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, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ, ycf3 Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, rpl22, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps12_copy2, rps14, rps15, rps16, rps18, rps19, rps19_copy2, 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 None Conserved open reading frames ycf1a, ycf1b, ycf2, ycf2_copy2, ycf4, ycf68, ycf68_copy2 Other genes orf57, orf57_copy2 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 rps2 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 ycf1, 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) [13456:13599](-) [12266:12676](-) clpP (3/3) [71237:71305](-) [70145:70438](-) [69238:69489](-) ndhA (2/2) [120851:121408](-) [119180:119719](-) ndhB (2/2) [95787:96563](-) [94329:95084](-) ndhB_copy2 (2/2) [140562:141338](+) [142041:142796](+) petB (1/2) [75028:75684](+) petD (1/2) [76614:77177](+) rpl16 (1/2) [80350:80760](-) rpl2 (2/2) [84774:85160](-) [83683:84114](-) rpl2_copy2 (2/2) [151965:152351](+) [153011:153442](+) rpoC1 (2/2) [23319:23750](-) [20935:22551](-) rps12 (2/3) [68995:69111](-) [97964:98206](-) rps12_copy2 (2/3) [68995:69111](-) [138919:139161](+) rps16 (2/2) [5594:5633](-) [4535:4743](-) ycf3 (3/3) [44691:44819](-) [43741:43968](-) [42850:43002](-) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: ycf68 2 [101889:101930](+) [101962:102372](+)] ycf68_copy2 2 [135195:135236](-) [134753:135163](-)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon petB ATT rpl16 ATC rps19 GTG rpl2 ATA orf57 ATC ndhD ATC orf57_copy2 ATC rpl2_copy2 ATA rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 135 genes (114 unique genes). Including: 89 protein-coding genes (80 are unique) 38 tRNA genes (30 are unique) 8 rRNA genes (4 are unique) Details are as follows: 89 protein-coding genes (80 are unique) Genes Length Location accD 1467 [57321:58787](+) atpA 1524 [10663:12186](-) atpB 1497 [52770:54266](-) atpE 405 [52369:52773](-) atpF 555 [13456:13599](-) [12266:12676](-) atpH 246 [14023:14268](-) atpI 744 [14753:15496](-) ccsA 960 [113709:114668](+) cemA 690 [60526:61215](+) clpP 615 [71237:71305](-) [70145:70438](-) [69238:69489](-) matK 1563 [1646:3208](-) ndhA 1098 [120851:121408](-) [119180:119719](-) ndhB 1533 [95787:96563](-) [94329:95084](-) ndhB_copy2 1533 [140562:141338](+) [142041:142796](+) ndhC 363 [50447:50809](-) ndhD 1506 [114888:116393](-) ndhE 306 [117213:117518](-) ndhF 2214 [109565:111778](-) ndhG 531 [117666:118196](-) ndhH 1182 [121410:122591](-) ndhI 543 [118549:119091](-) ndhJ 477 [49123:49599](-) ndhK 747 [49710:50456](-) orf57 174 [102942:103115](-) orf57_copy2 174 [134010:134183](+) petA 963 [61423:62385](+) petB 657 [75028:75684](+) petD 564 [76614:77177](+) petG 114 [65485:65598](+) petL 96 [65201:65296](+) petN 90 [29086:29175](+) psaA 2253 [40063:42315](-) psaB 2205 [37833:40037](-) psaC 246 [116511:116756](-) psaI 111 [59225:59335](+) psaJ 129 [66417:66545](+) psbA 1062 [81:1142](-) psbB 1527 [71766:73292](+) psbC 1422 [34346:35767](+) psbD 1062 [33337:34398](+) psbE 252 [64075:64326](-) psbF 120 [63938:64057](-) psbH 222 [73897:74118](+) psbI 111 [8161:8271](+) psbJ 123 [63551:63673](-) psbK 186 [7512:7697](+) psbL 117 [63799:63915](-) psbM 105 [30014:30118](-) psbN 132 [73650:73781](-) psbT 102 [73477:73578](+) psbZ 189 [36354:36542](+) rbcL 1461 [55052:56512](+) rpl14 369 [79854:80222](-) rpl16 411 [80350:80760](-) rpl2 819 [84774:85160](-) [83683:84114](-) rpl20 354 [67894:68247](-) rpl22 393 [82710:83102](-) rpl23 282 [85185:85466](-) rpl23_copy2 282 [151659:151940](+) rpl2_copy2 819 [151965:152351](+) [153011:153442](+) rpl32 174 [112649:112822](+) rpl33 201 [66927:67127](+) rpl36 114 [78938:79051](-) rpoA 1020 [77315:78334](-) rpoB 3213 [23777:26989](-) rpoC1 2049 [23319:23750](-) [20935:22551](-) rpoC2 4140 [16624:20763](-) rps11 417 [78403:78819](-) rps12 360 [68995:69111](-) [97964:98206](-) rps12_copy2 360 [68995:69111](-) [138919:139161](+) rps14 303 [37404:37706](-) rps15 270 [122705:122974](-) rps16 249 [5594:5633](-) [4535:4743](-) rps18 306 [67300:67605](+) rps19 279 [83150:83428](-) rps19_copy2 279 [153697:153975](+) rps3 663 [82000:82662](-) rps4 606 [45710:46315](-) rps7 468 [96882:97349](-) rps7_copy2 468 [139776:140243](+) rps8 399 [79235:79633](-) ycf1a 5280 [123306:128585](-) ycf1b 1059 [108540:109598](+) ycf2 6873 [85797:92669](+) ycf2_copy2 6873 [144456:151328](-) ycf3 510 [44691:44819](-) [43741:43968](-) [42850:43002](-) ycf4 555 [59670:60224](+) ycf68 453 [101889:101930](+) [101962:102372](+) ycf68_copy2 453 [135195:135236](-) [134753:135163](-) 38 tRNA genes (30 are unique) Genes Location trnK-UUU [3931:3967](-) [1391:1425](-) trnQ-UUG [7106:7177](-) trnS-GCU [8310:8397](-) trnG-TCC [9564:9586](+) [10285:10333](+) trnR-UCU [10472:10543](+) trnC-GCA [28239:28309](+) trnD-GUC [31209:31282](-) trnY-GUA [31559:31641](-) trnE-UUC [31701:31773](-) trnT-GGU [32131:32202](+) trnS-UGA [35914:36000](-) trnG-UCC [36822:36892](+) trnfM-CAU [37173:37246](-) trnS-GGA [45332:45419](+) trnT-UGU [46656:46728](-) trnL-UAA [47732:47766](+) [48072:48121](+) trnF-GAA [48380:48452](+) trnV-UAC [51926:51962](-) [51291:51327](-) trnM-CAU [52122:52194](+) trnW-CCA [65716:65789](-) trnP-UGG [65981:66054](-) trnH-GUG [83566:83639](+) trnI-CAU [85632:85705](-) trnL-CAA [93693:93773](-) trnV-GAC [99659:99730](+) trnI-GAU [101748:101784](+) [102719:102753](+) trnA-UGC [102818:102855](+) [103671:103705](+) trnR-ACG [107432:107505](+) trnN-GUU [108119:108190](-) trnL-UAG [113551:113630](+) trnN-GUU_copy2 [128935:129006](+) trnR-ACG_copy2 [129620:129693](-) trnA-UGC_copy2 [134270:134307](-) [133420:133454](-) trnI-GAU_copy2 [135341:135377](-) [134372:134406](-) trnV-GAC_copy2 [137395:137466](-) trnL-CAA_copy2 [143352:143432](+) trnI-CAU_copy2 [151420:151493](+) trnH-GUG_copy2 [153486:153559](-) 8 rRNA genes (4 are unique) Genes Location rrn16 [99956:101446](+) rrn23 [103851:106661](+) rrn4.5 [106760:106862](+) rrn5 [107086:107206](+) rrn5_copy2 [129919:130039](-) rrn4.5_copy2 [130263:130365](-) rrn23_copy2 [130464:133274](-) rrn16_copy2 [135679:137169](-) This genome has 22 genes with intron(s). Details are as follows: 20 gene(s) have 1 intron(s) Genes Exons rps12 [68995:69111](-) [97964:98206](-) rps16 [5594:5633](-) [4535:4743](-) atpF [13456:13599](-) [12266:12676](-) rpoC1 [23319:23750](-) [20935:22551](-) rps12_copy2 [68995:69111](-) [138919:139161](+) rpl2 [84774:85160](-) [83683:84114](-) ndhB [95787:96563](-) [94329:95084](-) ycf68 [101889:101930](+) [101962:102372](+) ndhA [120851:121408](-) [119180:119719](-) ycf68_copy2 [135195:135236](-) [134753:135163](-) ndhB_copy2 [140562:141338](+) [142041:142796](+) rpl2_copy2 [151965:152351](+) [153011:153442](+) trnK-UUU [3931:3967](-) [1391:1425](-) trnG-TCC [9564:9586](+) [10285:10333](+) trnL-UAA [47732:47766](+) [48072:48121](+) trnV-UAC [51926:51962](-) [51291:51327](-) trnI-GAU [101748:101784](+) [102719:102753](+) trnA-UGC [102818:102855](+) [103671:103705](+) trnA-UGC_copy2 [134270:134307](-) [133420:133454](-) trnI-GAU_copy2 [135341:135377](-) [134372:134406](-) 2 gene(s) have 2 intron(s) Genes Exons ycf3 [44691:44819](-) [43741:43968](-) [42850:43002](-) clpP [71237:71305](-) [70145:70438](-) [69238:69489](-)