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, rpl14_copy2, rpl16, rpl16_copy2, rpl2, rpl20, rpl22, rpl22_copy2, rpl23, rpl23_copy2, rpl2_copy2, rpl33, rpl36 Small subunit of ribosome rps11, rps12, rps12_copy2, rps14, rps15, rps16, rps18, rps19, rps19_copy2, rps2, rps3, rps3_copy2, rps4, rps7, rps7_copy2, rps8, rps8_copy2 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, 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 rpl32 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 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) [42382:42525](+) [43267:43677](+) clpP (3/3) [72443:72513](-) [71353:71641](-) [70357:70602](-) ndhA (2/2) [122761:123313](-) [121206:121744](-) ndhB (2/2) [96443:97219](-) [94986:95741](-) ndhB_copy2 (2/2) [143426:144202](+) [144904:145659](+) petB (2/2) [75415:75419](+) [76202:76844](+) petD (2/2) [77053:77059](+) [77766:78262](+) rpl16 (2/2) [82979:82987](-) [81600:81998](-) rpl16_copy2 (2/2) [157658:157666](+) [158647:159045](+) rpl2 (2/2) [85834:86224](-) [84740:85173](-) rpl2_copy2 (2/2) [154421:154811](+) [155472:155905](+) rpoC1 (2/2) [31545:31976](+) [32734:34344](+) rps12 (3/3) [70081:70194](-) [98636:98867](-) [98069:98094](-) rps12_copy2 (3/3) [70081:70194](-) [141778:142009](+) [142551:142576](+) rps16 (2/2) [1197:1237](+) [2110:2335](+) ycf3 (3/3) [9829:9953](+) [10682:10910](+) [11673:11825](+) ### The exon column shows the number of (actual exons/expected exons). ### Uncommon intron-contained genes: rps4 2 [160491:160493](+) [1:630](+)] 4. Genes with internal stop codon: None 5. Genes with nonstandard start codon: Genes Start codon rps19 GTG rpl2 ACG ndhD ACG rpl2_copy2 ACG rps19_copy2 GTG 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 133 genes (110 unique genes). Including: 89 protein-coding genes (77 are unique) 36 tRNA genes (29 are unique) 8 rRNA genes (4 are unique) Details are as follows: 89 protein-coding genes (77 are unique) Genes Length Location accD 1449 [58042:59490](+) atpA 1524 [43744:45267](+) atpB 1503 [53510:55012](-) atpE 402 [53112:53513](-) atpF 555 [42382:42525](+) [43267:43677](+) atpH 246 [41707:41952](+) atpI 744 [39833:40576](+) ccsA 960 [115706:116665](+) cemA 690 [61897:62586](+) clpP 606 [72443:72513](-) [71353:71641](-) [70357:70602](-) matK 1533 [3977:5509](+) ndhA 1092 [122761:123313](-) [121206:121744](-) ndhB 1533 [96443:97219](-) [94986:95741](-) ndhB_copy2 1533 [143426:144202](+) [144904:145659](+) ndhC 363 [50518:50880](-) ndhD 1503 [116920:118422](-) ndhE 306 [119018:119323](-) ndhF 2220 [111443:113662](-) ndhG 534 [119578:120111](-) ndhH 1182 [123315:124496](-) ndhI 543 [120578:121120](-) ndhJ 477 [49158:49634](-) ndhK 684 [49776:50459](-) petA 969 [62790:63758](+) petB 648 [75415:75419](+) [76202:76844](+) petD 504 [77053:77059](+) [77766:78262](+) petG 114 [66546:66659](+) petL 96 [66278:66373](+) petN 90 [26563:26652](-) psaA 2253 [12523:14775](+) psaB 2205 [14801:17005](+) psaC 246 [118558:118803](-) psaI 111 [60119:60229](+) psaJ 135 [67469:67603](+) psbA 1062 [6098:7159](+) psbB 1527 [72913:74439](+) psbC 1422 [19198:20619](-) psbD 1062 [20567:21628](-) psbE 252 [64665:64916](-) psbF 120 [64536:64655](-) psbH 222 [75074:75295](+) psbI 111 [8614:8724](+) psbJ 123 [64155:64277](-) psbK 186 [7992:8177](+) psbL 117 [64397:64513](-) psbM 105 [25798:25902](+) psbN 132 [74843:74974](-) psbT 108 [74638:74745](+) psbZ 189 [18349:18537](-) rbcL 1428 [55841:57268](+) rpl14 369 [81089:81457](-) rpl14_copy2 369 [159188:159556](+) rpl16 408 [82979:82987](-) [81600:81998](-) rpl16_copy2 408 [157658:157666](+) [158647:159045](+) rpl2 825 [85834:86224](-) [84740:85173](-) rpl20 354 [68929:69282](-) rpl22 540 [83801:84340](-) rpl22_copy2 540 [156305:156844](+) rpl23 282 [86243:86524](-) rpl23_copy2 282 [154121:154402](+) rpl2_copy2 825 [154421:154811](+) [155472:155905](+) rpl33 201 [68020:68220](+) rpl36 114 [80041:80154](-) rpoA 996 [78437:79432](-) rpoB 3213 [28306:31518](+) rpoC1 2043 [31545:31976](+) [32734:34344](+) rpoC2 4152 [34512:38663](+) rps11 417 [79511:79927](-) rps12 372 [70081:70194](-) [98636:98867](-) [98069:98094](-) rps12_copy2 372 [70081:70194](-) [141778:142009](+) [142551:142576](+) rps14 303 [17135:17437](+) rps15 273 [124712:124984](-) rps16 267 [1197:1237](+) [2110:2335](+) rps18 306 [68363:68668](+) rps19 279 [84400:84678](-) rps19_copy2 279 [155967:156245](+) rps2 708 [38883:39590](+) rps3 657 [83160:83816](-) rps3_copy2 657 [156829:157485](+) rps4 633 [160491:160493](+) [1:630](+) rps7 468 [97543:98010](-) rps7_copy2 468 [142635:143102](+) rps8 399 [80465:80863](-) rps8_copy2 399 [159782:160180](+) ycf1 5697 [125398:131094](-) ycf2 6879 [86832:93710](+) ycf2_copy2 6879 [146935:153813](-) ycf3 507 [9829:9953](+) [10682:10910](+) [11673:11825](+) ycf4 555 [60693:61247](+) 36 tRNA genes (29 are unique) Genes Location trnK-UUU [3163:3199](+) [5772:5806](+) trnH-GUG [7386:7460](+) trnQ-UUG [7580:7651](-) trnS-GGA [8860:8946](-) trnfM-CAU [17600:17673](+) trnG-GCC [17860:17930](-) trnS-UGA [18911:19003](+) trnT-GGU [23246:23317](-) trnE-UUC [24010:24082](+) trnY-GUA [24144:24227](+) trnD-GUC [24646:24719](+) trnC-GCA [27112:27182](-) trnR-UCU [45395:45466](-) trnG-UCC [46418:46440](-) [45612:45659](-) trnS-GCU [47021:47108](-) trnL-UAA [47803:47837](+) [48343:48392](+) trnF-GAA [48795:48867](+) trnV-UAC [52591:52628](-) [51971:52005](-) trnM-CAU [52803:52875](+) trnW-CCA [66804:66877](-) trnP-UGG [67044:67117](-) trnI-CAU [86690:86763](-) trnL-CAA [94345:94425](-) trnV-GAC [100629:100700](+) trnI-GAU [102716:102752](+) [103702:103736](+) trnA-UGC [103801:103838](+) [104654:104688](+) trnR-ACG [108452:108525](+) trnN-GUU [109156:109227](-) trnL-UAG [115518:115597](+) trnN-GUU_copy2 [131418:131489](+) trnR-ACG_copy2 [132120:132193](-) trnA-UGC_copy2 [136807:136844](-) [135957:135991](-) trnI-GAU_copy2 [137893:137929](-) [136909:136943](-) trnV-GAC_copy2 [139945:140016](-) trnL-CAA_copy2 [146220:146300](+) trnI-CAU_copy2 [153882:153955](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [100931:102421](+) rrn23 [104841:107653](+) rrn4.5 [107752:107854](+) rrn5 [108080:108200](+) rrn5_copy2 [132445:132565](-) rrn4.5_copy2 [132791:132893](-) rrn23_copy2 [132992:135804](-) rrn16_copy2 [138224:139714](-) This genome has 25 genes with intron(s). Details are as follows: 21 gene(s) have 1 intron(s) Genes Exons rps4 [160491:160493](+) [1:630](+) rps16 [1197:1237](+) [2110:2335](+) rpoC1 [31545:31976](+) [32734:34344](+) atpF [42382:42525](+) [43267:43677](+) petB [75415:75419](+) [76202:76844](+) petD [77053:77059](+) [77766:78262](+) rpl16 [82979:82987](-) [81600:81998](-) rpl2 [85834:86224](-) [84740:85173](-) ndhB [96443:97219](-) [94986:95741](-) ndhA [122761:123313](-) [121206:121744](-) ndhB_copy2 [143426:144202](+) [144904:145659](+) rpl2_copy2 [154421:154811](+) [155472:155905](+) rpl16_copy2 [157658:157666](+) [158647:159045](+) trnK-UUU [3163:3199](+) [5772:5806](+) trnG-UCC [46418:46440](-) [45612:45659](-) trnL-UAA [47803:47837](+) [48343:48392](+) trnV-UAC [52591:52628](-) [51971:52005](-) trnI-GAU [102716:102752](+) [103702:103736](+) trnA-UGC [103801:103838](+) [104654:104688](+) trnA-UGC_copy2 [136807:136844](-) [135957:135991](-) trnI-GAU_copy2 [137893:137929](-) [136909:136943](-) 4 gene(s) have 2 intron(s) Genes Exons rps12 [70081:70194](-) [98636:98867](-) [98069:98094](-) ycf3 [9829:9953](+) [10682:10910](+) [11673:11825](+) rps12_copy2 [70081:70194](-) [141778:142009](+) [142551:142576](+) clpP [72443:72513](-) [71353:71641](-) [70357:70602](-)