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, ycf3 Large subunit of ribosome rpl14, rpl16, rpl2, rpl22, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps12_copy2, 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 infA Conserved open reading frames ycf1, ycf2, ycf2_copy2, ycf4 Other genes lhbA 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 psbZ Large subunit of ribosome rpl20 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 None None None 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [13264:13408](-) [12129:12538](-) clpP (3/3) [70847:70915](-) [69682:69972](-) [68904:69131](-) ndhA (2/2) [119424:119975](-) [117790:118323](-) ndhB (2/2) [95298:96074](-) [93864:94619](-) ndhB_copy2 (2/2) [138932:139708](+) [140387:141142](+) petB (2/2) [73800:73805](+) [74616:75263](+) petD (2/2) [75458:75466](+) [76192:76665](+) rpl16 (2/2) [81532:81540](-) [80107:80505](-) rpl2 (2/2) [84354:84744](-) [83258:83691](-) rpl2_copy2 (2/2) [150262:150652](+) [151315:151748](+) rpoC1 (2/2) [23299:23733](-) [20933:22591](-) rps12 (3/3) [68641:68754](-) [97481:97711](-) [96917:96943](-) rps12_copy2 (3/3) [68641:68754](-) [137295:137524](+) [138062:138089](+) rps16 (2/2) [5847:5888](-) [4827:5054](-) ycf3 (3/3) [44908:45036](-) [43976:44203](-) [43088:43240](-) ### 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 rpl22 AAG rps19 GTG ycf2 GTG ndhD AAC ndhH ATC ycf2_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 128 genes (111 unique genes). Including: 84 protein-coding genes (78 are unique) 36 tRNA genes (29 are unique) 8 rRNA genes (4 are unique) Details are as follows: 84 protein-coding genes (78 are unique) Genes Length Location accD 1479 [56715:58193](+) atpA 1524 [10547:12070](-) atpB 1497 [52445:53941](-) atpE 402 [52047:52448](-) atpF 555 [13264:13408](-) [12129:12538](-) atpH 246 [13793:14038](-) atpI 735 [14740:15474](-) ccsA 960 [112546:113505](+) cemA 690 [60218:60907](+) clpP 588 [70847:70915](-) [69682:69972](-) [68904:69131](-) infA 243 [78681:78923](-) lhbA 189 [36336:36524](+) matK 1512 [1929:3440](-) ndhA 1086 [119424:119975](-) [117790:118323](-) ndhB 1533 [95298:96074](-) [93864:94619](-) ndhB_copy2 1533 [138932:139708](+) [140387:141142](+) ndhC 363 [49861:50223](-) ndhD 1500 [113778:115277](-) ndhE 306 [115931:116236](-) ndhF 2211 [108944:111154](-) ndhG 531 [116422:116952](-) ndhH 1197 [119977:121173](-) ndhI 504 [117209:117712](-) ndhJ 477 [48541:49017](-) ndhK 747 [49124:49870](-) petA 963 [61126:62088](+) petB 654 [73800:73805](+) [74616:75263](+) petD 483 [75458:75466](+) [76192:76665](+) petG 114 [65190:65303](+) petL 96 [64918:65013](+) petN 90 [28901:28990](+) psaA 2253 [40212:42464](-) psaB 2205 [37982:40186](-) psaC 246 [115409:115654](-) psaI 114 [58722:58835](+) psaJ 135 [66065:66199](+) psbA 1062 [342:1403](-) psbB 1527 [71353:72879](+) psbC 1422 [34335:35756](+) psbD 1062 [33326:34387](+) psbE 252 [63614:63865](-) psbF 120 [63485:63604](-) psbH 222 [73454:73675](+) psbI 111 [8360:8470](+) psbJ 123 [63089:63211](-) psbK 186 [7779:7964](+) psbL 117 [63346:63462](-) psbM 111 [30005:30115](-) psbN 132 [73220:73351](-) psbT 102 [73058:73159](+) rbcL 1428 [54637:56064](+) rpl14 369 [79600:79968](-) rpl16 408 [81532:81540](-) [80107:80505](-) rpl2 825 [84354:84744](-) [83258:83691](-) rpl22 378 [82502:82879](-) rpl23 282 [84768:85049](-) rpl23_copy2 282 [149957:150238](+) rpl2_copy2 825 [150262:150652](+) [151315:151748](+) rpl32 159 [111738:111896](+) rpl33 201 [66595:66795](+) rpl36 114 [78447:78560](-) rpoA 1017 [76832:77848](-) rpoB 3213 [23770:26982](-) rpoC1 2094 [23299:23733](-) [20933:22591](-) rpoC2 4158 [16612:20769](-) rps11 417 [77914:78330](-) rps12 372 [68641:68754](-) [97481:97711](-) [96917:96943](-) rps12_copy2 372 [68641:68754](-) [137295:137524](+) [138062:138089](+) rps14 303 [37566:37868](-) rps15 279 [121262:121540](-) rps16 270 [5847:5888](-) [4827:5054](-) rps18 306 [66956:67261](+) rps19 279 [82925:83203](-) rps2 711 [15665:16375](-) rps3 657 [81688:82344](-) rps4 606 [45587:46192](-) rps7 468 [96396:96863](-) rps7_copy2 468 [138143:138610](+) rps8 405 [79045:79449](-) ycf1 5166 [121942:127107](-) ycf2 6831 [85377:92207](+) ycf2_copy2 6831 [142799:149629](-) ycf3 510 [44908:45036](-) [43976:44203](-) [43088:43240](-) ycf4 555 [59064:59618](+) 36 tRNA genes (29 are unique) Genes Location trnH-GUG [1:72](-) trnK-UUU [4142:4178](-) [1642:1676](-) trnQ-UUG [7375:7446](-) trnS-GCU [8638:8725](-) trnR-UCU [10418:10489](+) trnC-GCA [27988:28066](+) trnD-GUC [31137:31210](-) trnY-GUA [31511:31594](-) trnE-UUC [31654:31726](-) trnT-GGU [32569:32640](+) trnS-UGA [35940:36032](-) trnG-UCC [37111:37181](+) trnfM-CAU [37323:37396](-) trnS-GGA [45292:45378](+) trnT-UGU [46528:46600](-) trnL-UAA [47009:47045](+) [47555:47604](+) trnF-GAA [47879:47951](+) trnV-UAC [51591:51628](-) [50997:51033](-) trnM-CAU [51797:51869](+) trnW-CCA [65425:65498](-) trnP-UGG [65647:65721](-) trnI-CAU [85215:85288](-) trnL-CAA [93206:93284](-) trnV-GAC [98949:99020](+) trnI-GAU [101034:101076](+) [102015:102049](+) trnA-UGC [102118:102155](+) [102993:103027](+) trnR-ACG [106776:106849](+) trnN-GUU [107443:107515](-) trnL-UAG [112393:112472](+) trnN-GUU_copy2 [127491:127563](+) trnR-ACG_copy2 [128157:128230](-) trnA-UGC_copy2 [132851:132888](-) [131979:132013](-) trnI-GAU_copy2 [133930:133972](-) [132957:132991](-) trnV-GAC_copy2 [135986:136057](-) trnL-CAA_copy2 [141722:141800](+) trnI-CAU_copy2 [149718:149791](+) 8 rRNA genes (4 are unique) Genes Location 16rrn [99248:100737](+) 23rrn [103180:105989](+) 4.5rrn [106088:106190](+) 5rrn [106410:106530](+) 5rrn_copy2 [128476:128596](-) 4.5rrn_copy2 [128816:128918](-) 23rrn_copy2 [129017:131826](-) 16rrn_copy2 [134268:135757](-) This genome has 22 genes with intron(s). Details are as follows: 18 gene(s) have 1 intron(s) Genes Exons rps16 [5847:5888](-) [4827:5054](-) atpF [13264:13408](-) [12129:12538](-) rpoC1 [23299:23733](-) [20933:22591](-) petB [73800:73805](+) [74616:75263](+) petD [75458:75466](+) [76192:76665](+) rpl16 [81532:81540](-) [80107:80505](-) rpl2 [84354:84744](-) [83258:83691](-) ndhB [95298:96074](-) [93864:94619](-) ndhA [119424:119975](-) [117790:118323](-) ndhB_copy2 [138932:139708](+) [140387:141142](+) rpl2_copy2 [150262:150652](+) [151315:151748](+) trnK-UUU [4142:4178](-) [1642:1676](-) trnL-UAA [47009:47045](+) [47555:47604](+) trnV-UAC [51591:51628](-) [50997:51033](-) trnI-GAU [101034:101076](+) [102015:102049](+) trnA-UGC [102118:102155](+) [102993:103027](+) trnA-UGC_copy2 [132851:132888](-) [131979:132013](-) trnI-GAU_copy2 [133930:133972](-) [132957:132991](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [68641:68754](-) [97481:97711](-) [96917:96943](-) ycf3 [44908:45036](-) [43976:44203](-) [43088:43240](-) rps12_copy2 [68641:68754](-) [137295:137524](+) [138062:138089](+) clpP [70847:70915](-) [69682:69972](-) [68904:69131](-)