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, psbT, psbZ, ycf3 Large subunit of ribosome rpl14, rpl16, rpl2, rpl20, rpl22, rpl22_copy2, 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 pbf1 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 psbN 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 5568 [108169:113737](+) ycf1_copy2 1209 [127301:128510](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [11818:11961](-) [10634:11044](-) clpP (3/3) [70806:70874](-) [69728:70018](-) [68828:69058](-) ndhA (2/2) [115612:116154](+) [117204:117734](+) ndhB (2/2) [95409:96185](-) [93953:94708](-) ndhB_copy2 (2/2) [140495:141271](+) [141972:142727](+) petB (2/2) [73739:73744](+) [74543:75184](+) petD (2/2) [75387:75395](+) [76136:76651](+) rpl16 (2/2) [81481:81489](-) [80091:80492](-) rpl2 (2/2) [84410:84814](-) [83318:83749](-) rpl2_copy2 (2/2) [151866:152270](+) [152931:153362](+) rpoC1 (2/2) [21810:22237](-) [19507:21118](-) rps12 (3/3) [68567:68680](-) [97599:97827](-) [97023:97048](-) rps12_copy2 (3/3) [68567:68680](-) [138853:139081](+) [139632:139657](+) rps16 (2/2) [5621:5660](-) [4564:4775](-) ycf3 (3/3) [43192:43323](-) [42242:42469](-) [41342:41500](-) ### 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 cemA TTG rps19 GTG rpl2 ATA ndhD ATC rpl2_copy2 ATA rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 134 genes (113 unique genes). Including: 88 protein-coding genes (79 are unique) 38 tRNA genes (30 are unique) 8 rRNA genes (4 are unique) Details are as follows: 88 protein-coding genes (79 are unique) Genes Length Location accD 1455 [56097:57551](+) atpA 1524 [9029:10552](-) atpB 1497 [51914:53410](-) atpE 405 [51513:51917](-) atpF 555 [11818:11961](-) [10634:11044](-) atpH 246 [12425:12670](-) atpI 744 [13287:14030](-) ccsA 972 [122167:123138](-) cemA 642 [61047:61688](-) clpP 591 [70806:70874](-) [69728:70018](-) [68828:69058](-) infA 234 [78680:78913](-) matK 1530 [1663:3192](-) ndhA 1074 [115612:116154](+) [117204:117734](+) ndhB 1533 [95409:96185](-) [93953:94708](-) ndhB_copy2 1533 [140495:141271](+) [141972:142727](+) ndhC 366 [48984:49349](-) ndhD 1506 [120439:121944](+) ndhE 306 [119427:119732](+) ndhF 2208 [125115:127322](+) ndhG 537 [118726:119262](+) ndhH 1182 [114429:115610](+) ndhI 534 [117835:118368](+) ndhJ 477 [47662:48138](-) ndhK 753 [48244:48996](-) pbf1 132 [73156:73287](-) petA 963 [59869:60831](-) petB 648 [73739:73744](+) [74543:75184](+) petD 525 [75387:75395](+) [76136:76651](+) petG 114 [65047:65160](+) petL 96 [64769:64864](+) petN 90 [27200:27289](+) psaA 2253 [38466:40718](-) psaB 2205 [36236:38440](-) psaC 246 [120075:120320](+) psaI 111 [58279:58389](+) psaJ 129 [65872:66000](+) psbA 1062 [78:1139](-) psbB 1527 [71296:72822](+) psbC 1422 [32823:34244](+) psbD 1062 [31814:32875](+) psbE 252 [63150:63401](-) psbF 120 [63020:63139](-) psbH 222 [73399:73620](+) psbI 111 [7065:7175](+) psbJ 123 [62633:62755](-) psbK 186 [6573:6758](+) psbL 117 [62881:62997](-) psbM 105 [28434:28538](-) psbT 108 [72983:73090](+) psbZ 189 [34813:35001](+) rbcL 1443 [54019:55461](+) rpl14 369 [79599:79967](-) rpl16 411 [81481:81489](-) [80091:80492](-) rpl2 837 [84410:84814](-) [83318:83749](-) rpl20 366 [67456:67821](-) rpl22 309 [82370:82678](-) rpl22_copy2 309 [154002:154310](+) rpl23 282 [84821:85102](-) rpl23_copy2 282 [151578:151859](+) rpl2_copy2 837 [151866:152270](+) [152931:153362](+) rpl32 162 [124080:124241](-) rpl33 201 [66500:66700](+) rpl36 114 [78444:78557](-) rpoA 1026 [76801:77826](-) rpoB 3204 [22264:25467](-) rpoC1 2040 [21810:22237](-) [19507:21118](-) rpoC2 4041 [15299:19339](-) rps11 417 [77895:78311](-) rps12 369 [68567:68680](-) [97599:97827](-) [97023:97048](-) rps12_copy2 369 [68567:68680](-) [138853:139081](+) [139632:139657](+) rps14 303 [35796:36098](-) rps15 273 [114064:114336](+) rps16 252 [5621:5660](-) [4564:4775](-) rps18 306 [66893:67198](+) rps19 279 [82789:83067](-) rps19_copy2 279 [153613:153891](+) rps2 714 [14278:14991](-) rps3 654 [81646:82299](-) rps4 606 [44330:44935](-) rps7 468 [96497:96964](-) rps7_copy2 468 [139716:140183](+) rps8 399 [79030:79428](-) ycf1 5568 [108170:113737](+) ycf1_copy2 1209 [127302:128510](-) ycf2 6891 [85410:92300](+) ycf2_copy2 6891 [144380:151270](-) ycf3 519 [43192:43323](-) [42242:42469](-) [41342:41500](-) ycf4 561 [58744:59304](+) 38 tRNA genes (30 are unique) Genes Location trnK-UUU [3972:4008](-) [1368:1402](-) trnQ-UUG [6175:6246](-) trnS-GCU [7327:7414](-) trnG-UCC [7928:7950](+) [8679:8726](+) trnR-UCU [8830:8901](+) trnC-GCA [26685:26755](+) trnD-GUC [29516:29589](-) trnY-GUA [29953:30036](-) trnE-UUC [30096:30168](-) trnT-GGU [30761:30832](+) trnS-UGA [34378:34470](-) trnG-GCC [35339:35409](+) trnfM-CAU [35563:35636](-) trnS-GGA [43946:44032](+) trnT-UGU [45265:45337](-) trnL-UAA [46240:46274](+) [46796:46845](+) trnF-GAA [47222:47294](+) trnV-UAC [51080:51118](-) [50460:50496](-) trnM-CAU [51282:51354](+) trnW-CCA [65273:65346](-) trnP-UGG [65510:65583](-) trnH-GUG [83200:83274](+) trnI-CAU [85268:85341](-) trnL-CAA [93313:93393](-) trnV-GAC [99646:99717](+) trnI-GAU [101738:101779](+) [102710:102744](+) trnA-UGC [102800:102837](+) [103640:103674](+) trnR-ACG [107420:107493](+) trnN-GUU [107774:107845](-) trnL-UAG [123219:123297](-) trnN-GUU_copy2 [128835:128906](+) trnR-ACG_copy2 [129187:129260](-) trnA-UGC_copy2 [133843:133880](-) [133006:133040](-) trnI-GAU_copy2 [134901:134942](-) [133936:133970](-) trnV-GAC_copy2 [136963:137034](-) trnL-CAA_copy2 [143287:143367](+) trnI-CAU_copy2 [151339:151412](+) trnH-GUG_copy2 [153406:153480](-) 8 rRNA genes (4 are unique) Genes Location rrn16 [99945:101435](+) rrn23 [104090:106638](+) rrn4.5 [106737:106839](+) rrn5 [107050:107170](+) rrn5_copy2 [129510:129630](-) rrn4.5_copy2 [129841:129943](-) rrn23_copy2 [130042:132590](-) rrn16_copy2 [135245:136735](-) This genome has 23 genes with intron(s). Details are as follows: 19 gene(s) have 1 intron(s) Genes Exons rps16 [5621:5660](-) [4564:4775](-) atpF [11818:11961](-) [10634:11044](-) rpoC1 [21810:22237](-) [19507:21118](-) petB [73739:73744](+) [74543:75184](+) petD [75387:75395](+) [76136:76651](+) rpl16 [81481:81489](-) [80091:80492](-) rpl2 [84410:84814](-) [83318:83749](-) ndhB [95409:96185](-) [93953:94708](-) ndhA [115612:116154](+) [117204:117734](+) ndhB_copy2 [140495:141271](+) [141972:142727](+) rpl2_copy2 [151866:152270](+) [152931:153362](+) trnK-UUU [3972:4008](-) [1368:1402](-) trnG-UCC [7928:7950](+) [8679:8726](+) trnL-UAA [46240:46274](+) [46796:46845](+) trnV-UAC [51080:51118](-) [50460:50496](-) trnI-GAU [101738:101779](+) [102710:102744](+) trnA-UGC [102800:102837](+) [103640:103674](+) trnA-UGC_copy2 [133843:133880](-) [133006:133040](-) trnI-GAU_copy2 [134901:134942](-) [133936:133970](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [68567:68680](-) [97599:97827](-) [97023:97048](-) ycf3 [43192:43323](-) [42242:42469](-) [41342:41500](-) rps12_copy2 [68567:68680](-) [138853:139081](+) [139632:139657](+) clpP [70806:70874](-) [69728:70018](-) [68828:69058](-)