Plastid genomes of four species of Iris from subgenus Scorpiris
DOI:
https://doi.org/10.54981/PDCA/vol2_iss2/a4Keywords:
chloroplast genome, nucleotide divergence, phylogenic markers, phylogeny, IrisAbstract
The taxonomic complexity of Iris (Iridaceae) is high, and its molecular phylogeny remains largely unknown. With the growing availability of full plastid genomes of species representing major taxonomic groups within Iris, it will become possible to produce a robust phylogenetic tree and reconstruct the evolutionary history of the genus. With this objective in mind, we sequenced and analyzed the chloroplast genomes of four species from subgenus Scorpiris native to Uzbekistan: Iris austrotschatkalica, I. pseudocapnoides, I. victoris and I. hippolyti. The phylogenetic tree obtained agreed well with those produced earlier with a limited number of chloroplast markers. We suggest as the most useful for phylogenetic analyses of Iris the following loci that show high variability and lack of loop structures: atpF/atpH, rps15/ycf1, atpA/atpF, trnL-UAA/trnF-GAA, trnG-UCC/trnR-UCU, and psaA/ycf3.
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Aligned length (bp) Indel (bp) Num ber of indel event s 9;6 Number of polymorphic sites Total Ts Tv Nucleoti de diversity 0.00136 0.00314 0.00724 0.00397 0.00269 0.00612 0.00525 0.00931 0.00271 0.00224 0.0075 0.00508 0.00325 0.00353 0.00345 0.0027 0.00529 0.0033 0.0037 0.00266 0.00196 0.0055 0.0014 0.00382 0.00872 0.00741 0.00401 0.00486 0.00414 0.00601 0.00901 0.00314 0.0026 0.00265 0.00694 0.00585 0.00388 0.00498 0.00708 0.00471 Ks Ka Ka/Ks Identity (%) Diversit y (%) 0.00685 0.00785 0.01082 0.0042 0.00338 0.00468 0.0028 0.002 0.0187 0.00945 0.0058 0.00413 0.00735 0.00842 0.01202 0.0075 0.05763 0.00417 0.00713 0.005 0.00365 0.00807 0.00668 0.00912 0.00353 0.00175 0.0087 0.0052 0.00338 0.00445 0.00393 0.00353 0.007 0.0042 0.0048 0.00345 0.00255 0.00147 0.0018 0.00492 0.00875 0.008 0.00515 0.0051 0.00325 0.00773 0.0093 0.00398 0.00325 0.00353 0.00953 0.00753 0.00515 0.00325 0.00712 0.0018 0.90871 0.84258 0.41667 2.57397 1.11111 1.20833 1.96667 0.07843 0.92593 1.37931 1.23487 0.44218 1.10451 0.27038 0.94889 0.03123 99.7 99.7 99.2 99.6 99.7 99.4 99.5 99.1 99.7 99.8 99.2 99.3 99.7 99.6 99.7 99.7 99.5 99.7 99.6 99.7 99.8 99.4 99.9 99.6 99.1 99.3 99.6 99.5 99.4 99.1 99.7 99.7 99.7 99.3 99.4 99.6 99.5 99.3 99.5 0.3 0.3 0.8 0.4 0.3 0.6 0.5 0.9 0.3 0.2 0.8 0.7 0.3 0.4 0.3 0.3 0.5 0.3 0.4 0.3 0.2 0.6 0.1 0.4 0.9 0.7 0.4 0.5 0.6 0.9 0.3 0.3 0.3 0.7 0.6 0.4 0.5 0.7 0.5 clpP psbB psbT psbN psbH petB petD rpoA rps11 rpl36 infA rps8 rpl14 rpl16 rps3 rpl22 total IR rps19 rpl2 rpl23 ycf2 ndhB rps7 rrn16 rrn23 rrn4.5 rrn5 total SSC ndhF rpl32 ccsA ndhD psaC ndhE ndhG ndhI ndhA ndhH rps15 408Diversity of Central Asia. 04 (2023) 103–123 Plant 0.00191 0.00502 0.00663 0.00375 0.00641 0.00839 0.000418 0.01062 0.00355 0.01375 0.0040 0.00193 0.0034 0.00323 0.0082 0.01153 0.0033 0.00242 0.00598 0.00767 0.00468 0.00728 0.0108 0.0032 0.01368 0.00443 0.01182 0.0045 3.10017 2.2549 2.2549 0.39024 1.02486 1.1122 99.8 99.5 99.3 99.6 99.4 99.2 99.6 98.9 99.6 98.6 99.6 0.2 0.5 0.7 0.4 0.6 0.8 0.4 1.1 0.4 1.4 0.4 30;3;3;36 0.00179 0.00175 0.00065 0.0004 0.0016 0.0002 0.0023 0.0018 0.00085 0.0005 1.125 1.1250 99.8 99.1 99.9 99.9 0.2 0.9 0.1 0.1 0.00647 0.01245 0.00345 0.00719 0.00949 0.00327 0.00659 0.0043 0.00534 0.00508 0.00611 0.0026 0.03487 0.0025 0.003 0.01595 0.00987 0.00502 0.0051 0.00753 0.00737 0.00373 0.00848 0.01248 0.00422 0.00437 0.0028 0.00548 0.0051 0.00773 2.89744 0.21126 1.49333 2.82778 0.27377 0.28369 1.0923 99.4 98.8 99.7 99.3 99.1 99.7 99.3 99.6 99.5 99.5 99.4 0.6 1.2 0.3 0.7 0.9 0.3 0.7 0.4 0.5 0.5 0.6 ycf1 9;6;3; 21;6; 9,3;12; 12;3;3 0.01175 0.0145 0.01115 0.76897 total 0.00679 0.00778 0.00670 1.20539 99.2 0.72 TOTAL 0.00375 0.00375 0.00389 1.14754 99.6 0.4 Ts = transitions; Tv = transversions; Ks = the number of synonymous substitutions per synonymous site; Ka = the number of nonsynonymous substitutions per nonsynonymous site; LSC = large single copy; IR = inverted repeat; SSC = small single copy. Ortikov et al. Plastid genomes of the subgenus Scorpiris Table S2. Comparison of intergenic space regions among plastomes of I. austrotschatkalica (I.a.), I. pseudocapnoides (I.p.), I. victoris (I.v.), and I. hippolyti (I.h.) Align Number of Size (bp) Number ed Indel polymorphic sites Nucleotide Identity IGS of indel length (bp) diversity (%) events (I.a.) (I.p.) (I.v.) (I.h.) Total Ts Tv (bp) LSC /psbA 0.08658 91.3 psbA/trnK-UUU 0.01336 98.7 trnK-UUU/matK 0.00398 99.4 matK/trnK-UUU 2;1;1;32 0.00382 96.7 trnK-UUU/rps16 2;1;11;120;2;1;6;3 0.0546 88.3 rps16/trnQ-UUG 1;206;1 0,00967 82.9 trnQ-UUG/psbK 1;1 0.01114 98.5 psbK/psbI 2;1;4;2;1 0.02231 96.7 psbI/trnS-GCU 0.01693 98.3 trnS-GCU/trnG-UCC 15;7;15;2;9;1 0.01229 95.7 trnG-UCC/trnR-UCU 6;4;3 0.0202 94.4 trnR-UCU/atpA 1;1;13 0.00612 atpA/atpF 0.00714 93.2 atpF/atpH 1;99;2 0.03152 85.2 atpH/atpL 4;2;1;1;1;3;1 0.00245 98.7 atpL/rps2 0.00199 99.8 rps2/rpoC2 0.00279 99.4 rpoC2/rpoC1 0.01217 98.8 rpoC1/rpoB rpoB/trnC-GCA 2;3;2;1;1;1;1;3;1;6 0.00988 98.2 trnC-GCA/petN 3;3;1;9;1;2;6;6 0.01028 97.3 petN/psbM 1;1;1;4;1;2 0.00616 98.8 psbM/trnD-GUC 12;2;2;1;42 0.00916 95.8 trnD-GUC/trnY-GUA 0.00873 trnY-GUA/trnE-UUC trnE-UUC/trnT-GGU 9;25;15;1;1 0.01138 96.2 trnT-GGU/psbD 1;1;9;7;5;1;1 0.00994 97.7 psbD/psbC psbC/trnS-UGA 0.01587 98.9 trnS-UGA/psbZ 0.01372 98.6 psbZ/trnG-GCC 22;16 0.00671 95.5 trnG-GCC/trnfM-CAU 7;1;20;6 0.01353 92.2 trnfM-CAU/rps14 0.00633 99.4 rps14/psaB 0.00494 99.5 psaB/psaA psaA/ycf3 6;1;2;4;24;4 0.00473 95.6 ycf3/trnS-GGA 0.01165 98.7 trnS-GGA/rps4 6;1 0.00758 98.1 rps4/trnT-UGU 0.01266 98.5 Diversit y (%) 8.7 1.3 0.6 3.3 11.7 17.1 1.5 3.3 1.7 4.3 5.6 6.8 14.8 1.3 0.2 0.6 1.2 1.8 2.7 1.2 4.2 3.8 2.3 1.1 1.4 4.5 7.8 0.6 0.5 4.4 1.3 1.9 1.5 trnT-UGU/trnL-UAA trnL-UAA/trnF-GAA trnF-GAA/ndhJ ndhJ/ndhK ndhK/ndhC ndhC/trnV-UAC trnV-UAC/trnM-CAU trnM-CAU/atpE atpE/atpB atpB/rbcL rbcL/accD accD/psaI psaI/ycf4 ycf4/cemA cemA/petA petA/psbJ psbJ/psbL psbL/psbF psbF/psbE psbE/petL petL/petG petG/trnW-CCA trnW-CCA/trnP-UGG trnP-UGG/psaJ psaJ/rpl33 rpl33/rps18 rps18/rpl20 rpl20/rps12-2 rps12-2/clpP clpP/psbB psbB/psbT psbT/psbN psbN/psbH psbH/petB petB/petD petD/rpoA rpoA/rps11 rps11/rpl36 rpl36/infA infA/rps8 rps8/rpl14 rpl14/rpl16 rpl16/rps3 rps3/rpl22 rpl22/rps19 total 12;2;1;11;4;1;7;9;3 2;5;35 3;2;1 4;3;2 5;3;4 1;1 5;1;7;134 1;16;2;1;2;1 4;2;1 9;1;1 6;1 2;1 1;10 1;1;26;6 0.01166 0.01153 0.00648 0.00305 0.00423 0.0144 0.00802 0.01238 0.00768 0.05971 0.024 0.00819 0.02841 0.00641 0.00707 0.00609 0.00922 0.00877 0.01292 0.00468 0.00725 0.00116 0.00402 0.00889 0.00901 0.00242 0.01738 0.01563 0.01061 0.02119 0.02108 0.00352 0.01935 0.0625 0.01852 0.011876 96.1 93.3 96.2 99.7 98.9 99.6 97.7 98.7 98.2 98.8 88.6 97.6 98.3 97.2 98.9 97.6 97.8 97.8 98.7 97.4 99.5 99.3 99.6 99.6 99.1 99.1 99.4 98.4 98.9 97.9 93.2 99.6 98.1 86.4 95.5 97.19 3.9 6.7 3.8 0.3 1.1 0.4 2.3 1.3 1.8 1.2 11.4 2.4 1.7 2.8 1.1 2.4 2.2 2.2 1.3 2.6 0.5 0.7 0.4 0.4 0.9 0.9 0.6 1.6 1.1 2.1 6.8 0.4 1.9 13.6 4.5 2.81 IR rps19/trnH-GUG trnH-GUG/rpl2 0.02326 97.7 rpl2/rpl23 rpl23/trnI-CAU trnI-CAU/ycf2 ycf2/trnL-CAA 99.4 trnL-CAA/ndhB 0.00298 ndhB/rps7 rps7/rps12-2 rps12-2/trnV-GAC 5;12 0.00149 99.4 trnV-GAC/rrn16 0.00221 99.8 rrn16/trnI-GAU trnI-GAU/trnA-UGC trnA-UGC/rrn23 rrn23/rrn4.5 99.5 rrn4.5/rrn5 0.00314 97.4 rrn5/trnR-ACG 0.00392 99.6 trnR-ACG/trnN-GUU 8;9 0.00171 trnN-GUU/ycf1 0.00154 99.8 total 0.00211 99.4 SSC ndhF/rpl32 1;5;5;5;5;2,1;12,5;9,4 0.00978 96.2 rpl32/trnL-UAG 82;1;18,13;9;1;2,1 0.01507 96.1 trnL-UAG/ccsA 0.00595 99.4 ccsA/ndhD 0.00735 97.1 ndhD/psaC 0.0042 97.4 psaC/ndhE 1;6;2 0.00872 97.7 ndhE/ndhG ndhG/ndhI 0.00629 99.2 ndhI/ndhA 0.00588 99.4 ndhA/ndhH ndhH/rps15 0.01449 98.6 rps15/ycf1 2;25,13,4;1;4;5;2;2,1;36 0.04088 88.7 total 0.009884 97.5 TOTAL 36374 36851 36641 36644 37237 0.007959 98.0 Ts = transitions; Tv = transversions; LSC = large single copy; IR = inverted repeat; SSC = small single copy; “-“ = no integenic sequence between psbD and psbC genes. 2.3 0.6 0.6 0.2 0.5 2.6 0.4 0.2 0.6 3.8 3.9 0.6 2.9 2.6 2.3 0.8 0.6 1.4 11.3 2.5 2.0 Plastid genomes of the subgenus Scorpiris Ortikov et al. Table S3. Comparison of introns among plastomes of I. austrotschatkalica (I.a.), I. pseudocapnoides (I.p.), I. victoris (I.v.), and I. hippolyti (I.h.) Region LSC Intron Indel (bp) Number of indel events Number of polymorphic sites Total Ts Tv Nucleotide diversity Identity (%) Diversity (%) (I.p.) (I.v.) (I.h.) trnK-UUU rps16 trnG-UCC atpF rpoC1 ycf3 ycf3 trnL-UAA trnV-UAC clpP clpP petB petD rpl16 1;3;2,1;1;32 3;1;4;6 5;1 2;2;1 1;1;2;13,3 1;1;2;5 8,4;1;1;2,1 2,1;2,1;5 1;4;6 1;5;2 5;1;3;12,6 0.00593 0.00749 0.00624 0.00722 0.0046 0.00609 0.00461 0.00471 0.01016 0.00253 0.01019 0.00712 0.00618 0.0059 98.5 98.2 98.8 98.9 98.2 98.7 99.3 99.4 99.4 97.7 99.2 98.6 97.9 98.6 1.5 1.8 1.2 1.1 1.8 1.3 0.7 0.6 0.6 2.3 0.8 1.4 2.1 1.4 rpl2 ndhB rps12-2 trnI-GAU trnA-UGC 0.00096 0.00124 0.00044 99.5 99.9 99.8 99.84 0.5 0.1 0.2 0.16 ndhA 2;1;8 0.00822 0.00822 98.7 98.7 1.3 1.3 0.00486 99.1 0.9 IR total SSC TOTAL Aligned length (bp) (I.a.) total total Size (bp) Ts = transitions; Tv = transversions; LSC = large single copy; IR = inverted repeat; SSC = small single copy.
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