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Barkodlama Bölgesi Olarak Potentilla L. Cinsinde psbA-trnH IGS Sekanslarının Değerlendirmesi

Yıl 2024, Cilt: 27 Sayı: 4, 773 - 781, 15.08.2024

Aykut Yılmaz

https://doi.org/10.18016/ksutarimdoga.vi.1329172

Öz

Potentilla cinsi 400’den fazla türle, morfolojik değişimlere neden olan geniş bir yayılışa sahiptir. Geniş yayılışın yanı sıra, cinsteki hibridizasyon, introgression, otopoliploidi ve allopoliploidi gibi birçok durum gözlemlenir. Bunlar, yanlış tanımlamalara ve taksonomik problemlere yol açabilir. DNA barkodlama çalışmaları, tür tanımlama ve taksonomik problemlerin çözümünde önemlidir. Ancak, tercih edilen DNA sekansları, bitki grupları arasında farklı etkilere sahip olabilir. Bu nedenle, hangi DNA bölgelerinin tercih edilmesi gerektiği daha kapsamlı sonuçlar elde etmek için önemlidir. Bu çalışmada, Potentilla taksonlarına ait psbA-trnH IGS sekansları uyumlulukları açısından incelendi ve variable bölgeler, parsim-info bölgeler ve ilgili bölge için nükleotit frekansları (%) Molecular Evolutionary Genetics Analysis (MEGA 11) kullanılarak analiz edildi. Son olarak, Maximum Parsimony (MP) dendrogram taksonomik ve filogenetik olarak Potentilla taksonlarını değerlendirmek için oluşturuldu. Çalışmanın sonucu olarak Potentilla cinsine ait taksonların dendrogramda iyi gruplandığı ve psbA-trnH IGS sekanslarının daha sonraki çalışmalarda kullanımının fayda sağlayacağı söylenebilir.

Anahtar Kelimeler

Potentilla DNA barkodlama psbA-trnH IGS MEGA 11 Dendrogram

Kaynakça

  • Bean, A. R. (2015). Notes on Potentilla (Rosaceae) and related genera in Australia. Muelleria, 33, 75-83.
  • Dobes, C., & Paule, J. (2010). A comprehensive chloroplast DNA-based phylogeny of the genus Potentilla (Rosaceae): Implications for its geographic origin, phylogeography and generic circumscription. Molecular Phylogenetics and Evolution, 56(1), 156-175. DOI: 10.1016/j.ympev. 2010.03.031
  • Eriksson, T., Lundberg, M., Töpel, M., Östensson, P., & Smedmark, J. E. E. (2015). Sibbaldia: a molecular phylogenetic study of a remarkably polyphyletic genus in Rosaceae. Plant Systematics and Evolution, 301(1), 171-184. DOI: 10.1007/s00606-014-1063-7
  • Eriksson, T., Persson, N. L., & Smedmark, J. E. E. (2022). What is Potentilla? A phylogeny-based taxonomy for Potentillinae (Rosaceae). Taxon, 71(3), 493-505. DOI: 10.1002/tax.12822
  • Feng, T., Moore, M. J., Sun, Y., Meng, A., Chu, H., Li, J., & Wang, H. (2014). A new species of Argentina (Rosaceae, Potentilleae) from Southeast Tibet, concerning the taxonomic status of the genus. Plant Syst Evol, 301(3), 911-921. DOI: 10.1007/s00606-014-1063-7
  • Feng, T., Moore, M. J., Yan, M. H., Sun, Y. X., Zhang, H. J., Meng, A. P., Li, X. D., Jian, S. G., Li, J. Q., & Wang, H. C. (2017). Phylogenetic study of the tribe Potentilla (Rosaceae), with further insight into the disintegration of Sibbaldia. Journal of Systematics and Evolution, 55(3), 177-191. DOI: 10.1111/jse.12233
  • Gontcharov, A. A., Marin, B., & Melkonian, M. (2004). Are Combined Analyses Better Than Single Gene Phylogenies? A Case Study Using SSU rDNA and rbcL Sequence Comparisons in the Zygnematophyceae (Streptophyta). Molecular Biology and Evolution, 21(3), 612-624. DOI: 10.1093/molbev/msh049
  • IPCN. Index to Plant Chromosome Numbers. (1979). In IPCN Database: Goldblatt, P., Johnson, D. E., eds. St. Louis, MO: Missouri Botanical Garden: USA, Available online: www.tropicos.org/project/ ipcn (accessed on 21 June 2023).
  • Kalkman, C. (2004). Potentilla. In: Kubitzki K, ed. Flowering plants-Dicotyledons: Celastrales, Oxalidales, Rosales, Cornales, Ericales. Berlin: Springer, 366.
  • Kechaykin, A. A., Skaptsov, M. V., Smirnov, S. V., Kutsev, M. G., & Shmakov, A. I. (2016). Study of genome size representatives of the genus Potentilla L. (Rosaceae Juss.). Biol. Bull. Bogdan Chmelnitskiy Melitopol State Pedagog. Univ., 6, 229-233.
  • Loera Sanchez, M., Studer, B., & Kölliker, R. (2020). DNA barcode trnH psbA is a promising candidate for the efficient identification of forage legumes and grasses. BMC Research Notes, 13, 35. DOI: 10.1186/s13104-020-4891-y
  • Lundberg, M., Töpel, M., Eriksen, B., Nylander, J. A., & Eriksson, T. (2009). Allopolyploidy in Fragariinae (Rosaceae): Comparing four DNA sequence regions, with comments on classification. Molecular Phylogenetics and Evolution, 51(2), 269-280. DOI: 10.1016/j.ympev.2008.12.003 NCBI, National Centre of Biotechnology Information, https://www.ncbi.nlm.nih.gov/genbank.
  • Paule, J., Sharbel, T. F., & Dobeš, C. (2011). Apomictic and sexual lineages of the Potentilla argentea L. group (Rosaceae): cytotype and molecular genetic differentiation. Taxon, 60, 721-732.
  • Paule, J., Scherbantin, A., & Dobeš, C. (2012). Implications of hybridization and cytotypic differentiation in speciation assessed by AFLP and plastid haplotypes–a case study of Potentilla alpicola La Soie. BMC Evolutionary Biology, 12, 132. DOI: 10.1186/1471-2148-12-132
  • Persson, N. L., Toresen, I., Andersen, H. L., Smedmark, J. E. E., & Eriksson, T. (2020a). Detecting destabilizing species in the phylogenetic backbone of Potentilla (Rosaceae) using low-copy nuclear markers. Annals of Botany Plants, 12(3), plaa017. DOI: 10.1093/aobpla/plaa017
  • Persson, N. L., Eriksson, T., & Smedmark, J. E. E. (2020b). Complex patterns of reticulate evolution in opportunistic weeds (Potentilla L., Rosaceae), as revealed by low-copy nuclear markers. BMC Evolutionary Biology, 20, 38. DOI: 10.1186/s12862-020-01614-w
  • Potter, D., Eriksson, T., Evans, R. C., Oh, S., Smedmark, J. E. E., Morgan, D. R., Kerr, M., Robertson, K. R., Arsenault, M., Dickinson, T. A., & Campbell, C. S. (2007). Phylogeny and classification of Rosaceae. Plant Systematics and Evolution, 266(1-2), 5-43. DOI: 10.1007/s00606-006-0510-2
  • Santos, C., & Pereira, F. (2018). Identification of plant species using variable length chloroplast DNA sequences. Forensic Science International: Genetics, 36, 1-12. DOI: 10.1016/j.fsigen.2018.04.013
  • Schanzer, I. A., Fedorova, A. V., Shelepova, O. V., & Suleymanova, G. F. (2020). Molecular Phylogeny and Phylogeography of Potentilla multifida L. agg. (Rosaceae) in Northern Eurasia with a Special Focus on Two Rare and Critically Endangered Endemic Species, P. volgarica and P. eversmanniana. Plants, 9, 1798. DOI: 10.3390/plants9121798
  • Soják, J. (2008). Notes on Potentilla XXI. A new division of the tribe Potentilla (Rosaceae) and notes on generic delimitations. Botanische Jahrbücher für Systematik, Pflanzengeschichte und Pflanzengeographie, 127(3), 349-358. DOI: 10.1127/0006-8152/2008/0127-0349
  • Sojak, J. (2009). Potentilla (Rosaceae) in the former USSR; second part: comments. Notes on Potentilla XXIV. Feddes Repertorium, 120, 185-217.
  • Sojak, J. (2010). Argentina Hill., a genus distinct from Potentilla (Rosaceae). Thaiszia-J. Bot., 20, 91-97.
  • Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA 11: Molecular Evolutionary Genetics Analysis Version 11. Molecular Biology and Evolution, 38(7), 3022-3027. DOI: 10.1093/molbev/msab121
  • Töpel, M., Lundberg, M., Eriksson, T., & Eriksen, B. (2011). Molecular data and ploidal levels indicate several putative allopolyploidization events in the genus Potentilla (Rosaceae). PLoS Currents, 3, RRN1237. DOI: 10.1371/currents.RRN1237
  • Yılmaz, A., & Yeltekin, Y. (2022). The Evaluations Of Taxonomic Classifications In The Genus Trifolium L. Based On ITS Sequences. Sakarya University Journal of Science, 26(3), 545-553. DOI: 10.16984/saufenbilder.971792
  • Yılmaz, A. (2021). The Evaluations and Comparisons of Nuclear and Chloroplast DNA Regions Based on Species Identification and Phylogenetic Relationships of Crocus L. Taxa. Journal of the Institute of Science and Technology, 11(2), 1504-1518.
  • Yılmaz, A. (2023a). The importance of trnL/trnF IGS region in the taxonomy of the genus Potentilla L. Trakya Univ J Nat Sci, 24(1), 71-76. DOI: 10.33483/trkjnat.101080
  • Yılmaz, A. (2023b). The importance of ITS1-ITS2 sequences in the phylogenetic evaluation of Potentilla L. taxa and comparison of these sequences as noncoding regions. International Studies in Health Sciences. DOI: 10.1016/j.hj.2022.03.005
  • Yılmaz, A. (2023c). Phylogenetic relationships of Potentilla L. taxa based on rbcL sequences. Scope and Importance of Agricultural Studies. DOI: 10.1016/j.hj.2022.03.005.

The Evaluation of psbA-trnH IGS Sequences in The Genus Potentilla L. as Barcoding Region

Yıl 2024, Cilt: 27 Sayı: 4, 773 - 781, 15.08.2024

Aykut Yılmaz

https://doi.org/10.18016/ksutarimdoga.vi.1329172

Öz

With more than 400 species, the genus Potentilla has a wide distribution causing morphological variations. Besides the wide distribution, many conditions such as hybridization, introgression, autopolyploidy, and allopolyploidy are observed in the genus. These can lead to misidentifications and taxonomic problems. DNA barcoding studies are important for species identification and solving taxonomic problems. However, preferred DNA sequences may have different effects among plant groups. Therefore, which DNA regions should be preferred is important to obtain more comprehensive results. In this research, psbA-trnH IGS sequences belonging to the Potentilla taxa were examined based on their compatibility and analyzed variable sites, passim-info sites, and nucleotide frequencies (%) for the region relevant by using Molecular Evolutionary Genetics Analysis (MEGA 11). Finally, a Maximum Parsimony (MP) dendrogram was performed to evaluate the Potentilla taxa taxonomically and phylogenetically. As a result of this study, it can be stated that the taxa belonging to the genus Potentilla were well grouped in the dendrogram and the use of psbA-trnH IGS sequences is strongly recommended for further studies.

Anahtar Kelimeler

Potentilla DNA barcoding psbA-trnH IGS MEGA 11 Dendrogram

Teşekkür

The author would like to thank to NCBI for sequence information used in this study and the authors sharing the sequence informations in NCBI.

Kaynakça

  • Bean, A. R. (2015). Notes on Potentilla (Rosaceae) and related genera in Australia. Muelleria, 33, 75-83.
  • Dobes, C., & Paule, J. (2010). A comprehensive chloroplast DNA-based phylogeny of the genus Potentilla (Rosaceae): Implications for its geographic origin, phylogeography and generic circumscription. Molecular Phylogenetics and Evolution, 56(1), 156-175. DOI: 10.1016/j.ympev. 2010.03.031
  • Eriksson, T., Lundberg, M., Töpel, M., Östensson, P., & Smedmark, J. E. E. (2015). Sibbaldia: a molecular phylogenetic study of a remarkably polyphyletic genus in Rosaceae. Plant Systematics and Evolution, 301(1), 171-184. DOI: 10.1007/s00606-014-1063-7
  • Eriksson, T., Persson, N. L., & Smedmark, J. E. E. (2022). What is Potentilla? A phylogeny-based taxonomy for Potentillinae (Rosaceae). Taxon, 71(3), 493-505. DOI: 10.1002/tax.12822
  • Feng, T., Moore, M. J., Sun, Y., Meng, A., Chu, H., Li, J., & Wang, H. (2014). A new species of Argentina (Rosaceae, Potentilleae) from Southeast Tibet, concerning the taxonomic status of the genus. Plant Syst Evol, 301(3), 911-921. DOI: 10.1007/s00606-014-1063-7
  • Feng, T., Moore, M. J., Yan, M. H., Sun, Y. X., Zhang, H. J., Meng, A. P., Li, X. D., Jian, S. G., Li, J. Q., & Wang, H. C. (2017). Phylogenetic study of the tribe Potentilla (Rosaceae), with further insight into the disintegration of Sibbaldia. Journal of Systematics and Evolution, 55(3), 177-191. DOI: 10.1111/jse.12233
  • Gontcharov, A. A., Marin, B., & Melkonian, M. (2004). Are Combined Analyses Better Than Single Gene Phylogenies? A Case Study Using SSU rDNA and rbcL Sequence Comparisons in the Zygnematophyceae (Streptophyta). Molecular Biology and Evolution, 21(3), 612-624. DOI: 10.1093/molbev/msh049
  • IPCN. Index to Plant Chromosome Numbers. (1979). In IPCN Database: Goldblatt, P., Johnson, D. E., eds. St. Louis, MO: Missouri Botanical Garden: USA, Available online: www.tropicos.org/project/ ipcn (accessed on 21 June 2023).
  • Kalkman, C. (2004). Potentilla. In: Kubitzki K, ed. Flowering plants-Dicotyledons: Celastrales, Oxalidales, Rosales, Cornales, Ericales. Berlin: Springer, 366.
  • Kechaykin, A. A., Skaptsov, M. V., Smirnov, S. V., Kutsev, M. G., & Shmakov, A. I. (2016). Study of genome size representatives of the genus Potentilla L. (Rosaceae Juss.). Biol. Bull. Bogdan Chmelnitskiy Melitopol State Pedagog. Univ., 6, 229-233.
  • Loera Sanchez, M., Studer, B., & Kölliker, R. (2020). DNA barcode trnH psbA is a promising candidate for the efficient identification of forage legumes and grasses. BMC Research Notes, 13, 35. DOI: 10.1186/s13104-020-4891-y
  • Lundberg, M., Töpel, M., Eriksen, B., Nylander, J. A., & Eriksson, T. (2009). Allopolyploidy in Fragariinae (Rosaceae): Comparing four DNA sequence regions, with comments on classification. Molecular Phylogenetics and Evolution, 51(2), 269-280. DOI: 10.1016/j.ympev.2008.12.003 NCBI, National Centre of Biotechnology Information, https://www.ncbi.nlm.nih.gov/genbank.
  • Paule, J., Sharbel, T. F., & Dobeš, C. (2011). Apomictic and sexual lineages of the Potentilla argentea L. group (Rosaceae): cytotype and molecular genetic differentiation. Taxon, 60, 721-732.
  • Paule, J., Scherbantin, A., & Dobeš, C. (2012). Implications of hybridization and cytotypic differentiation in speciation assessed by AFLP and plastid haplotypes–a case study of Potentilla alpicola La Soie. BMC Evolutionary Biology, 12, 132. DOI: 10.1186/1471-2148-12-132
  • Persson, N. L., Toresen, I., Andersen, H. L., Smedmark, J. E. E., & Eriksson, T. (2020a). Detecting destabilizing species in the phylogenetic backbone of Potentilla (Rosaceae) using low-copy nuclear markers. Annals of Botany Plants, 12(3), plaa017. DOI: 10.1093/aobpla/plaa017
  • Persson, N. L., Eriksson, T., & Smedmark, J. E. E. (2020b). Complex patterns of reticulate evolution in opportunistic weeds (Potentilla L., Rosaceae), as revealed by low-copy nuclear markers. BMC Evolutionary Biology, 20, 38. DOI: 10.1186/s12862-020-01614-w
  • Potter, D., Eriksson, T., Evans, R. C., Oh, S., Smedmark, J. E. E., Morgan, D. R., Kerr, M., Robertson, K. R., Arsenault, M., Dickinson, T. A., & Campbell, C. S. (2007). Phylogeny and classification of Rosaceae. Plant Systematics and Evolution, 266(1-2), 5-43. DOI: 10.1007/s00606-006-0510-2
  • Santos, C., & Pereira, F. (2018). Identification of plant species using variable length chloroplast DNA sequences. Forensic Science International: Genetics, 36, 1-12. DOI: 10.1016/j.fsigen.2018.04.013
  • Schanzer, I. A., Fedorova, A. V., Shelepova, O. V., & Suleymanova, G. F. (2020). Molecular Phylogeny and Phylogeography of Potentilla multifida L. agg. (Rosaceae) in Northern Eurasia with a Special Focus on Two Rare and Critically Endangered Endemic Species, P. volgarica and P. eversmanniana. Plants, 9, 1798. DOI: 10.3390/plants9121798
  • Soják, J. (2008). Notes on Potentilla XXI. A new division of the tribe Potentilla (Rosaceae) and notes on generic delimitations. Botanische Jahrbücher für Systematik, Pflanzengeschichte und Pflanzengeographie, 127(3), 349-358. DOI: 10.1127/0006-8152/2008/0127-0349
  • Sojak, J. (2009). Potentilla (Rosaceae) in the former USSR; second part: comments. Notes on Potentilla XXIV. Feddes Repertorium, 120, 185-217.
  • Sojak, J. (2010). Argentina Hill., a genus distinct from Potentilla (Rosaceae). Thaiszia-J. Bot., 20, 91-97.
  • Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA 11: Molecular Evolutionary Genetics Analysis Version 11. Molecular Biology and Evolution, 38(7), 3022-3027. DOI: 10.1093/molbev/msab121
  • Töpel, M., Lundberg, M., Eriksson, T., & Eriksen, B. (2011). Molecular data and ploidal levels indicate several putative allopolyploidization events in the genus Potentilla (Rosaceae). PLoS Currents, 3, RRN1237. DOI: 10.1371/currents.RRN1237
  • Yılmaz, A., & Yeltekin, Y. (2022). The Evaluations Of Taxonomic Classifications In The Genus Trifolium L. Based On ITS Sequences. Sakarya University Journal of Science, 26(3), 545-553. DOI: 10.16984/saufenbilder.971792
  • Yılmaz, A. (2021). The Evaluations and Comparisons of Nuclear and Chloroplast DNA Regions Based on Species Identification and Phylogenetic Relationships of Crocus L. Taxa. Journal of the Institute of Science and Technology, 11(2), 1504-1518.
  • Yılmaz, A. (2023a). The importance of trnL/trnF IGS region in the taxonomy of the genus Potentilla L. Trakya Univ J Nat Sci, 24(1), 71-76. DOI: 10.33483/trkjnat.101080
  • Yılmaz, A. (2023b). The importance of ITS1-ITS2 sequences in the phylogenetic evaluation of Potentilla L. taxa and comparison of these sequences as noncoding regions. International Studies in Health Sciences. DOI: 10.1016/j.hj.2022.03.005
  • Yılmaz, A. (2023c). Phylogenetic relationships of Potentilla L. taxa based on rbcL sequences. Scope and Importance of Agricultural Studies. DOI: 10.1016/j.hj.2022.03.005.
Toplam 29 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Bitki Biyoteknolojisi, Bitki Hücresi ve Moleküler Biyoloji, Bitki Bilimi (Diğer)
Bölüm ARAŞTIRMA MAKALESİ (Research Article)
Yazarlar

Aykut Yılmaz 0000-0002-0327-8388

Erken Görünüm Tarihi 23 Nisan 2024
Yayımlanma Tarihi 15 Ağustos 2024
Gönderilme Tarihi 18 Temmuz 2023
Kabul Tarihi 3 Aralık 2023
Yayımlandığı Sayı Yıl 2024Cilt: 27 Sayı: 4

Kaynak Göster

APA Yılmaz, A. (2024). The Evaluation of psbA-trnH IGS Sequences in The Genus Potentilla L. as Barcoding Region. Kahramanmaraş Sütçü İmam Üniversitesi Tarım Ve Doğa Dergisi, 27(4), 773-781. https://doi.org/10.18016/ksutarimdoga.vi.1329172
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