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Journals / Turkish Journal of Bioscience and Collections / 2023 / Volume: 7 Issue: 2

Genetic Structure and Phylogenetic Analysis of Liquidambar orientalis Mill. (Altingiaceae) Populations Based on Non-Coded psaA/ycf3 Intergenic Region in The Chloroplast Genome in Türkiye

Taylan Doğaroğlu(Muğla Sıtkı Koçman University, Ula Vocational School, Department of Bee Breeding)0000-0002-4671-1372
Evin Günenç(Muğla Sıtkı Koçman University, Institue of Science, Department of Molecular Biology and Genetics)0000-0001-6201-1256
Rumeysa Yeşim Manap(Muğla Sıtkı Koçman University, Institue of Science, Department of Molecular Biology and Genetics)0000-0003-4975-7234
Vatan Taşkın(Muğla Sıtkı Koçman University, Faculty of Science, Department of Biology)0000-0002-5122-0885
Belgin Göçmen Taşkın(Muğla Sıtkı Koçman University, Faculty of Science, Department of Biology)0000-0003-1239-5751
Ersin Doğaç(Muğla Sıtkı Koçman University, Institue of Science, Department of Molecular Biology and Genetics)0000-0003-4426-2187
Pages
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Publication Date
2023-09-07
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AI Summary & Key Takeaways

AI Insight
⚡ TL;DR(Too Long; Didn't Read)

According to the results of our research, the gene flow level (Nm) among the populations was 1.40.

📌 3 Key Takeaways

🎯
Objective & Hypothesis:Objective: The genus Liquidambar, is one of many woody genera with morphologically similar species in America, Southeast Europe, and Asia and is thought to have existed on Earth for about 65 million years.
📊
Key Findings & Data:With this study, it was aimed to reveal the sequence differences of the psaA/ycf3 inter-gene space region of chloroplast DNA (cpDNA) in L. orientalis populations for the first time in the scientific literature.
💡
Conclusion & Impact:According to the results of our research, the gene flow level (Nm) among the populations was 1.40.
🔬Design:Research Article
📍Scope:154 samples
⚙️Variables:Liquidambar · Sweetgum tree · cpDNA

Abstract

Objective: The genus Liquidambar, is one of many woody genera with morphologically similar species in America, Southeast Europe, and Asia and is thought to have existed on Earth for about 65 million years. Liquidambar orientalis (Anatolian sweetgum tree) is distributed in southwestern Türkiye. With this study, it was aimed to reveal the sequence differences of the psaA/ycf3 inter-gene space region of chloroplast DNA (cpDNA) in L. orientalis populations for the first time in the scientific literature. Materials and Methods: In addition, the polymorphism levels, and the molecular evolution of the studied gene region of the L. orientalis populations were investigated. 154 samples were collected from 12 different populations belonging to four provinces, Muğla, Burdur, Antalya, and Aydın, and were studied and the psaA/ycf3 gene encoded by chloroplast DNA was analysed by partial base sequence analysis. Results: Haplotype diversity (h) and the average nucleotide diversity (π) values for all populations were found to be 0.52933 ± 0.011, and 0.00086 ± 0.0001, respectively. According to the results of our research, the gene flow level (Nm) among the populations was 1.40. FST values revealed statistically significant genetic differences between the Fethiye-Yanıklar population of Muğla province and other studied populations. Conclusion: According to the results of the study, Fethiye-Yanıklar, Marmaris-National Park, and Fethiye-İnlice locations, where the highest genetic diversities detected among the studied populations, were found to be important in terms of conservation studies.

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Cite This Article

Doğaroğlu, T., Günenç, E., Manap, R. Y., Taşkın, V., Taşkın, B. G., Doğaç, E. (2023). Genetic Structure and Phylogenetic Analysis of Liquidambar orientalis Mill. (Altingiaceae) Populations Based on Non-Coded psaA/ycf3 Intergenic Region in The Chloroplast Genome in Türkiye. Turkish Journal of Bioscience and Collections, Volume: 7 Issue: 2. https://doi.org/10.26650/tjbc.1327318

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References (71)

  1. Acar, M.I., (1989). (Liquidambar orientalis Mill.) Balsamı (sığla yağı) eterik yağının gc-ms-ds sistemi ile analiz edilerek birleşiminin belirlenmesi. Ormancılık Enstitüsü Yayınları, Teknik Raporlar Serisi, 33, 5-21. google scholar
  2. Acatay, A., (1963). Sığla Ağacı (Liquidambar orientalis Mill.)’nın Türkiye’de yayılışı, yeni tespit edilen Liquidambar orientalis (var. suber) varyetesi ve sığla ağacına musallat olan böcekler. İstanbul Üniversitesi Orman Fakültesi Dergisi, Seri A, 8(2), 40-56. google scholar
  3. Akman, Y., Ketenoğlu, O. & Kurt, L. (1992). Fethiye-Marmaris ve Bucak çevrelerinde yetişen Liquidambar orientalis mill. topluluklarının floristik yapısı. Turkish Journal Botany, 16, 273-86. google scholar
  4. Alan, M. & Kaya, Z. (2003). EUFORGEN-Technical Guidelines for genetic conservation and use for oriental sweet gum (Liquidambar orientalis). Bioversity International. https://doi. org/10.31195/ejejfs.1132874 google scholar
  5. Arslan, M.B. & Şahin, H.T. (2016). Unutulan bir orman ürünü kaynağı: Anadolu sığla ağacı (Liquidambar orientalis Miller). Bartın Orman Fakültesi Dergisi, 18(1), 103-117 google scholar
  6. Atay, I. (1985). Sığla ağacının (Liquidambar orientalis mill.) önemi ve sivikültürel özellikleri. İstanbul Üniversitesi Orman Fakültesi Dergisi, 35, 15-21. google scholar
  7. Aydıngöz, M. & Bulut, S. (2014). Egenin gizli kalmış şifa iksiri: sığla. Afyon Kocatepe Üniversitesi Fen ve Mühendislik Bilimleri Dergisi, 012201, 1-6. google scholar
  8. Bandelt, H.J., Forster, P. & Rohl, A. (1999). Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37-48. https://doi.org/10.1093/oxfordjoumals. molbev.a026036 google scholar
  9. Beatty, G. E. & Provan, J. I. M. (2010). Refugial persistence and postglacial recolonization ofNorth America by the cold-tolerant herbaceous plant Orthilia secunda. Molecular Ecology, 19(22), 5009-5021. https://doi.org/10.1111/j.1365-294X.2010.04859.x google scholar
  10. Beaumont, M. & Wang, J. (2019). Conservation Genetics In: D. Balding, I. Moltke, J. Marioni (Ed.), Handbook of Statistical Genomics: Two Volume Set, 4th edn. Wiley, (pp 457-500). Oxford, https://doi.org/10.1002/9781119487845.ch16 google scholar
  11. Bozkurt, Y., Göker, Y. & Kurtoğlu, A. (1989). Sığla ağacının bazı özellikleri. Journal of the Faculty of Forestry Istanbul University, 39(1), 43-52. google scholar
  12. Crawford, D.J., Stuessy, T.F., Haines, D.W., Cosner, M.B., O., M.S. & Lopez, P. (1992). Allozyme diversity within and divergence among four species of Robinsonia (Asteraceae: Senecioneae), a genus endemic to the juan Fernandez islands, Chile. American Journal of Botany, 79, 962-966. https://doi. org/10.1002/j.1537-2197.1992.tb13680.x google scholar
  13. Doğaç, E. 2008. Türkiye’deki relikt endemik sığla ağacı (Liquidambar orientalis Mill. var. orientalis ve L. orientalis Mill. var. integriloba fiori) populasyonlarındaki genetik çeşitliliğin RAPD (Rastgele Üretilen Polimorfik DNA) belirteçleri yardımıyla belirlenmesi. Master’s Dissertation, Muğla Sıtkı Koçman University. google scholar
  14. Doyle, J. J. & Doyle, J. L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 19, 11-15. google scholar
  15. Durkovic, J. & Lux, A. (2010). Micropropagation with a novel pattern of adventitious rooting in American sweetgum (Liquidambar styraciflua L.). Trees, 24, 491-497. https://doi.org/10.1007/ s00468-010-0418-9 google scholar
  16. Efe, A. (1987). Liquidambar orientalis Mill. (Sığla Ağacı)’ın morfolojik ve palinolojik özellikleri üzerine araştırmalar. Journal of the Faculty of Forestry Istanbul University, 37(2), 273-286. google scholar
  17. Excoffier, L., Laval, G. & Schneider, S. (2007). ARLEQUIN (ver. 3.0): An integrated software package for population genetics data analysis. Evolutionary Bioinformatics, 1, 47-50. google scholar
  18. Frankham, R. (2019). Conservation Genetics. In: B. Fath (Ed.) Encyclopedia of Ecology, 2nd edn. Elsevier. https://doi. org/10.1016/B978-0-12-409548-9.10559-7 google scholar
  19. Günal, N. (1994). Liquidambar orientalis (Anadolu Sığla Ağacı)’İn Güneybatı Anadolu’daki yayılışında relief, iklim ilişkileri. Turkish Geographical Review, 29, 175-190. google scholar
  20. Günal, N. (2006). Aksu Çayının orta kesimindeki sığla (Liquidambar orientalis) Toplulukları. Turkish Geographical Review, 46, 41-48. google scholar
  21. Hamrick, J., Godt, M. & Shermen-Broyless, S. (1990). Factors influencing levels of genetic diversity in woody plant species. New Forests, 6, 95-124. https://doi.org/10.1007/BF00120641 google scholar
  22. Hedrick P. W. (2001). Conservation genetics: where are we now? Trends in Ecology & Evolution, 16(11), 629-636. https://doi. org/10.1016/S0169-5347(01)02282-0 google scholar
  23. Hedrick, P.W. & Hurt, C.R. (2012). Conservation genetics and evolution in an endangered species: research in Sonoran topminnows. Evolutionary Applications, 5(8), 806-19. https:// doi.org/10.1111/j.1752-4571.2012.00259.x google scholar
  24. Hoey, M. T. & Parks, C. R. (1990). Isozyme inheritance in the genus Liquidambar L. Journal of Heredity, 81(5), 393-397. https:// doi.org/10.1093/oxfordjournals.jhered.a111007 google scholar
  25. Hoey, M.T. & Parks, C.R. (1991). Isozyme divergence between eastern Asian, North American, and Turkish species of Liquidambar (Hamamelidaceae). American Journal of Botany, 78, 938-947. https://doi.org/10.1002/j.15372197.1991.tb14497.x google scholar
  26. Hoey, M.T. & Parks, C.R. (1994). Genetic Divergence in Liquidambar styraciflua, L. formosana, and L. acalycina (Hamamelidaceae). Systematic Botany, 19(2), 308-316. https:// doi.org/10.2307/2419604 google scholar
  27. Hristova, V, Ivanov D. (2009). Palynological data of the fossil flora from Sofia neogene basin (southwest Bulgaria)-Preliminary results. C R Academia Bulgare Science, 62(3), 379-3 84. google scholar
  28. Huş, S. (1949). Sığla Ağacı’nın (Liquidambar orientalis Mill) ormancılık bakımından önemi ve sığla yağının kimyasal araştırılması. Orman Genel Müdürlüğü Yayınları, Istanbul. google scholar
  29. Ickert-Bond, S. M., Pigg, K. B. & Wen, J. (2005). Comparative infructescence morphology in Liquidambar (Altingiaceae) and its evolutionary significance. American Journal of Botany, 92(8), 1234-1255. https://doi.org/10.3732/ajb.92.8.1234 google scholar
  30. Ickert-Bond, S.M. & Wen, J. (2006). Phylogeny and biogeography of Altingiaceae: evidence from combined analysis of five non-coding chloroplast regions. Molecular Phylogenetics and Evolution, 39, 512-528. https://doi.org/10.1016/j. ympev.2005.12.003 google scholar
  31. İstek, A. & Hafızoğlu, H. (1998). Sığla Ağacı (Liquidambar orientalis Mill.) odununun anatomik özelliklerinin belirlenmesi. Z.K.Ü. Bartın Orman. Fakültesi Dergisi, 1, ISSN 1302-0056. google scholar
  32. Jiao, Z. & Li, J. (2009). Phylogenetics and biogeography of eastern Asian- North American disjunct genus Pachysandra (Buxaceae) inferred from nucleotide sequences. Journal of Systematics and Evolution, 47(3), 191-201. https://doi.org/10.1111/j.1759-6831.2009.00021.x google scholar
  33. Joannin, S., Quillevere, F., Suc, J.P., Lecuyer, C. & Martineau, F. (2007). Early Pleistocene climate changes in the central Mediterranean region as inferred from integrated pollen and planktonie foraminiferal stable isotope analyses. Quaternary Research, 67, 264-274. https://doi.org/10.1016/j. yqres.2006.11.001 google scholar
  34. Kasapligil, B. (1976). Late tertiary cone bearing-green leaved forests around Guvem Village Near Kizilcahamam. MTA Report, Ankara. google scholar
  35. Kramer, A.T. & Havens, K. (2009). Plant conservation genetics in a changing world. Trends in Plant Science, 14(11), 599-607. https://doi.org/10.1016/j.tplants.2009.08.005. google scholar
  36. Kumar, S., Stecher, G. & Tamura, K. (2016). MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870-1874. https:// doi.org/10.1093/molbev/msw054 google scholar
  37. Li, J. & Donoghue, M.J. (1999). More molecular evidence for interspecific relationships in Liquidambar (Hamamelidaceae). Rhodora, 101, 87-91. google scholar
  38. Li, J., Bogle, A.L. & Klein, A.S. (1997a). Interspecific relationships and genetic divergence of the disjunct genus Liquidambar (Hamamelidaceae) inferred from DNA sequences of plastid gene MatK. Rhodora, 99(899), 229-240. google scholar
  39. Li, J., Bogle, A.L. & Klein, A.S. (1997b). Phylogenetic relationships of the Hamamelidaceae inferred from sequences of internal transcribed spacers (ITS) of nuclear ribosomal DNA. American Journal ofBotany, 86, 1027-1037. google scholar
  40. Librado, P. & Rozas, J. (2009). DnaSP v5: A Software for Comprehensive Analysis of DNA Polymorphism Data, Bioinformatics, 25, 1451-1452. https://doi.org/10.1093/ bioinformatics/btp187 google scholar
  41. Milne, R.I. (2004). Phylogeny and biogeography of Rhododendron subsection Pontica, a group with a Tertiary relict distribution. Molecular Phylogenetics and Evolution, 33, 389-401. https:// doi.org/10.1016/j.ympev.2004.06.009 google scholar
  42. Moritz, C. (1999). Conservation units and translocations: Strategies for conserving evolutionary processes. Hereditas, 130, 217-228. https://doi.org/10.1111/j.1601-5223.1999.00217.x google scholar
  43. Nei, M. (1987). Molecular Evolutionary Genetics. Columbia university press. google scholar
  44. Or, M. 2007. Kloroplast genomundaki kodlanmayan trn bölgelerinin karşılaştırılması yapılarak Liquidambar orientalis mill. varyetelerinin filogenetik analizi. Master’s Dissertation. Middle East Technical University. google scholar
  45. Örtel, E. (1988). Sığla ormanlarımızın durumu. Turkish Journal of Forestry Research, 68, 93-96. google scholar
  46. Ouborg, N.J., Pertoldi, C., Loeschcke, V., Bijlsma, R. & Hedrick, P.W. (2010). Conservation genetics in transition to conservation genomics. Trends in Genetics, 26(4), 177-187. https://doi. org/10.1016/j.tig.2010.01.001 google scholar
  47. Özdilek, A. 2007. Kloroplast genomundaki matK gen bölgesine göre Liquidambar orientalis mill. varyetelerinin genetik farklılaşması. Master’s Dissertation. Middle East Technical University. google scholar
  48. Özdilek, A., Cengel, B., Kandemir, G., Tayanc, Y., Velioğlu, E. & Kaya, Z. (2012). Molecular phylogeny of relict-endemic Liquidambar orientalis Mill based on sequence diversity of the chloroplast-encoded matK gene. Plant Systematics and Evolution, 298, 337-349. https://doi.org/10.1007/s00606-011-0548-6 google scholar
  49. Öztürk, E. 2008. Türkiye’deki relikt endemik sığla ağacı (Liquidambar orientalis Mill. var orientalis ve L. orientalis Mill. var. integriloba Fiori) populasyonlarında izoenzim polimorfizminin polyakrilamid jel elektroforezi (page) yöntemi ile saptanması. Master’s Dissertation, Muğla Sıtkı Koçman University. google scholar
  50. Pauls, S.U., Nowak, C., Balint, M. & Pfenninger, M. (2013). The impact of global climate change on genetic diversity within populations and species. Molecular Ecology, 22, 925-946. https://doi.org/10.1111/mec.12152 google scholar
  51. Polzin, T. & Daneschmand, S.V. (2003). On steiner trees and minimum spanning trees in hypergraphs. Operations Research Letters, 31, 12-20. https://doi.org/10.1016/S0167-6377(02)00185-2 google scholar
  52. Sadori, L., Giardini, M., Chiarini, E., Mattei, M., Papasodaro, F. & Porreca, M. (2010). Pollen and macrofossil analyses of Pliocene lacustrine sediments (Saltoriver valley, Central Italy). Quaternary International, 225, 44-57. https://doi.org/10.1016/j. quaint.2009.05.008 google scholar
  53. Sakala, J. & Prive-Gill, C. (2004). Oligocene angiosperm woods from northwestern Bohemia, Czech Republic. IAWA Journal, 25(3), 369-380. https://doi.org/10.1163/22941932-90000372 google scholar
  54. Schmickl, R., Jorgensen, M.H., Brysting, A.K. & Koch, M.A. (2010). The evolutionary history of the Arabidobsis lyrata complex: a hybrid in the amphi-Beringian area closes a large distribution gap and builds up a genetic barrier. BMC Evolutionary Biology, 10, 98. https://doi.org/10.1186/1471-2148-10-98 google scholar
  55. Shi, S., Chang, H. T., Chen, Y., Qu, L. & Wen, J. (1998). Phylogeny of the Hamamelidaceae based on the ITS sequences of nuclear ribosomal DNA. Biochemical Systematics and Ecology, 26(1), 55-69. https://doi.org/10.1016/S0305-1978(97)00075-6 google scholar
  56. Shi, S., Huang, Y., Zhong, Y., Du, Y., Zhang, Q., Chang, H. & Boufford, D.E. (2001). Phylogeny of the Altingiaceae based on cpDNA matK PY-IGS and nrDNA ITS sequences. Plant Systematics and Evolution, 230, 13-24. https://doi.org/10.1007/ s006060170002 google scholar
  57. Sun, R., Lin, F., Huang, P., Ye, X., Lai, J. & Zheng, Y. (2019). Phylogeographical structure of Liquidambar formosana hance revealed by chloroplast phylogeography and species distribution models. Forests, 10(10), 858. https://doi.org/10.3390/f10100858 google scholar
  58. Thorpe, J. P. (1982). The molecular clock hypothesis: biochemical evolution, genetic differentiation and systematics. Annual Review of Ecology and Systematics, 13(1), 139-168. https:// doi.org/10.1146/annurev.es.13.110182.001035 google scholar
  59. Tiffney, B.H. (1985). The Eocene of North Atlantic land bridge: its importance in Tertiary and modern phytogeography of the northern hemisphere. Journal of the Arnold Arboretum, 66, 24373. google scholar
  60. Tiffney, B.H. (2000). Geographic and climatic influence on the Creataceous and Tertiary history of Euroamerican floristic similarity. Acta Universitatis Carolinae, Geologica, 44, 5-16. google scholar
  61. Tong, Y.W., Lewis, B.J., Zhou, W.M., Mao, C.R., Wang, Y., Zhou, L., Yu, D.P., Dai, L.M. & Qi, L. (2020). Genetic diversity and population structure of natural Pinus koraiensis populations. Forests, 11(1), 39. https://doi.org/10.3390/f11010039 google scholar
  62. Ürker, O., Yılmaz, T., Öztürk, Ş., & Çobanoğlu, N. (2014). Anadolu Sığla Ormanları’nın Çevre Sosyolojisi Kapsamında İncelenmesi. Sosyoloji Araştırmaları Dergisi, 17(2). google scholar
  63. Velioğlu, E., Kandemir, G., Tayanç, Y., Çengel, B., Alan, M. & Kaya, Z. (2008). Türkiye’deki sığla (Liquidambar orientalis Mill.) populasyonlarının genetik yapısının moleküler belirteçlerle belirlenmesi ve koruma stratejileri geliştirilmesi. Orman Ağaçları ve Tohumları Islah Araştırma Müdürlüğü, Technical Bulletin, 20, 43. google scholar
  64. Wang, G., Yang, Z., Chen, P. & Lu, C. (2020). Differences in seedling distribution patterns between wind-dispersed Liquidambar formosana and rodent-dispersed Quercus acutissima. Pakistan Journal of Botany, 52(2). http://dx.doi.org/10.30848/PJB2020-2(39) google scholar
  65. Wen, J. (1999). Evolution of eastern Asian and eastern North American disjunct distributions in flowering plants. Annual Review of Ecology, 30, 421-455. google scholar
  66. Wen, J. & Zimmer, E.A. (1996). Phylogeny and biogeography of Panax L. (the ginseng genus, Araliaceae): inferences from ITS sequences of nuclear ribosomal DNA. Molecular Phylogenetics and Evolution, 6(2), 167-77. https://doi.org/10.1006/ mpev.1996.0069 google scholar
  67. Willi, Y., Kristensen, T.N., Sgro, C.M., Weeks, A.R., 0rsted, M. & Hoffmann, A.A. (2022). Conservation genetics as a management tool: The five best-supported paradigms to assist the management of threatened species. Proceedings of the National Academy of Sciences, 119(1), e2105076119. https:// doi.org/10.1073/pnas.2105076119 google scholar
  68. Witzenberger, K.A. & Hochkirch, A. (2011). Ex situ conservation genetics: a review of molecular studies on the genetic consequences of captive breeding programmes for endangered animal species. Biodiversity and Conservation, 20, 1843-1861. https://doi.org/10.1007/s10531-011-0074-4 google scholar
  69. Worobic, E. & Gedl, P. (2010). Spore-pollen and phytoplankton analysis of the upper Miocene deposits from Jefina (Krakow-Silesia Upland, Poland). Geological Quarterly, 54(1), 41-53. google scholar
  70. Wright, S. (1931). Evolution in Mendelian populations. Genetics, 16, 97-159. https://doi.Org/10.1093/genetics/16.2.97 google scholar
  71. Yüzer, Ö. (2019). Muğla iline ait Liquidambar orientalis Mill. popülasyonlarının genetik çeşitliliğinin ISSR belirteçleri kullanılarak belirlenmesi. Master’s Dissertation. Muğla Sıtkı Koçman University. google scholar