Phylogenetic Analysis of Rare and Endangered Tulipa Species (Liliaceae) of Kazakhstan Based on Universal Barcoding Markers
Abstract
:Simple Summary
Abstract
1. Introduction
2. Results
2.1. Single-Nucleotide Polymorphisms of the ITS, rbcL, and matK DNA Sequences in Tulipa
2.2. Nuclear rDNA Phylogeny
2.3. Chloroplast Genome Phylogeny
2.4. Combined, rbcL, psbA-trnH, matK, and ITS Data Set of 8 Species of Kazakhstan Tulips
3. Discussion
3.1. Incongruent Placement of T. patens in nrDNA and cpDNA Phylogenies
3.2. Placement of T. kaufmanniana in Section Vinistriatae (Raamsd.) Zonn
3.3. Using a Combined Data Set to Optimize Phylogenetic Analysis
4. Materials and Methods
4.1. Sample Collection and Data Acquisition
4.2. DNA Isolation, Amplification, and Sequencing
4.3. Data Analyses
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Species | Sequence ID | Coordinates | Altitude | Source | Collection Date | rbcL | trnH-psbA | matK | ITS |
---|---|---|---|---|---|---|---|---|---|
Subg. Tulipa T. greigii | T. greigii A-Zh KZ* | 42.2039 N, 70.2529 E | 1830 m. | Aksu-Zhabagly Nature State Reserve | 14-May-2021 | ON010708 (583 bp) | ON423208 (464 bp) | ON423211 (732 bp) | OP279724 (727 bp) |
Subg. Tulipa, T. kaufmanniana | T. kaufmanniana A-Zh KZ* | 42.205 N, 70.289 E | 2050 m. | Aksu-Zhabagly Nature State Reserve | 14-May-2021 | ON186589 (582 bp) | ON423207 (481 bp) | ON952472 (693 bp) | OP279725 (725 bp) |
Subg. Eriostemones T. turkestanica | T. turkestanica A-Zh KZ* | 42.2550 N, 70.2247 E | 1340 m. | Aksu-Zhabagly Nature State Reserve | 14-May-2021 | ON186590 (577 bp) | ON423209 (449 bp) | ON952473 (678 bp) | OP279723 (744 bp) |
Subg. Eriostemones T. bifloriformis | T. bifloriformis A-Zh KZ* | 42.2334 N, 70.3713 E | 1960 m. | Aksu-Zhabagly Nature State Reserve | 15-May-2021 | ON186591 (582 bp) | ON423210 (492 bp) | ON952474 (598 bp) | OQ733258 (607 bp) |
Subg. Eriostemones T. patens | T. patens AKM KZ* | 51.1112 N, 66.4362 E | 272 m. | Akmola Region | 28-Apr-2021 | OP261551 (574 bp) | OQ718219 (520 bp) | OP261547 (865 bp) | OP279727 (725 bp) |
Subg. Tulipa, T. dubia | T. dubia A-Zh KZ* | 42.247 N, 70.3543 E | 1910 m. | Aksu-Zhabagly Nature State Reserve | 18-May-2021 | OP261549 (585 bp) | ON983982 (487 bp) | OQ718220 (818 bp) | OQ733267 (681 bp) |
Subg. Tulipa, T. alberti | T. alberti Karatau KZ* | 43.3816 N, 68.3746 E | 710 m. | Karatau Nature State Reserve | 16-May-2022 | OP261548 (564 bp) | ON983980 (528 bp) | OQ718218 (861 bp) | OP279728 (715 bp) |
Subg. Tulipa, T. schrenkii | T. schrenkii KOS KZ* | 50.2949 N, 65.5801 E | 660 m. | Kostanay region | 18-Aug-2022 | OP261550 (590 bp) | ON983981 (487 bp) | OP261546 (863 bp) | OP279726 (737 bp) |
Parameters | rbcL | matK | ITS |
---|---|---|---|
No. of taxa | 60 | 52 | 65 |
Alignment length (bp) | 471 | 564 | 485 |
Conserved sites | 461 | 542 | 397 |
Variable sites | 10 | 16 | 80 |
Parsimony informative sites | 5 | 6 | 64 |
Singleton sites | 5 | 10 | 16 |
Overall nucleotide divergence (Pi) | 0.002 | 0.007 | 0.05 |
G + C contents (%) | 44.6 | 34.0 | 60.0 |
Species | ITS | rbcL | matK | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
28 | 34 | 53 | 260 | 339 | 350 | 362 | 399 | 405 | 426 | 435 | 441 | 117 | 212 | 255 | 174 | 302 | 314 | |
T. greigii | T | C | A | C | T | C | - | G | T | G | T | A | C | G | A | G | A | A |
T. kaufmanniana | T | T | A | C | T | C | - | G | T | G | T | A | C | G | A | G | A | A |
T. turkestanica | C | T | G | C | T | A | G | G | T | G | A | G | T | A | A | G | G | A |
T. bifloriformis | C | T | G | C | C | A | G | G | T | G | A | G | T | A | G | G | G | A |
T. patens | T | T | A | T | T | C | - | G | T | A | T | A | C | G | A | G | A | A |
T. dubia | T | T | A | C | T | C | - | A | C | G | T | A | T | A | A | A | A | A |
T. alberti | T | T | A | T | T | C | - | G | T | A | T | A | C | G | A | G | A | A |
T. schrenkii | T | T | A | C | T | C | - | A | C | G | T | A | T | A | A | A | A | T |
Primer Name | Nucleotide Sequence of Primer (5′-3′) | Barcoding Locus | Tm (°C) |
---|---|---|---|
3F_KIMf [48] | CGTACAGTACTTTTGTGTTTACGAG | matK | 50 |
1R_KIMr [48] | ACCCCATTCATCTGGAAATCTTGGTTC | matK | 50 |
rbcLa_F [49] | ATGTCACCAACAAACAGAGACTAAAGC | rbcL | 58 |
rbcLa_R [49] | GTAAAATCAAGTCCACCRCG | rbcL | 58 |
psbA3f [50] | GTTATGCATGGTGGATTCACAATCC | trnH-psbA | 53 |
trnHf_05 [50] | CGCGCATGGTGGATTCACAATCC | trnH-psbA | 53 |
ITS4 [51] | TCCTCCGCTTATTGATATGC | ITS1 and ITS2 | 55 |
ITS5 [51] | GGAAGTAAAAGTCGTAACAAG | ITS1 and ITS2 | 55 |
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Sutula, M.; Kakanay, A.; Tussipkan, D.; Dzhumanov, S.; Manabayeva, S. Phylogenetic Analysis of Rare and Endangered Tulipa Species (Liliaceae) of Kazakhstan Based on Universal Barcoding Markers. Biology 2024, 13, 365. https://doi.org/10.3390/biology13060365
Sutula M, Kakanay A, Tussipkan D, Dzhumanov S, Manabayeva S. Phylogenetic Analysis of Rare and Endangered Tulipa Species (Liliaceae) of Kazakhstan Based on Universal Barcoding Markers. Biology. 2024; 13(6):365. https://doi.org/10.3390/biology13060365
Chicago/Turabian StyleSutula, Maxim, Ayan Kakanay, Dilnur Tussipkan, Samatulla Dzhumanov, and Shuga Manabayeva. 2024. "Phylogenetic Analysis of Rare and Endangered Tulipa Species (Liliaceae) of Kazakhstan Based on Universal Barcoding Markers" Biology 13, no. 6: 365. https://doi.org/10.3390/biology13060365