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 None 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, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ, ycf3 Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, rpl22, rpl22_copy2, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl36 Small subunit of ribosome rps11, rps12, rps12_copy2, rps14, rps15, rps16, rps18, rps19, rps19_copy2, rps2, rps3, rps4, rps7, rps7_copy2, rps8 DNA dependent RNA polymerase rpoA, rpoB, rpoC1 Subunit of rubisco rbcL c-type cytochrom synthesis gene None Envelop membrane protein cemA Maturase None 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 ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK Subunits of cytochrome b/f complex None Subunits of photosystem I None Subunits of photosystem II None Large subunit of ribosome rpl33 Small subunit of ribosome None DNA dependent RNA polymerase rpoC2 Subunit of rubisco None c-type cytochrom synthesis gene ccsA Envelop membrane protein None Maturase matK 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 rpl2 864 join{[75755:76149](-), [74663:75133](-)} rpl2_copy2 861 join{[126279:126670](+), [127295:127765](+)} 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [11340:11475](-) [10107:10516](-) clpP (3/3) [62093:62163](-) [60912:61205](-) [60037:60262](-) petB (2/2) [65244:65249](+) [66028:66669](+) petD (2/2) [66839:66846](+) [67584:68058](+) rpl16 (2/2) [72712:72720](-) [71255:71689](-) rpl2 (2/2) [75756:76149](-) [74664:75133](-) rpl2_copy2 (2/2) [126280:126670](+) [127296:127765](+) rpoC1 (2/2) [21174:21605](-) [18796:20403](-) rps12 (3/3) [59778:59891](-) [86097:86328](-) [85524:85549](-) rps12_copy2 (3/3) [59778:59891](-) [116101:116332](+) [116880:116905](+) rps16 (2/2) [5765:5804](-) [4559:4806](-) ycf3 (3/3) [40907:41035](-) [39881:40110](-) [38922:39072](-) ### 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 psbL ACG rps19 GTG rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 114 genes (95 unique genes). Including: 70 protein-coding genes (63 are unique) 36 tRNA genes (28 are unique) 8 rRNA genes (4 are unique) Details are as follows: 70 protein-coding genes (63 are unique) Genes Length Location accD 1494 [49241:50734](+) atpA 1524 [8507:10030](-) atpB 1464 [45132:46595](-) atpE 396 [44710:45105](-) atpF 546 [11340:11475](-) [10107:10516](-) atpH 252 [11861:12112](-) atpI 741 [12697:13437](-) cemA 705 [52224:52928](+) clpP 591 [62093:62163](-) [60912:61205](-) [60037:60262](-) petA 978 [53119:54096](+) petB 648 [65244:65249](+) [66028:66669](+) petD 483 [66839:66846](+) [67584:68058](+) petG 114 [56381:56494](+) petL 96 [56118:56213](+) petN 90 [26072:26161](+) psaA 2250 [36020:38269](-) psaB 2208 [33765:35972](-) psaC 246 [98769:99014](-) psaI 111 [50915:51025](+) psaJ 141 [57339:57479](+) psbA 1062 [86:1147](-) psbB 1524 [62792:64315](+) psbC 1464 [30244:31707](+) psbD 1062 [29277:30338](+) psbE 252 [55006:55257](-) psbF 120 [54875:54994](-) psbH 219 [64889:65107](+) psbI 117 [7485:7601](+) psbJ 123 [54480:54602](-) psbK 189 [6873:7061](+) psbL 117 [54736:54852](-) psbM 117 [26557:26673](-) psbN 132 [64657:64788](-) psbT 114 [64491:64604](+) psbZ 189 [32498:32686](+) rbcL 1428 [47260:48687](+) rpl14 366 [70784:71149](-) rpl16 444 [72712:72720](-) [71255:71689](-) rpl2 864 [75756:76149](-) [74664:75133](-) rpl20 444 [58534:58977](-) rpl22 393 [73892:74284](-) rpl22_copy2 393 [128145:128537](+) rpl23 291 [76163:76453](-) rpl23_copy2 291 [125976:126266](+) rpl2_copy2 861 [126280:126670](+) [127296:127765](+) rpl32 165 [96954:97118](+) rpl36 111 [69916:70026](-) rpoA 1014 [68229:69242](-) rpoB 3204 [21632:24835](-) rpoC1 2040 [21174:21605](-) [18796:20403](-) rps11 417 [69309:69725](-) rps12 372 [59778:59891](-) [86097:86328](-) [85524:85549](-) rps12_copy2 372 [59778:59891](-) [116101:116332](+) [116880:116905](+) rps14 300 [33329:33628](-) rps15 228 [99728:99955](-) rps16 288 [5765:5804](-) [4559:4806](-) rps18 294 [58009:58302](+) rps19 282 [74327:74608](-) rps19_copy2 282 [127821:128102](+) rps2 708 [13597:14304](-) rps3 663 [72952:73614](-) rps4 609 [41908:42516](-) rps7 468 [84999:85466](-) rps7_copy2 468 [116963:117430](+) rps8 414 [70233:70646](-) ycf1 5520 [100089:105608](-) ycf2 6789 [76796:83584](+) ycf2_copy2 6789 [118845:125633](-) ycf3 510 [40907:41035](-) [39881:40110](-) [38922:39072](-) ycf4 564 [51170:51733](+) 36 tRNA genes (28 are unique) Genes Location trnK-UUU [3952:3991](-) [1331:1365](-) trnQ-UUG [6569:6640](-) trnS-GCU [7694:7781](-) trnR-UCU [8225:8296](+) trnC-GCA [25281:25353](+) trnD-GUC [27179:27252](-) trnY-GUA [27731:27813](-) trnE-UUC [27878:27950](-) trnT-GGU [28476:28547](+) trnS-UGA [31978:32070](-) trnG-GCC [32896:32966](+) trnfM-CAU [33108:33181](-) trnS-GGA [41535:41621](+) trnT-UGU [42702:42774](-) trnL-UAA [43291:43327](+) [43854:43903](+) trnF-GAA [44171:44243](+) trnM-CAU [44393:44465](+) trnW-CCA [56610:56683](-) trnP-UGG [56898:56971](-) trnH-GUG [73811:73884](+) trnI-CAU [76634:76707](-) trnL-CAA [84018:84098](-) trnV-GAC [88114:88185](+) trnI-GAU [90218:90251](+) [91132:91170](+) trnA-UGC [91233:91271](+) [92069:92103](+) trnR-ACG [95836:95909](+) trnN-GUU [96497:96568](-) trnL-UAG [97377:97456](+) trnN-GUU_copy2 [105861:105932](+) trnR-ACG_copy2 [106520:106593](-) trnA-UGC_copy2 [111158:111196](-) [110326:110360](-) trnI-GAU_copy2 [112178:112211](-) [111259:111297](-) trnV-GAC_copy2 [114244:114315](-) trnL-CAA_copy2 [118331:118411](+) trnI-CAU_copy2 [125722:125795](+) trnH-GUG_copy2 [128545:128618](-) 8 rRNA genes (4 are unique) Genes Location rrn16S [88408:89905](+) rrn23S [92252:95063](+) rrn4.5S [95163:95264](+) rrn5S [95479:95600](+) rrn5S_copy2 [106829:106950](-) rrn4.5S_copy2 [107165:107266](-) rrn23S_copy2 [107366:110177](-) rrn16S_copy2 [112524:114021](-) This genome has 18 genes with intron(s). Details are as follows: 14 gene(s) have 1 intron(s) Genes Exons rps16 [5765:5804](-) [4559:4806](-) atpF [11340:11475](-) [10107:10516](-) rpoC1 [21174:21605](-) [18796:20403](-) petB [65244:65249](+) [66028:66669](+) petD [66839:66846](+) [67584:68058](+) rpl16 [72712:72720](-) [71255:71689](-) rpl2 [75756:76149](-) [74664:75133](-) rpl2_copy2 [126280:126670](+) [127296:127765](+) trnK-UUU [3952:3991](-) [1331:1365](-) trnL-UAA [43291:43327](+) [43854:43903](+) trnI-GAU [90218:90251](+) [91132:91170](+) trnA-UGC [91233:91271](+) [92069:92103](+) trnA-UGC_copy2 [111158:111196](-) [110326:110360](-) trnI-GAU_copy2 [112178:112211](-) [111259:111297](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [59778:59891](-) [86097:86328](-) [85524:85549](-) ycf3 [40907:41035](-) [39881:40110](-) [38922:39072](-) rps12_copy2 [59778:59891](-) [116101:116332](+) [116880:116905](+) clpP [62093:62163](-) [60912:61205](-) [60037:60262](-)