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, petB_copy2, petD, petD_copy2, petG, petL, petN Subunits of photosystem I psaA, psaB, psaC, psaI, psaJ Subunits of photosystem II psbA, psbB, psbB_copy2, psbC, psbD, psbE, psbF, psbH, psbH_copy2, psbI, psbJ, psbK, psbL, psbM, psbN, psbN_copy2, psbT, psbT_copy2, psbZ, ycf3 Large subunit of ribosome rpl14, rpl14_copy2, rpl16, rpl16_copy2, rpl2, rpl20, rpl22, rpl22_copy2, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36, rpl36_copy2 Small subunit of ribosome rps11, rps11_copy2, 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 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, infA_copy2 Conserved open reading frames ycf1, ycf15, ycf15_copy2, 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 None Subunits of photosystem II None Large subunit of ribosome None Small subunit of ribosome None DNA dependent RNA polymerase rpoA 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 None Other genes None 2. Multicopy genes with different lengths: Genes Length Location rpl2 816 join{[86357:86739](-), [85264:85698](-)} rpl2_copy2 828 join{[152643:153036](+), [153695:154130](+)} 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [12621:12780](-) [11504:11913](-) clpP (3/3) [73048:73116](-) [72018:72308](-) [71043:71285](-) ndhA (2/2) [116693:117259](+) [118308:118847](+) ndhB (2/2) [96012:96788](-) [94562:95320](-) ndhB_copy2 (2/2) [142607:143383](+) [144075:144833](+) petB (2/2) [76048:76053](+) [76818:77471](+) petB_copy2 (2/2) [163342:163347](-) [161924:162577](-) petD (2/2) [77669:77676](+) [78360:78855](+) petD_copy2 (2/2) [161719:161726](-) [160540:161035](-) rpl16 (2/2) [83529:83537](-) [82305:82703](-) rpl16_copy2 (2/2) [155858:155866](+) [156692:157090](+) rpl2 (2/2) [86358:86739](-) [85265:85698](-) rpl2_copy2 (2/2) [152644:153036](+) [153696:154130](+) rpoC1 (2/2) [22790:23245](-) [20420:22039](-) rps12 (3/3) [70413:70526](-) [98199:98430](-) [97637:97662](-) rps12_copy2 (3/3) [70413:70526](-) [140965:141196](+) [141733:141758](+) rps16 (2/2) [6052:6091](-) [4960:5156](-) ycf3 (3/3) [44770:44898](-) [43828:44055](-) [42927:43079](-) ### 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 psbT ATC psbH ATC rps19 GTG rpl2 ACG rpl2_copy2 ATA rps19_copy2 GTG psbH_copy2 ATC psbT_copy2 ATC 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 147 genes (113 unique genes). Including: 101 protein-coding genes (79 are unique) 38 tRNA genes (30 are unique) 8 rRNA genes (4 are unique) Details are as follows: 101 protein-coding genes (79 are unique) Genes Length Location accD 1707 [58948:60654](+) atpA 1524 [9918:11441](-) atpB 1497 [54589:56085](-) atpE 402 [54191:54592](-) atpF 570 [12621:12780](-) [11504:11913](-) atpH 246 [13247:13492](-) atpI 744 [14252:14995](-) ccsA 966 [123396:124361](-) cemA 690 [62376:63065](+) clpP 603 [73048:73116](-) [72018:72308](-) [71043:71285](-) infA 246 [80880:81125](-) infA_copy2 246 [158270:158515](+) matK 1530 [2093:3622](-) ndhA 1107 [116693:117259](+) [118308:118847](+) ndhB 1536 [96012:96788](-) [94562:95320](-) ndhB_copy2 1536 [142607:143383](+) [144075:144833](+) ndhC 363 [51108:51470](-) ndhD 1554 [121604:123157](+) ndhE 306 [120670:120975](+) ndhF 2235 [126237:128471](+) ndhG 531 [119909:120439](+) ndhH 1182 [115510:116691](+) ndhI 507 [118926:119432](+) ndhJ 477 [49788:50264](-) ndhK 678 [50371:51048](-) petA 969 [63287:64255](+) petB 660 [76048:76053](+) [76818:77471](+) petB_copy2 660 [163342:163347](-) [161924:162577](-) petD 504 [77669:77676](+) [78360:78855](+) petD_copy2 504 [161719:161726](-) [160540:161035](-) petG 114 [66904:67017](+) petL 96 [66626:66721](+) petN 90 [28617:28706](+) psaA 2253 [40196:42448](-) psaB 2205 [37966:40170](-) psaC 246 [121271:121516](+) psaI 111 [61148:61258](+) psaJ 135 [67820:67954](+) psbA 1062 [534:1595](-) psbB 1527 [73534:75060](+) psbB_copy2 1527 [164335:165861](-) psbC 1422 [34438:35859](+) psbD 1062 [33429:34490](+) psbE 252 [65127:65378](-) psbF 120 [64998:65117](-) psbH 246 [75683:75928](+) psbH_copy2 246 [163467:163712](-) psbI 111 [7645:7755](+) psbJ 123 [64621:64743](-) psbK 186 [7033:7218](+) psbL 117 [64859:64975](-) psbM 105 [29352:29456](-) psbN 132 [75467:75598](-) psbN_copy2 132 [163797:163928](+) psbT 111 [75238:75348](+) psbT_copy2 111 [164047:164157](-) psbZ 189 [36525:36713](+) rbcL 1428 [56828:58255](+) rpl14 369 [81810:82178](-) rpl14_copy2 369 [157217:157585](+) rpl16 408 [83529:83537](-) [82305:82703](-) rpl16_copy2 408 [155858:155866](+) [156692:157090](+) rpl2 816 [86358:86739](-) [85265:85698](-) rpl20 354 [69261:69614](-) rpl22 519 [84334:84852](-) rpl22_copy2 519 [154543:155061](+) rpl23 282 [86758:87039](-) rpl23_copy2 282 [152356:152637](+) rpl2_copy2 828 [152644:153036](+) [153696:154130](+) rpl32 159 [125065:125223](-) rpl33 198 [68409:68606](+) rpl36 114 [80646:80759](-) rpl36_copy2 114 [158636:158749](+) rpoB 3213 [23251:26463](-) rpoC1 2076 [22790:23245](-) [20420:22039](-) rpoC2 4137 [16116:20252](-) rps11 465 [80059:80523](-) rps11_copy2 465 [158872:159336](+) rps12 372 [70413:70526](-) [98199:98430](-) [97637:97662](-) rps12_copy2 372 [70413:70526](-) [140965:141196](+) [141733:141758](+) rps14 303 [37534:37836](-) rps15 273 [115119:115391](+) rps16 237 [6052:6091](-) [4960:5156](-) rps18 303 [68773:69075](+) rps19 288 [84906:85193](-) rps19_copy2 288 [154202:154489](+) rps2 711 [15203:15913](-) rps3 657 [83693:84349](-) rps3_copy2 657 [155046:155702](+) rps4 606 [46149:46754](-) rps7 468 [97121:97588](-) rps7_copy2 468 [141807:142274](+) rps8 399 [81260:81658](-) rps8_copy2 399 [157737:158135](+) ycf1 5562 [109213:114774](+) ycf15 228 [93916:94143](+) ycf15_copy2 228 [145252:145479](-) ycf2 6174 [87622:93795](+) ycf2_copy2 6174 [145600:151773](-) ycf3 510 [44770:44898](-) [43828:44055](-) [42927:43079](-) ycf4 555 [61666:62220](+) 38 tRNA genes (30 are unique) Genes Location trnH-GUG [1:75](-) trnK-UUU [4344:4380](-) [1807:1841](-) trnQ-UUG [6623:6694](-) trnS-GCU [7921:8008](-) trnG-UCC [8745:8767](+) [9497:9533](+) trnR-UCU [9723:9794](+) trnC-GCA [27669:27749](+) trnD-GUC [30671:30744](-) trnY-GUA [31134:31217](-) trnE-UUC [31277:31348](-) trnT-GGU [32006:32077](+) trnS-UGA [36076:36168](-) trnG-GCC [37056:37126](+) trnfM-CAU [37297:37370](-) trnS-GGA [45768:45854](+) trnT-UGU [47165:47237](-) trnL-UAA [48001:48035](+) [48525:48574](+) trnF-GAA [48999:49071](+) trnV-UAC [53680:53718](-) [53054:53091](-) trnM-CAU [53911:53982](+) trnT-GGU_copy2 [53916:53974](+) trnW-CCA [67143:67216](-) trnP-UGG [67373:67446](-) trnI-CAU [87222:87295](-) trnL-CAA [94159:94239](-) trnV-GAC [100125:100196](+) trnI-GAU [102215:102256](+) [103196:103230](+) trnA-UGC [103295:103332](+) [104133:104167](+) trnR-ACG [107928:108001](+) trnN-GUU [108482:108553](-) trnL-UAG [124457:124536](-) trnN-GUU_copy2 [130842:130913](+) trnR-ACG_copy2 [131394:131467](-) trnA-UGC_copy2 [136063:136100](-) [135228:135262](-) trnI-GAU_copy2 [137139:137180](-) [136165:136199](-) trnV-GAC_copy2 [139199:139270](-) trnL-CAA_copy2 [145156:145236](+) trnI-CAU_copy2 [152100:152173](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [100424:101914](+) rrn23 [104296:107099](+) rrn4.5 [107198:107300](+) rrn5 [107526:107646](+) rrn5_copy2 [131749:131869](-) rrn4.5_copy2 [132095:132197](-) rrn23_copy2 [132296:135099](-) rrn16_copy2 [137481:138971](-) This genome has 26 genes with intron(s). Details are as follows: 22 gene(s) have 1 intron(s) Genes Exons rps16 [6052:6091](-) [4960:5156](-) atpF [12621:12780](-) [11504:11913](-) rpoC1 [22790:23245](-) [20420:22039](-) petB [76048:76053](+) [76818:77471](+) petD [77669:77676](+) [78360:78855](+) rpl16 [83529:83537](-) [82305:82703](-) rpl2 [86358:86739](-) [85265:85698](-) ndhB [96012:96788](-) [94562:95320](-) ndhA [116693:117259](+) [118308:118847](+) ndhB_copy2 [142607:143383](+) [144075:144833](+) rpl2_copy2 [152644:153036](+) [153696:154130](+) rpl16_copy2 [155858:155866](+) [156692:157090](+) petD_copy2 [161719:161726](-) [160540:161035](-) petB_copy2 [163342:163347](-) [161924:162577](-) trnK-UUU [4344:4380](-) [1807:1841](-) trnG-UCC [8745:8767](+) [9497:9533](+) trnL-UAA [48001:48035](+) [48525:48574](+) trnV-UAC [53680:53718](-) [53054:53091](-) trnI-GAU [102215:102256](+) [103196:103230](+) trnA-UGC [103295:103332](+) [104133:104167](+) trnA-UGC_copy2 [136063:136100](-) [135228:135262](-) trnI-GAU_copy2 [137139:137180](-) [136165:136199](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [70413:70526](-) [98199:98430](-) [97637:97662](-) ycf3 [44770:44898](-) [43828:44055](-) [42927:43079](-) rps12_copy2 [70413:70526](-) [140965:141196](+) [141733:141758](+) clpP [73048:73116](-) [72018:72308](-) [71043:71285](-)