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, 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 clpP Subunit of Acetyl-CoA-carboxylase accD Translational initiation factor infA Conserved open reading frames ycf1, ycf1_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 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 None Conserved open reading frames ycf15 Other genes None 2. Multicopy genes with different lengths: Genes Length Location ycf1 3897 [112798:116695](+) ycf1_copy2 5448 [130855:136303](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [12323:12467](-) [11087:11511](-) clpP (3/3) [74756:74815](-) [73587:73892](-) [72686:72937](-) ndhA (2/2) [128297:128858](-) [126685:127202](-) ndhB (2/2) [99634:100415](-) [98183:98960](-) ndhB_copy2 (2/2) [148687:149468](+) [150142:150919](+) petB (2/2) [77823:77828](+) [78609:79256](+) petD (2/2) [79455:79462](+) [80205:80679](+) rpl16 (2/2) [85653:85661](-) [84207:84608](-) rpl2 (2/2) [88738:89128](-) [87645:88087](-) rpl2_copy2 (2/2) [159974:160364](+) [161015:161457](+) rpoC1 (2/2) [23323:23751](-) [20964:22589](-) rps12 (3/3) [72408:72521](-) [101812:102040](-) [101246:101271](-) rps12_copy2 (3/3) [72408:72521](-) [147062:147290](+) [147831:147856](+) rps16 (2/2) [5860:5899](-) [4914:5125](-) ycf3 (3/3) [45923:46046](-) [44980:45180](-) [44025:44191](-) ### 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 rpl2 ACG ndhD ATC rpl2_copy2 ACG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 133 genes (111 unique genes). Including: 87 protein-coding genes (79 are unique) 38 tRNA genes (28 are unique) 8 rRNA genes (4 are unique) Details are as follows: 87 protein-coding genes (79 are unique) Genes Length Location accD 1533 [60138:61670](+) atpA 1524 [9504:11027](-) atpB 1488 [55569:57056](-) atpE 408 [55165:55572](-) atpF 570 [12323:12467](-) [11087:11511](-) atpH 246 [12967:13212](-) atpI 744 [14647:15390](-) ccsA 990 [120825:121814](+) cemA 690 [63726:64415](+) clpP 618 [74756:74815](-) [73587:73892](-) [72686:72937](-) infA 234 [82743:82976](-) matK 1548 [1770:3317](-) ndhA 1080 [128297:128858](-) [126685:127202](-) ndhB 1560 [99634:100415](-) [98183:98960](-) ndhB_copy2 1560 [148687:149468](+) [150142:150919](+) ndhC 363 [52275:52637](-) ndhD 1506 [122085:123590](-) ndhE 306 [124628:124933](-) ndhF 2217 [116721:118937](-) ndhG 531 [125136:125666](-) ndhH 1182 [128860:130041](-) ndhI 543 [126049:126591](-) ndhJ 480 [50945:51424](-) ndhK 753 [51532:52284](-) petA 963 [64652:65614](+) petB 654 [77823:77828](+) [78609:79256](+) petD 483 [79455:79462](+) [80205:80679](+) petG 114 [68744:68857](+) petL 96 [68475:68570](+) petN 90 [29002:29091](+) psaA 2253 [41153:43405](-) psaB 2205 [38923:41127](-) psaC 246 [123715:123960](-) psaI 111 [62177:62287](+) psaJ 129 [69659:69787](+) psbA 1062 [126:1187](-) psbB 1527 [75275:76801](+) psbC 1422 [35554:36975](+) psbD 1062 [34545:35606](+) psbE 252 [66998:67249](-) psbF 120 [66868:66987](-) psbH 222 [77408:77629](+) psbI 111 [7383:7493](+) psbJ 123 [66485:66607](-) psbK 186 [6704:6889](+) psbL 117 [66729:66845](-) psbM 105 [30432:30536](-) psbN 132 [77156:77287](-) psbT 108 [76989:77096](+) psbZ 189 [37568:37756](+) rbcL 1464 [57868:59331](+) rpl14 369 [83716:84084](-) rpl16 411 [85653:85661](-) [84207:84608](-) rpl2 834 [88738:89128](-) [87645:88087](-) rpl20 429 [71256:71684](-) rpl22 390 [86531:86920](-) rpl23 282 [89147:89428](-) rpl23_copy2 282 [159674:159955](+) rpl2_copy2 834 [159974:160364](+) [161015:161457](+) rpl32 174 [119598:119771](+) rpl33 201 [70367:70567](+) rpl36 114 [82512:82625](-) rpoA 1032 [80866:81897](-) rpoB 3228 [23778:27005](-) rpoC1 2055 [23323:23751](-) [20964:22589](-) rpoC2 4128 [16646:20773](-) rps11 417 [81969:82385](-) rps12 369 [72408:72521](-) [101812:102040](-) [101246:101271](-) rps12_copy2 369 [72408:72521](-) [147062:147290](+) [147831:147856](+) rps14 303 [38471:38773](-) rps15 273 [130144:130416](-) rps16 252 [5860:5899](-) [4914:5125](-) rps18 336 [70757:71092](+) rps19 279 [87096:87374](-) rps19_copy2 279 [161728:162006](+) rps2 711 [15674:16384](-) rps3 657 [85812:86468](-) rps4 606 [47044:47649](-) rps7 468 [100720:101187](-) rps7_copy2 468 [147915:148382](+) rps8 399 [83086:83484](-) ycf1 3897 [112799:116695](+) ycf1_copy2 5448 [130856:136303](-) ycf2 6810 [89797:96606](+) ycf2_copy2 6810 [152496:159305](-) ycf3 492 [45923:46046](-) [44980:45180](-) [44025:44191](-) ycf4 555 [62639:63193](+) 38 tRNA genes (28 are unique) Genes Location trnK-UUU [4144:4180](-) [1455:1490](-) trnQ-UUG [6288:6360](-) trnS-GCU [7627:7714](-) trnG-GCC [8417:8439](+) [9142:9188](+) trnR-UCU [9316:9387](+) trnC-GCA [28093:28173](+) trnD-GUC [31612:31685](-) trnY-GUA [32121:32204](-) trnE-UUC [32259:32331](-) trnT-UGU [33192:33263](+) trnS-UGA [37124:37215](-) trnG-UCC [37991:38061](+) trnfM-CAU [38240:38313](-) trnS-GCU_copy2 [46683:46769](+) trnT-UGU_copy2 [48114:48186](-) trnL-UAA [49346:49380](+) [49914:49963](+) trnF-GAA [50291:50363](+) trnV-UAC [54700:54737](-) [54065:54101](-) trnM-CAU [54921:54992](+) trnW-CCA [68988:69061](-) trnP-UGG [69214:69287](-) trnH-GUG [87525:87599](+) trnI-CAU [89594:89667](-) trnL-CAA [97620:97700](-) trnV-GAC [103959:104030](+) trnI-GAU [106054:106095](+) [107031:107065](+) trnA-UGC [107129:107166](+) [107934:107968](+) trnR-ACG [111750:111823](+) trnN-GUU [112402:112473](-) trnL-UAG [120637:120716](+) trnN-GUU_copy2 [136629:136700](+) trnR-ACG_copy2 [137279:137352](-) trnA-UGC_copy2 [141936:141973](-) [141134:141168](-) trnI-GAU_copy2 [143007:143048](-) [142037:142071](-) trnV-GAC_copy2 [145072:145143](-) trnL-CAA_copy2 [151402:151482](+) trnI-CAU_copy2 [159435:159508](+) trnH-GUG_copy2 [161503:161577](-) 8 rRNA genes (4 are unique) Genes Location rrn16 [104258:105748](+) rrn23 [108114:110921](+) rrn4.5 [111033:111135](+) rrn5 [111364:111484](+) rrn5_copy2 [137618:137738](-) rrn4.5_copy2 [137967:138069](-) rrn23_copy2 [138170:140977](-) rrn16_copy2 [143354:144844](-) This genome has 23 genes with intron(s). Details are as follows: 19 gene(s) have 1 intron(s) Genes Exons rps16 [5860:5899](-) [4914:5125](-) atpF [12323:12467](-) [11087:11511](-) rpoC1 [23323:23751](-) [20964:22589](-) petB [77823:77828](+) [78609:79256](+) petD [79455:79462](+) [80205:80679](+) rpl16 [85653:85661](-) [84207:84608](-) rpl2 [88738:89128](-) [87645:88087](-) ndhB [99634:100415](-) [98183:98960](-) ndhA [128297:128858](-) [126685:127202](-) ndhB_copy2 [148687:149468](+) [150142:150919](+) rpl2_copy2 [159974:160364](+) [161015:161457](+) trnK-UUU [4144:4180](-) [1455:1490](-) trnG-GCC [8417:8439](+) [9142:9188](+) trnL-UAA [49346:49380](+) [49914:49963](+) trnV-UAC [54700:54737](-) [54065:54101](-) trnI-GAU [106054:106095](+) [107031:107065](+) trnA-UGC [107129:107166](+) [107934:107968](+) trnA-UGC_copy2 [141936:141973](-) [141134:141168](-) trnI-GAU_copy2 [143007:143048](-) [142037:142071](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [72408:72521](-) [101812:102040](-) [101246:101271](-) ycf3 [45923:46046](-) [44980:45180](-) [44025:44191](-) rps12_copy2 [72408:72521](-) [147062:147290](+) [147831:147856](+) clpP [74756:74815](-) [73587:73892](-) [72686:72937](-)