Molecular phylogenetic analysis of Tulipa (Liliaceae) from Aksu-Zhabagly Nature Reserve
DOI:
https://doi.org/10.14719/pst.2153Keywords:
Tulipa, Phylogeny, ITS, matK, ycf1Abstract
Barcodes are conserved sequences of genomic, plastid and mitochondrial DNA that can be utilized to uniquely identify an unidentified specimen to its species when conventional identification methods are inapplicable. Among prokaryotic and eukaryotic species, nuclear ribosomal internal transcribed spacer (ITS) sections are one of the most often utilized DNA markers in DNA barcoding and phylogenetic research. In addition to the ribosomal genes, the plastid genes are the most suitable for identifying plant species. The Aksu-Zhabagly Nature Reserve is the oldest nature reserve in Central Asia and is home to 1,312 vascular plant species, 44 of which are categorized as threatened or endangered in Kazakhstan's red data book. In this study, a collection of specimens of uncommon tulip species was compiled, along with their morphological identification and DNA barcoding. The ITS region and parts of the matK and ycf1b genes of tulip plastid DNA were sequenced. The evolutionary link between species of tulips was investigated. Phylogenetic study predicted two Tulipa subclades. Tulipa species have substantially preserved MatK genes. Tulips' ycf1b gene has evolved more slowly than other Liliaceae family members. Nuclear and plastid DNA sequences investigated Tulipa species evolutionary relationships. The findings about the ITS region of nuclear DNA were more definite. Overall, our work shows that genetic data will be important in determining species concepts in this genus, however, even with a molecular perspective pulling apart closely related taxa can be extremely challenging.
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References
Smith WW. The Genus Tulipa. Nature. 1940; 1940/09/01;146(3699): pp. 379-80. https://doi.org/10.1038/146379a0.
Christenhusz MJM, Govaerts R, David JC, Hall T, Borland K, Roberts PS et al. Tiptoe through the tulips - cultural history, molecular phylogenetics and classification of Tulipa (Liliaceae). Botanical Journal of the Linnean Society. 2013; 07/01;172(3): pp. 280-328. https://doi.org/10.1111/boj.12061.
Raamsdonk LWDv, Vries Td. Biosystematic studies in Tulipa sect.Eriostemones (Liliaceae). Plant Systematics and Evolution. 2004;179pp. 27-41. https://doi.org/10.1007/BF00938017.
Raamsdonk LWD, Vries Td. Species relationships and taxonomy in Tulipa subg. Tulipa (Liliaceae). Plant Systematics and Evolution. 2004;195pp. 13-44. https://doi.org/10.1007/BF00982313.
Zarrei M, Wilkin P, Ingrouille M, Leitch I, Buerki S, Fay M et al. Speciation and evolution in the Gagea reticulata species complex (Tulipeae; Liliaceae). Molecular phylogenetics and evolution. 2011; 11/17;62pp. 624-39. https://doi.org/10.1016/j.ympev.2011.11.003.
Kiani M, Memariani F, Zarghami H. Molecular analysis of species of Tulipa L. from Iran based on ISSR markers. Plant Systematics and Evolution. 2012; 10/01;298pp. https://doi.org/10.1007/s00606-012-0654-0.
Morgil H, ?ik L, Erol O. Genetic diversity by AFLP analysis within Tulipa orphanidea L. (Liliaceae) populations in Manisa. Celal Bayar University Journal of Science. 2017; 11/21;13pp. 913-17. https://doi.org/10.18466/cbayarfbe.334831.
Hebert PD, Cywinska A, Ball SL, deWaard JR. Biological identifications through DNA barcodes. Proceedings Biological sciences. 2003 Feb 7;270(1512): pp. 313-21. PubMed PMID: 12614582. Pubmed Central PMCID: PMC1691236. https://doi.org/10.1098/rspb.2002.2218.
de Vere N, Rich T, Trinder S, Long C. DNA barcoding for plants. Methods in molecular biology (Clifton, NJ). 2015; 01/01;1245pp. 101-18. https://doi.org/10.1007/978-1-4939-1966-6_8.
Ahrens D, Monaghan MT, Vogler AP. DNA-based taxonomy for associating adults and larvae in multi-species assemblages of chafers (Coleoptera: Scarabaeidae). Mol Phylogenet Evol. 2007; Jul;44(1): pp. 436-49. PubMed PMID: 17420144. https://doi.org/10.1016/j.ympev.2007.02.024.
Kesanakurti PR, Fazekas AJ, Burgess KS, Percy DM, Newmaster SG, Graham SW et al. Spatial patterns of plant diversity below-ground as revealed by DNA barcoding. Molecular ecology. 2011 Mar;20(6): pp. 1289-302. PubMed PMID: 21255172. https://doi.org/10.1111/j.1365-294X.2010.04989.x.
Hollingsworth PM, Graham SW, Little DP. Choosing and Using a Plant DNA Barcode. PloS one. 2011;6(5): pp. https://doi.org/10.1371/journal.pone.0019254.
de Groot GA, During HJ, Maas JW, Schneider H, Vogel JC, Erkens RHJ. Use of rbcL and trnL-F as a Two-Locus DNA Barcode for Identification of NW-European Ferns: An Ecological Perspective. PloS one. 2011;6(1): pp. e16371. https://doi.org/10.1371/journal.pone.0016371.
Ebihara A, Nitta JH, Ito M. Molecular Species Identification with Rich Floristic Sampling: DNA Barcoding the Pteridophyte Flora of Japan. PloS one. 2010;5(12): pp. e15136. https://doi.org/10.1371/journal.pone.0015136.
Li F-W, Kuo L-Y, Rothfels CJ, Ebihara A, Chiou W-L, Windham MD et al. rbcL and matK Earn Two Thumbs Up as the Core DNA Barcode for Ferns. PloS one. 2011;6(10): pp. e26597. https://doi.org/10.1371/journal.pone.0026597.
Nitta JH. Exploring the utility of three plastid loci for biocoding the filmy ferns (Hymenophyllaceae) of Moorea. TAXON. 2008;57(3): pp. 725-36. https://doi.org/10.1002/tax.573006.
Mes THM, Kuperus P, Kirschner J, Stepanek J, Oosterveld P, Storchová H, et al. Hairpins involving both inverted and direct repeats are associated with homoplasious indels in non-coding chloroplast DNA of Taraxacum (Lactuceae: Asteraceae). Genome / National Research Council Canada = Génome / Conseil national de recherches Canada. 2000; 09/01;43pp. 634-41. https://doi.org/10.1139/g99-135.
Navarro F, Suárez-Santiago VN, Blanca G. A new species of Haplophyllum A. Juss. (Rutaceae) from the Iberian Peninsula: evidence from morphological, karyological and molecular analyses. Annals of Botany. 2004;94 4pp. 571-82. https://doi.org/10.1093/aob/mch176.
Alvarez I, Wendel JF. Ribosomal ITS sequences and plant phylogenetic inference. Mol Phylogenet Evol. 2003 Dec;29(3): pp. 417-34. PubMed PMID: 14615184. https://doi.org/10.1016/s1055-7903(03)00208-2.
Turktas M, Metin ÖK, Ba?tu? B, Ertu?rul F, Saraç YI, Kaya E. Molecular phylogenetic analysis of Tulipa (Liliaceae) based on noncoding plastid and nuclear DNA sequences with an emphasis on Turkey. Botanical Journal of the Linnean Society. 2013; 2013/04/25;172(3): pp. 270-79. https://doi.org/10.1111/boj.12040.
Kalendar R, Boronnikova S, Seppänen M. Isolation and Purification of DNA from Complicated Biological Samples. In: Besse P, editor. Molecular Plant Taxonomy: Methods and Protocols. New York, NY: Springer US; 2021; p. 57-67. https://doi.org/10.1007/978-1-0716-0997-2_3
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. Journal of Molecular Biology. 1990 Oct 5;215(3): pp. 403-10. PubMed PMID: 2231712. https://doi.org/10.1016/s0022-2836(05)80360-2.
Tamura K, Stecher G, Kumar S. MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution. 2021;38(7): pp. 3022-27. https://doi.org/10.1093/molbev/msab120.
Lewin B. Chromatin and gene expression: constant questions, but changing answers. Cell. 1994 Nov 4;79(3): pp. 397-406. PubMed PMID: 7954807. https://doi.org/10.1016/0092-8674(94)90249-6.
Baldwin B, Sanderson M, Porter J, Wojciechowski M, Campbell C, Donoghue M. The its Region of Nuclear Ribosomal DNA: A Valuable Source of Evidence on Angiosperm Phylogeny. Annals of the Missouri Botanical Garden. 1995; 01/01;82pp. 247. https://doi.org/10.2307/2399880.
Nieto Feliner G, Rosselló JA. Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Mol Phylogenet Evol. 2007 Aug;44(2): pp. 911-19. PubMed PMID: 17383902. https://doi.org/10.1016/j.ympev.2007.01.013.
Schultz J, Müller T, Achtziger M, Seibel PN, Dandekar T, Wolf M. The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses. Nucleic Acids Research. 2006 Jul 1;34(Web Server issue), pp. W704-07. PubMed PMID: 16845103. Pubmed Central PMCID: PMC1538906. https://doi.org/10.1093/nar/gkl129.
Drouin G, Daoud H, Xia J. Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants. Mol Phylogenet Evol. 2008 Dec;49(3): pp. 827-31. PubMed PMID: 18838124. https://doi.org/10.1016/j.ympev.2008.09.009.
Dubouzet JG, Shinoda K. Phylogenetic analysis of the internal transcribed spacer region of Japanese Lilium species. Theoretical and Applied Genetics. 1999;98pp. 954-60. https://doi.org/10.1007/s001220051155.
Cronn RC, Small RL, Haselkorn TS, Wendel JF. Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes. American Journal of Botany. 2002;89 4pp. 707-25. https://doi.org/10.3732/ajb.89.4.707.
Fazekas AJ, Burgess KS, Kesanakurti PR, Graham SW, Newmaster SG, Husband BC et al. Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. PloS one. 2008 Jul 30;3(7): pp. e2802. PubMed PMID: 18665273. Pubmed Central PMCID: PMC2475660. https://doi.org/10.1371/journal.pone.0002802.
Chase MW, Knapp S, Cox AV, Clarkson JJ, Butsko Y, Joseph J et al. Molecular systematics, GISH and the origin of hybrid taxa in Nicotiana (Solanaceae). Ann Bot. 2003 Jul;92(1): pp. 107-27. PubMed PMID: 12824072. Pubmed Central PMCID: PMC4243627. https://doi.org/10.1093/aob/mcg087.
Neuhaus H, Link G. The chloroplast tRNALys(UUU) gene from mustard (Sinapis alba) contains a class II intron potentially coding for a maturase-related polypeptide. Current Genetics. 1987;11(4): pp. 251-57. PubMed PMID: 2834093. https://doi.org/10.1007/bf00355398.
Hilu KW, Borsch T, Müller K, Soltis DE, Soltis PS, Savolainen V et al. Angiosperm phylogeny based on matK sequence information. Am J Bot. 2003 Dec;90(12): pp. 1758-76. PubMed PMID: 21653353. https://doi.org/10.3732/ajb.90.12.1758.
Müller KF, Borsch T, Hilu KW. Phylogenetic utility of rapidly evolving DNA at high taxonomical levels: contrasting matK, trnT-F and rbcL in basal angiosperms. Mol Phylogenet Evol. 2006 Oct;41(1): pp. 99-117. PubMed PMID: 16904914. https://doi.org/10.1016/j.ympev.2006.06.017.
Chase MW, Cowan RS, Hollingsworth PM, van den Berg C, Madrinan S, Petersen G et al. A proposal for a standardised protocol to barcode all land plants. Taxon. 2007 May;56(2): pp. 295-99. PubMed PMID: WOS:000247420000004. https://doi.org/10.1002/tax.562004.
Lahaye R, van der Bank M, Bogarin D, Warner J, Pupulin F, Gigot G, et al. DNA barcoding the floras of biodiversity hotspots. Proceedings of the National Academy of Sciences of the United States of America. 2008 Feb 26;105(8): pp. 2923-28. PubMed PMID: 18258745. Pubmed Central PMCID: PMC2268561. https://doi.org/10.1073/pnas.0709936105.
Qiu YL, Lee J, Bernasconi-Quadroni F, Soltis DE, Soltis PS, Zanis M et al. The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes. Nature. 1999 Nov 25;402(6760): pp. 404-47. PubMed PMID: 10586879. https://doi.org/10.1038/46536.
Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics (Oxford, England). 2009 Jun 1;25(11): pp. 1451-52. PubMed PMID: 19346325. https://doi.org/10.1093/bioinformatics/btp187.
Hausner G, Olson R, Simon D, Johnson I, Sanders ER, Karol KG et al. Origin and evolution of the chloroplast trnK (matK) intron: a model for evolution of group II intron RNA structures. Mol Biol Evol. 2006 Feb;23(2): pp. 380-91. PubMed PMID: 16267141. https://doi.org/10.1093/molbev/msj047.
Xiao-Xian L, Zhe-Kun Z. The higher-level phylogeny of monocots based on matK, rbcL and 18S rDNA sequences. Journal of Systematics and Evolution. 2007;45(2): pp. 113-33. https://doi.org/10.1360/aps06148.
Ya-Ling W, Yong L, Shou-Zhou Z, Xing-Sheng Y. The utility of matK gene in the phylogenetic analysis of the genus Magnolia. Journal of Systematics and Evolution. 2006;44(2): pp. 135-47. https://doi.org/10.1360/aps040013.
YU J, XUE J-H, ZHOU S-L. New universal matK primers for DNA barcoding angiosperms. Journal of Systematics and Evolution. 2011;49(3): pp. 176-81. https://doi.org/10.1111/j.1759-6831.2011.00134.x.
Kikuchi S, Bédard J, Hirano M, Hirabayashi Y, Oishi M, Imai M et al. Uncovering the protein translocon at the chloroplast inner envelope membrane. Science. 2013;339(6119): pp. 571-74. https://doi.org/10.1126/science.1229262.
Oliver MJ, Murdock AG, Mishler BD, Kuehl JV, Boore JL, Mandoli DF et al. Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes. BMC genomics. 2010;11(1): pp. 1-8. https://doi.org/10.1186/1471-2164-11-143.
Wolf PG, Der JP, Duffy AM, Davidson JB, Grusz AL, Pryer KM. The evolution of chloroplast genes and genomes in ferns. Plant Molecular Biology. 2011;76(3): pp. 251-61. https://doi.org/10.1007/s11103-010-9706-4.
Neubig KM, Whitten WM, Carlsward BS, Blanco MA, Endara L, Williams NH et al. Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK. Plant Systematics and Evolution. 2009;277(1): pp. 75-84. https://doi.org/10.1007/s00606-008-0105-0.
Gernandt DS, Hernández-León S, Salgado-Hernández E, Pérez de La Rosa JA. Phylogenetic relationships of Pinus subsection Ponderosae inferred from rapidly evolving cpDNA regions. Systematic Botany. 2009;34(3): pp. 481-91. https://doi.org/10.1600/036364409789271290.
Drew BT, Sytsma KJ. The South American radiation of Lepechinia (Lamiaceae): phylogenetics, divergence times and evolution of dioecy. Botanical Journal of the Linnean Society. 2013;171(1): pp. 171-90. https://doi.org/10.1111/j.1095-8339.2012.01325.x.
Dong W, Liu J, Yu J, Wang L, Zhou S. Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PloS one. 2012;7(4): pp. e35071. https://doi.org/10.1371/journal.pone.0035071.
Dong W, Xu C, Li C, Sun J, Zuo Y, Shi S et al. ycf1, the most promising plastid DNA barcode of land plants. Scientific Reports. 2015 2015/02/12;5(1): pp. 8348. https://doi.org/10.1038/srep08348.
Doyle JJ. Gene Trees and Species Trees: Molecular Systematics as One-Character Taxonomy. Systematic Botany. 1992;17pp. 144-63. https://doi.org/10.2307/2419070.
Potter D, Luby JJ, Harrison RE. Phylogenetic relationships among species of Fragaria (Rosaceae) inferred from non-coding nuclear and chloroplast DNA sequences. Systematic Botany. 2000;25(2): pp. 337-48, 12. https://doi.org/10.2307/2666646
Everett D, Fay MF, Christenhusz MJM, Wilford R, Royal Botanic Gardens K. The Genus Tulipa: Tulips of the World: Kew Publishing; 2013.
Raamsdonk LWD, Eikelboom W, Vries Td, Straathof TP editors. The systematics of the genus Tulipa 11997.
Cheng T, Xu C, Lei L, Li C, Zhang Y, Zhou S. Barcoding the Kingdom Plantae: New PCR primers for ITS regions of plants with improved universality and specificity. Molecular Ecology Resources. 2015; 07/03pp. https://doi.org/10.1111/1755-0998.12438.
Kalendar R. A guide to using FASTPCR software for PCR, in silico PCR and oligonucleotide analysis. In: Basu C editor. PCR Primer Design. New York, NY: Springer US; 2022; p. 223-43. https://doi.org/10.1007/978-1-0716-1799-1_16
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