](+) petB (2/2) [74571:74576](+) [75359:76000](+) petD (2/2) [76205:76212](+) [76945:77440](+) rpl16 (1/2) [80772:81182](-) rpl16_copy2 (1/2) [157649:158059](+) rpl2 (2/2) [84985:85387](-) [83900:84333](-) rpl2_copy2 (2/2) [153444:153846](+) [154498:154931](+) rpoC1 (2/2) [27098:27529](-) [24719:26329](-) rps12 (3/3) [69302:69415](-) [97744:97972](-) [97177:97232](-) rps12_copy2 (3/3) [69302:69415](-) [140859:141087](+) [141599:141654](+) rps16 (2/2) [1195:1234](+) [2123:2343](+) ycf3 (3/3) [49070:49193](-) [48114:48343](-) [47211:47363](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: rps4 2 [159497:159497](+) [1:632](+)] ycf2 2 [85983:86572](+) [87095:92816](+)] ycf1 3 [125807:128426](-) [125418:125776](-) [124524:125387](-)] ycf2_copy2 2 [152259:152848](-) [146015:151736](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon rpl16 ATC rps19 GTG rpl2 ATA ndhD ATA rpl2_copy2 ATA rps19_copy2 GTG rpl16_copy2 ATC 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 131 genes (106 unique genes). Including: 88 protein-coding genes (76 are unique) 35 tRNA genes (26 are unique) 8 rRNA genes (4 are unique) Details are as follows: 88 protein-coding genes (76 are unique) Genes Length Location accD 1443 [57409:58851](+) atpA 1524 [13827:15350](-) atpB 1503 [52875:54377](-) atpE 402 [52477:52878](-) atpF 555 [16569:16713](-) [15417:15826](-) atpH 246 [17149:17394](-) atpI 744 [18517:19260](-) ccsA 966 [114860:115825](+) cemA 690 [61101:61790](+) clpP 606 [71606:71676](-) [70519:70809](-) [69577:69820](-) matK 1530 [3792:5321](+) ndhA 1092 [121968:122520](-) [120427:120965](-) ndhB 1533 [95558:96332](-) [94098:94855](-) ndhB_copy2 1533 [142499:143273](+) [143976:144733](+) ndhC 363 [12028:12390](-) ndhD 1479 [116057:117535](-) ndhE 306 [118211:118516](-) ndhF 2235 [110369:112603](-) ndhG 534 [118798:119331](-) ndhH 1182 [122522:123703](-) ndhI 543 [119811:120353](-) ndhJ 477 [10676:11152](-) ndhK 678 [11287:11964](-) petA 969 [61998:62966](+) petB 648 [74571:74576](+) [75359:76000](+) petD 504 [76205:76212](+) [76945:77440](+) petG 114 [65791:65904](+) petL 96 [65511:65606](+) petN 90 [32362:32451](+) psaA 2253 [44219:46471](-) psaB 2205 [41989:44193](-) psaC 246 [117722:117967](-) psaJ 135 [66686:66820](+) psbA 1062 [5893:6954](+) psbB 1527 [72086:73612](+) psbC 1422 [38518:39939](+) psbD 1062 [37509:38570](+) psbE 252 [63889:64140](-) psbF 120 [63760:63879](-) psbH 222 [74230:74451](+) psbI 111 [8485:8595](+) psbJ 123 [63379:63501](-) psbK 186 [7897:8082](+) psbL 117 [63621:63737](-) psbM 105 [33247:33351](-) psbN 132 [73996:74127](-) psbT 108 [73802:73909](+) psbZ 189 [40554:40742](+) rbcL 1428 [55246:56673](+) rpl14 369 [80261:80629](-) rpl14_copy2 369 [158202:158570](+) rpl16 411 [80772:81182](-) rpl16_copy2 411 [157649:158059](+) rpl2 837 [84985:85387](-) [83900:84333](-) rpl20 354 [68157:68510](-) rpl22 486 [82962:83447](-) rpl22_copy2 486 [155384:155869](+) rpl23 282 [85394:85675](-) rpl23_copy2 282 [153156:153437](+) rpl2_copy2 837 [153444:153846](+) [154498:154931](+) rpl33 201 [67212:67412](+) rpl36 114 [79218:79331](-) rpoA 1020 [77592:78611](-) rpoB 3213 [27556:30768](-) rpoC1 2043 [27098:27529](-) [24719:26329](-) rpoC2 4152 [20400:24551](-) rps11 417 [78684:79100](-) rps12 399 [69302:69415](-) [97744:97972](-) [97177:97232](-) rps12_copy2 399 [69302:69415](-) [140859:141087](+) [141599:141654](+) rps14 303 [41556:41858](-) rps15 273 [123849:124121](-) rps16 261 [1195:1234](+) [2123:2343](+) rps18 306 [67601:67906](+) rps19 279 [83561:83839](-) rps19_copy2 279 [154992:155270](+) rps2 711 [19480:20190](-) rps3 657 [82321:82977](-) rps3_copy2 657 [155854:156510](+) rps4 633 [159497:159497](+) [1:632](+) rps7 468 [96656:97123](-) rps7_copy2 468 [141708:142175](+) rps8 399 [79645:80043](-) rps8_copy2 399 [158788:159186](+) ycf1 3843 [125807:128426](-) [125418:125776](-) [124524:125387](-) ycf2 6312 [85983:86572](+) [87095:92816](+) ycf2_copy2 6312 [152259:152848](-) [146015:151736](-) ycf3 507 [49070:49193](-) [48114:48343](-) [47211:47363](-) ycf4 555 [59948:60502](+) 35 tRNA genes (26 are unique) Genes Location trnK-UUU [2989:3026](+) [5578:5613](+) trnH-GUG [7290:7363](+) trnQ-UUG [7489:7560](-) trnS-GCU [8682:8769](-) trnL-UAA [9346:9380](+) [9874:9923](+) trnF-GAA [10063:10135](+) trnS-CGA [12688:12718](+) [13408:13467](+) trnR-UCU [13626:13697](+) trnC-GCA [31848:31918](+) trnD-GUC [34474:34547](-) trnY-GUA [34925:35008](-) trnE-UUC [35068:35140](-) trnT-GGU [35861:35932](+) trnS-UGA [40136:40228](-) trnG-GCC [41071:41141](+) trnM-CAU [41320:41393](-) trnS-GGA [50111:50197](+) trnM-CAU_copy2 [52149:52221](+) trnW-CCA [66050:66123](-) trnP-UGG [66287:66360](-) trnM-CAU_copy3 [85841:85914](-) trnL-CAA [93457:93537](-) trnV-GAC [99802:99873](+) trnI [101883:101914](+) [102862:102901](+) trnA-UGC [102966:103002](+) [103816:103851](+) trnR-ACG [107593:107666](+) trnN-GUU [108282:108353](-) trnL-UAG [114665:114744](+) trnN-GUU_copy2 [130478:130549](+) trnR-ACG_copy2 [131165:131238](-) trnA-UGC_copy2 [135829:135865](-) [134980:135015](-) trnI_copy2 [136917:136948](-) [135930:135969](-) trnV-GAC_copy2 [138958:139029](-) trnL-CAA_copy2 [145294:145374](+) trnM-CAU_copy4 [152917:152990](+) 8 rRNA genes (4 are unique) Genes Location rrn16S [100102:101592](+) rrn23S [104004:106813](+) rrn4.5S [106912:107014](+) rrn5S [107239:107359](+) rrn5S_copy2 [131472:131592](-) rrn4.5S_copy2 [131817:131919](-) rrn23S_copy2 [132018:134827](-) rrn16S_copy2 [137239:138729](-) This genome has 25 genes with intron(s). Details are as follows: 20 gene(s) have 1 intron(s) Genes Exons rps4 [159497:159497](+) [1:632](+) rps16 [1195:1234](+) [2123:2343](+) atpF [16569:16713](-) [15417:15826](-) rpoC1 [27098:27529](-) [24719:26329](-) petB [74571:74576](+) [75359:76000](+) petD [76205:76212](+) [76945:77440](+) rpl2 [84985:85387](-) [83900:84333](-) ycf2 [85983:86572](+) [87095:92816](+) ndhB [95558:96332](-) [94098:94855](-) ndhA [121968:122520](-) [120427:120965](-) ndhB_copy2 [142499:143273](+) [143976:144733](+) ycf2_copy2 [152259:152848](-) [146015:151736](-) rpl2_copy2 [153444:153846](+) [154498:154931](+) trnK-UUU [2989:3026](+) [5578:5613](+) trnL-UAA [9346:9380](+) [9874:9923](+) trnS-CGA [12688:12718](+) [13408:13467](+) trnI [101883:101914](+) [102862:102901](+) trnA-UGC [102966:103002](+) [103816:103851](+) trnA-UGC_copy2 [135829:135865](-) [134980:135015](-) trnI_copy2 [136917:136948](-) [135930:135969](-) 5 gene(s) have 2 intron(s) Genes Exons rps12 [69302:69415](-) [97744:97972](-) [97177:97232](-) ycf3 [49070:49193](-) [48114:48343](-) [47211:47363](-) rps12_copy2 [69302:69415](-) [140859:141087](+) [141599:141654](+) clpP [71606:71676](-) [70519:70809](-) [69577:69820](-) ycf1 [125807:128426](-) [125418:125776](-) [124524:125387](-)