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, rps12_copy3, rps14, rps15, rps16, rps18, rps19, 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 None 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 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 None Other genes None 2. Multicopy genes with different lengths: Genes Length Location rps12 141 [57965:58106](+) rps12_copy2 240 [101656:101896](-) rps12_copy3 240 [144902:145142](+) rpl2 864 join{[88476:88870](-), [87358:87828](-)} rpl2_copy2 861 join{[157928:158319](+), [158970:159440](+)} ndhB 1626 join{[99390:100260](-), [98045:98801](-)} ndhB_copy2 1533 join{[146538:147315](+), [147997:148753](+)} 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [13747:13909](-) [12480:12955](-) clpP (1/3) [74115:74705](-) ndhA (2/2) [125949:126522](-) [124262:124800](-) ndhB (2/2) [99391:100260](-) [98046:98801](-) ndhB_copy2 (2/2) [146539:147315](+) [147998:148753](+) petB (1/2) [78465:79163](+) petD (1/2) [80100:80624](+) rpl16 (1/2) [84167:84577](-) rpl2 (2/2) [88477:88870](-) [87359:87828](-) rpl2_copy2 (2/2) [157929:158319](+) [158971:159440](+) rpoC1 (2/2) [24620:25085](-) [22233:23869](-) rps12 (1/3) [57966:58106](+) rps12_copy2 (1/3) [101657:101896](-) rps12_copy3 (1/3) [144903:145142](+) rps16 (1/2) [5025:5210](-) ycf3 (3/3) [47110:47236](-) [46146:46375](-) [45251:45403](-) ### 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 rps16 ATC atpF ATA rpoC1 TTG psbC GTG psbT ATC psbN TTG petB ATT rps8 GTG rpl16 ATC rps19 GTG ycf15 ATT rps12_copy2 ATC ndhD GTG ndhA TTG ycf1 ATT rps12_copy3 ATC ycf15_copy2 ATT 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 129 genes (110 unique genes). Including: 87 protein-coding genes (79 are unique) 34 tRNA genes (27 are unique) 8 rRNA genes (4 are unique) Details are as follows: 87 protein-coding genes (79 are unique) Genes Length Location accD 1911 [69451:71361](-) atpA 1521 [10883:12403](-) atpB 1497 [55854:57350](-) atpE 402 [55456:55857](-) atpF 639 [13747:13909](-) [12480:12955](-) atpH 246 [14433:14678](-) atpI 744 [15898:16641](-) ccsA 972 [118755:119726](+) cemA 705 [66445:67149](-) clpP 591 [74115:74705](-) matK 1521 [2058:3578](-) ndhA 1113 [125949:126522](-) [124262:124800](-) ndhB 1626 [99391:100260](-) [98046:98801](-) ndhB_copy2 1533 [146539:147315](+) [147998:148753](+) ndhC 363 [53364:53726](-) ndhD 1521 [120175:121695](-) ndhE 306 [122309:122614](-) ndhF 2232 [114029:116260](-) ndhG 531 [122850:123380](-) ndhH 1182 [126512:127693](-) ndhI 504 [123675:124178](-) ndhJ 477 [51989:52465](-) ndhK 684 [52608:53291](-) petA 963 [65247:66209](-) petB 699 [78465:79163](+) petD 525 [80100:80624](+) petG 114 [61896:62009](-) petL 96 [62203:62298](-) petN 90 [30226:30315](+) psaA 2253 [42021:44273](-) psaB 2205 [39791:41995](-) psaC 246 [121818:122063](-) psaI 114 [69079:69192](-) psaJ 135 [60899:61033](-) psbA 1062 [389:1450](-) psbB 1527 [75199:76725](+) psbC 1452 [35910:37361](+) psbD 1062 [34931:35992](+) psbE 252 [63668:63919](+) psbF 120 [63929:64048](+) psbH 222 [77343:77564](+) psbI 111 [8422:8532](+) psbJ 123 [64347:64469](+) psbK 186 [7805:7990](+) psbL 117 [64081:64197](+) psbM 105 [31419:31523](-) psbN 216 [77114:77329](-) psbT 117 [76904:77020](+) psbZ 189 [38114:38302](+) rbcL 1455 [72266:73720](-) rpl14 375 [83668:84042](-) rpl16 411 [84167:84577](-) rpl2 864 [88477:88870](-) [87359:87828](-) rpl20 351 [58846:59196](+) rpl22 504 [86482:86985](-) rpl23 282 [88889:89170](-) rpl23_copy2 282 [157629:157910](+) rpl2_copy2 861 [157929:158319](+) [158971:159440](+) rpl32 207 [117063:117269](+) rpl33 201 [60224:60424](-) rpl36 114 [82472:82585](-) rpoA 1041 [80788:81828](-) rpoB 3213 [25082:28294](-) rpoC1 2103 [24620:25085](-) [22233:23869](-) rpoC2 4128 [17934:22061](-) rps11 417 [81902:82318](-) rps12 141 [57966:58106](+) rps12_copy2 240 [101657:101896](-) rps12_copy3 240 [144903:145142](+) rps14 303 [39350:39652](-) rps15 273 [127799:128071](-) rps16 186 [5025:5210](-) rps18 342 [59553:59894](-) rps19 285 [87024:87308](-) rps2 711 [16895:17605](-) rps3 663 [85835:86497](-) rps4 612 [48227:48838](-) rps7 468 [100579:101046](-) rps7_copy2 468 [145753:146220](+) rps8 405 [83082:83486](-) ycf1 5556 [128445:134000](-) ycf15 204 [96507:96710](+) ycf15_copy2 204 [150089:150292](-) ycf2 6792 [89645:96436](+) ycf2_copy2 6792 [150363:157154](-) ycf3 510 [47110:47236](-) [46146:46375](-) [45251:45403](-) ycf4 555 [68101:68655](-) 34 tRNA genes (27 are unique) Genes Location trnH-GTG [1:74](-) trnK-TTT [4282:4318](-) [1721:1755](-) trnQ-TTG [7370:7441](-) trnS-GCT [8612:8699](-) trnR-TCT [10514:10585](+) trnC-GCA [29429:29499](+) trnD-GTC [32295:32368](-) trnY-GTA [32686:32769](-) trnE-TTC [32830:32902](-) trnT-GGT [33587:33658](+) trnS-TGA [37667:37759](-) trnG-GCC [38832:38902](+) trnfM-CAT [39109:39182](-) trnS-GGA [47801:47887](+) trnT-TGT [49355:49427](-) trnF-GAA [51406:51478](+) trnM-CAT [55142:55214](+) trnP-TGG [61398:61471](+) trnW-CCA [61666:61739](+) trnI-CAT [89341:89414](-) trnL-CAA [97371:97451](-) trnV-GAC [103777:103848](+) trnI-GAT [105865:105906](+) [106862:106896](+) trnA-TGC [106960:106997](+) [107815:107849](+) trnR-ACG [111625:111698](+) trnN-GTT [112325:112396](-) trnL-TAG [118480:118559](+) trnN-GTT_copy2 [134403:134474](+) trnR-ACG_copy2 [135101:135174](-) trnA-TGC_copy2 [139802:139839](-) [138950:138984](-) trnI-GAT_copy2 [140893:140934](-) [139903:139937](-) trnV-GAC_copy2 [142951:143022](-) trnL-CAA_copy2 [149348:149428](+) trnI-CAT_copy2 [157385:157458](+) 8 rRNA genes (4 are unique) Genes Location rrn16S [104081:105571](+) rrn23S [108009:110818](+) rrn4.5S [110917:111019](+) rrn5S [111249:111369](+) rrn5S_copy2 [135420:135550](-) rrn4.5S_copy2 [135780:135882](-) rrn23S_copy2 [135981:138790](-) rrn16S_copy2 [141228:142718](-) This genome has 13 genes with intron(s). Details are as follows: 12 gene(s) have 1 intron(s) Genes Exons atpF [13747:13909](-) [12480:12955](-) rpoC1 [24620:25085](-) [22233:23869](-) rpl2 [88477:88870](-) [87359:87828](-) ndhB [99391:100260](-) [98046:98801](-) ndhA [125949:126522](-) [124262:124800](-) ndhB_copy2 [146539:147315](+) [147998:148753](+) rpl2_copy2 [157929:158319](+) [158971:159440](+) trnK-TTT [4282:4318](-) [1721:1755](-) trnI-GAT [105865:105906](+) [106862:106896](+) trnA-TGC [106960:106997](+) [107815:107849](+) trnA-TGC_copy2 [139802:139839](-) [138950:138984](-) trnI-GAT_copy2 [140893:140934](-) [139903:139937](-) 1 gene(s) have 2 intron(s) Genes Exons ycf3 [47110:47236](-) [46146:46375](-) [45251:45403](-)