Research Article
BibTex RIS Cite

Genetic Diversity Analysis of cpDNA in Turkish Abies Taxa

Year 2021, Volume: 21 Issue: 1, 41 - 54, 03.04.2021
https://doi.org/10.17475/kastorman.908630

Abstract

Aim of study: Five Abies taxa naturally distributed in Turkey. Abies nordmanniana has three subspecies and A. cilica has two subspecies. In this study, we aimed to show phylogenetic relationships both in Turkish taxa and in other Abies taxa from around the world based on cpDNA regions, trnR-trnN and rps18-rpl20 regions.
Material and methods: Following CTAB-based DNA isolation method, the relevant fir DNA regions were amplified and sequenced. Phylogenetic trees were constructed using maximum likelihood method with 1000 bootstrap replicates.
Main results: It was difficult to make distinctions among the Turkish Abies taxa based on the sequenced DNA regions. Based on rps18-rpl20 phylogenetic tree, some members of Abies cilicica subsp. isaurica, A. nordmanniana subsp. equi-trojani and A. cilicica subsp. cilicica were in the same clade with A. spectabilis and A. densa; However, some members of A. nordmanniana subsp. bornmuelleriana, A. cilicica subsp. isaurica and A. nordmanniana subsp. equi-trojani were placed in a clade with A. alba placed near Turkey and A. amabilis known from North America.
Highlights: This study provides new insights into the distribution of cpDNA variation in Abies species in Turkey and the genetic variation between firs in Turkey and the rest of the world.

Supporting Institution

Kastamonu University, Scientific Research Projects Coordination Department.

Project Number

KÜBAP-01/2012-11

References

  • Aguirre-Planter, É., Jaramillo-Correa, J. P., Gómez-Acevedo, S., Khasa, D. P., Bousquet, J. & Eguiarte, L. E. (2012). Phylogeny, diversification rates and species boundaries of Mesoamerican firs (Abies, Pinaceae) in a genus-wide context. Molecular Phylogenetics and Evolution, 62(1), 263-274.
  • Ateş, M. A. (2011). Molecular phylogenetics of Turkish Abies (pinaceae) species based on matK gene regions of chloroplast genome (Master's thesis, Dept. of Biological Sciences, Middle East Technical University, Ankara).
  • Davis, P. (1985). PH 1965-1985. Flora of Turkey and the East Aegean Islands. 1-9. Edinburg: Edinburgh University Press.
  • Fady, B., Arbez, M. & Marpeau, A. (1992). Geographic variability of terpene composition in Abies cephalonica Loudon and Abies species around the Aegean: hypotheses for their possible phylogeny from the Miocene. Trees-Structure and Function, 6(3), 162-171.
  • Farjon, A. (1990). Pinaceae. Drawings and descriptions of the genera Abies, Cedrus, Pseudolarix, Keteleeria, Nothotsuga, Tsuga, Cathaya, Pseudotsuga, Larix and Picea. Königstein: Koeltz Scientific Books.
  • Gülbaba, A. G., Velioğlu, E., Özer, A. S., Doğan, B., Doerksen, A. H. & Adams, W. T. (1996). Population Genetic Structure of Kazdağı Fir (Abies equitrojani Aschers et Sint.), A Narrow Endemic to Turkey: Implications for in situ Conservation. In Proceedings of the International Symposium of In situ Conservation of Plant Genetic Diversity.
  • Güner, A., Özhatay, N., Ekim, T. & Başer, H. K. C. (2000). Flora of Turkey and East Aegean Islands: v.11 Supplement 2. Edinburgh: Edinburgh University Press.
  • Güner, A., Aslan, S., Ekim, T., Vural, M. & Babaç, M. (2012). Turkey plant list (vascular plants). İstanbul: Nezahat Gökyiğit Botanical Garden and Flora Research Association Publication.
  • Hansen, O. K., Kjær, E. D. & Vendramin, G. (2005). Chloroplast microsatellite variation in Abies nordmanniana and simulation of causes for low differentiation among populations. Tree Genetics & Genomes, 1(3), 116-123.
  • Hrivnák, M., Paule, L., Krajmerová, D., Kulaç, Ş., Şevik, H., Turna, İ., ... & Gömöry, D. (2017). Genetic variation in Tertiary relics: The case of eastern‐Mediterranean Abies (Pinaceae). Ecology and Evolution, 7(23), 10018-10030.
  • Isoda, K., Shiraishi, S. & Kisanuki, H. (2000). Classifying Abies species (Pinaceae) based on the sequence variation of a tandemly repeated array found in the chloroplast DNA trnL and trnF intergenic spacer. Silvae Genetica, 49(3), 161-164.
  • Kaya, Z., Skaggs, A. & Neale, D. B. (2008). Genetic Differentiation of Abies equi-trojani (Asch. & Sint. ex Boiss) Mattf. populations from Kazdağı, Turkey and the genetic relationship between Turkish Firs belonging to the Abies nordmanniana Spach Complex. Turkish Journal of Botany, 32(1), 1-10.
  • Kormutak, A., Vookova, B., Ziegenhagen, B., Kwon, H. Y. & Hong, Y. P. (2004). Chloroplast DNA variation in some representatives of the Asian, North American and Mediterranean firs (Abies spp). Silvae Genetica, 53(1-6), 99-104.
  • Letunic, I. & Bork, P. (2016). Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Research, 44(1), 242-245.
  • Li, H.L. (1975). Flora of Taiwan, Epoch publishing, 2, 316p., Taiwan.
  • Liang, H. (2003). The Phylogenetic Reconstruction of the grass family (Poaceae) using matK gene sequences (Doctoral dissertation, Virginia Polytechnic Institute, Blacksburg).
  • Özdemir Değirmenci, F. (2011). Molecular phylogenetic position of Turkish abies (pinaceae) based on noncoding trn regions of chloroplast genome (Master's thesis, Dept. of Biological Sciences, Middle East Technical University, Ankara).
  • Parducci, L. & Szmidt, A. (1999). PCR-RFLP analysis of cpDNA in the genus Abies. TAG Theoretical and Applied Genetics, 98(5), 802-808.
  • Saghai-Maroof, M.A., Soliman, K.M., Jorgensen, R.A. & Allard, R. (1984). Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proceedings of the National Academy of Sciences, 81(24), 8014-8018.
  • Semerikova, S.A., Semerikov, V.L. & Lascoux, M. (2011). Post‐glacial history and introgression in Abies (Pinaceae) species of the Russian Far East inferred from both nuclear and cytoplasmic markers. Journal of Biogeography, 38(2), 326-340.
  • Semerikova, S.A. & Semerikov, V.L. (2014). Molecular phylogenetic analysis of the genus Abies (Pinaceae) based on the nucleotide sequence of chloroplast DNA. Russian Journal of Genetics, 50(1), 7-19.
  • Suyama, Y., Yoshimaru, H. & Tsumura, Y. (2000). Molecular phylogenetic position of Japanese Abies (Pinaceae) based on chloroplast DNA sequences. Molecular Phylogenetics and Evolution, 16(2), 271-277.
  • Şimşek, Y. (1992). Türkiye Orijinli Göknar Türlerinin Genetik Yapıları Üzerine Araştırmalar. Ormancılık Araştırma Enstitüsü, Teknik Bülten Serisi (221).
  • Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30(12), 2725-2729.
  • Tayanç, Y., Çengel, B., Kandemir, G. & Velioğlu, E. (2013). Türkiye’de Yayılış Gösteren Göknar (Abies spp.) Populasyonlarının Genetik Çeşitliliği ve Filogenetik Sınıflandırması. Orman Genel Müdürlüğü Orman Ağaçları ve Tohumları Islah Araştırma Enstitüsü Müdürlüğü Yayınları, (47).
  • Tozkar, C.Ö., Önde, S. & Kaya, Z. (2009). The phylogenetic relationship between populations of marginally and sympatrically located Pinus halepensis Mill. and Pinus brutia Ten. in Turkey, based on the ITS-2 region. Turkish Journal of Agriculture and Forestry, 33(4), 363-373.
  • Wang, X.R., Tsumura, Y., Yoshimaru, H., Nagasaka, K. & Szmidt, A.E. (1999). Phylogenetic relationships of Eurasian pines (Pinus, Pinaceae) based on chloroplast rbcL, matK, rpl20‐rps18 spacer, and trnV intron sequences. American Journal of Botany, 86(12), 1742-1753.
  • Xiang, Q.P., Xiang, Q.Y., Guo, Y.Y. & Zhang, X.C. (2009). Phylogeny of Abies (Pinaceae) inferred from nrITS sequence data. Taxon, 58(1), 141-152.
  • Xiang, Q.P., Xiang, Q.Y., Liston, A. & Zhang, X.C. (2004). Phylogenetic relationships in Abies (Pinaceae): evidence from PCR-RFLP of the nuclear ribosomal DNA internal transcribed spacer region. Botanical Journal of the Linnean Society, 145(4), 425-435.
  • Ziegenhagen, B., Fady, B., Kuhlenkamp, V. & Liepelt, S. (2005). Differentiating groups of Abies species with a simple molecular marker. Silvae Genetica, 54(1-6), 123-126.

Türk Göknar Taksonlarında Genetik Çeşitlilik Analizleri

Year 2021, Volume: 21 Issue: 1, 41 - 54, 03.04.2021
https://doi.org/10.17475/kastorman.908630

Abstract

Çalışmanın amacı: Beş Abies taksonu Türkiye'de doğal olarak dağılmıştır. Abies nordmanniana' nın üç alt türü ve A. cilica 'nın iki alt türü vardır. Bu çalışmada, cpDNA bölgeleri, trnR-trnN ve rps18-rpl20 bölgelerine göre hem Türk taksonlarında hem de dünyanın diğer Abies taksonlarında filogenetik ilişkileri göstermeyi amaçladık.
Materyal ve yöntem: CTAB metodu ile DNA izolasyonunun ardından ilgili göknar DNA bölgeleri çoğaltılmış ve dizilenmiştir. Filogenetik ağaçlar, 1000 tekrarlı maximum likelihood (maksimum olabilirlik) yöntemi kullanılarak oluşturulmuştur.
Temel sonuçlar: Türkiye’deki göknar taksonları arasında bu bölgeler bakımından ayrım yapmak zor gözükmektedir. rps18-rpl20 dizileri temelindeki filogenetik ağaca dayanarak, bazı Abies cilicica subsp. isaurica, A. nordmanniana subsp. equi-trojani ve A. cilicica subsp. cilicica üyeleri A. spectabilis ve A. densa ile aynı sınıfta yer alırken, bazı A. nordmanniana subsp. bornmulleriana, A. cilicica subsp. isaurica ve A. nordmanniana subsp. equi-trojani üyeleri ise Türkiye’ye yakın yayılış gösteren A. alba ve Kuzey Amerika’da yayılışı bilinen A. amabilis ile aynı sınıfta yer almıştır.
Araştırma Vurguları: Mevcut çalışma, Türkiye’deki göknar türleri arasında cpDNA çeşitliliğinin dağılımına ve Türkiye göknarları ile dünyada yayılış gösteren diğer göknar türleri arasındaki genetik çeşitliliğe yeni bir ışık tutmaktadır.

Project Number

KÜBAP-01/2012-11

References

  • Aguirre-Planter, É., Jaramillo-Correa, J. P., Gómez-Acevedo, S., Khasa, D. P., Bousquet, J. & Eguiarte, L. E. (2012). Phylogeny, diversification rates and species boundaries of Mesoamerican firs (Abies, Pinaceae) in a genus-wide context. Molecular Phylogenetics and Evolution, 62(1), 263-274.
  • Ateş, M. A. (2011). Molecular phylogenetics of Turkish Abies (pinaceae) species based on matK gene regions of chloroplast genome (Master's thesis, Dept. of Biological Sciences, Middle East Technical University, Ankara).
  • Davis, P. (1985). PH 1965-1985. Flora of Turkey and the East Aegean Islands. 1-9. Edinburg: Edinburgh University Press.
  • Fady, B., Arbez, M. & Marpeau, A. (1992). Geographic variability of terpene composition in Abies cephalonica Loudon and Abies species around the Aegean: hypotheses for their possible phylogeny from the Miocene. Trees-Structure and Function, 6(3), 162-171.
  • Farjon, A. (1990). Pinaceae. Drawings and descriptions of the genera Abies, Cedrus, Pseudolarix, Keteleeria, Nothotsuga, Tsuga, Cathaya, Pseudotsuga, Larix and Picea. Königstein: Koeltz Scientific Books.
  • Gülbaba, A. G., Velioğlu, E., Özer, A. S., Doğan, B., Doerksen, A. H. & Adams, W. T. (1996). Population Genetic Structure of Kazdağı Fir (Abies equitrojani Aschers et Sint.), A Narrow Endemic to Turkey: Implications for in situ Conservation. In Proceedings of the International Symposium of In situ Conservation of Plant Genetic Diversity.
  • Güner, A., Özhatay, N., Ekim, T. & Başer, H. K. C. (2000). Flora of Turkey and East Aegean Islands: v.11 Supplement 2. Edinburgh: Edinburgh University Press.
  • Güner, A., Aslan, S., Ekim, T., Vural, M. & Babaç, M. (2012). Turkey plant list (vascular plants). İstanbul: Nezahat Gökyiğit Botanical Garden and Flora Research Association Publication.
  • Hansen, O. K., Kjær, E. D. & Vendramin, G. (2005). Chloroplast microsatellite variation in Abies nordmanniana and simulation of causes for low differentiation among populations. Tree Genetics & Genomes, 1(3), 116-123.
  • Hrivnák, M., Paule, L., Krajmerová, D., Kulaç, Ş., Şevik, H., Turna, İ., ... & Gömöry, D. (2017). Genetic variation in Tertiary relics: The case of eastern‐Mediterranean Abies (Pinaceae). Ecology and Evolution, 7(23), 10018-10030.
  • Isoda, K., Shiraishi, S. & Kisanuki, H. (2000). Classifying Abies species (Pinaceae) based on the sequence variation of a tandemly repeated array found in the chloroplast DNA trnL and trnF intergenic spacer. Silvae Genetica, 49(3), 161-164.
  • Kaya, Z., Skaggs, A. & Neale, D. B. (2008). Genetic Differentiation of Abies equi-trojani (Asch. & Sint. ex Boiss) Mattf. populations from Kazdağı, Turkey and the genetic relationship between Turkish Firs belonging to the Abies nordmanniana Spach Complex. Turkish Journal of Botany, 32(1), 1-10.
  • Kormutak, A., Vookova, B., Ziegenhagen, B., Kwon, H. Y. & Hong, Y. P. (2004). Chloroplast DNA variation in some representatives of the Asian, North American and Mediterranean firs (Abies spp). Silvae Genetica, 53(1-6), 99-104.
  • Letunic, I. & Bork, P. (2016). Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Research, 44(1), 242-245.
  • Li, H.L. (1975). Flora of Taiwan, Epoch publishing, 2, 316p., Taiwan.
  • Liang, H. (2003). The Phylogenetic Reconstruction of the grass family (Poaceae) using matK gene sequences (Doctoral dissertation, Virginia Polytechnic Institute, Blacksburg).
  • Özdemir Değirmenci, F. (2011). Molecular phylogenetic position of Turkish abies (pinaceae) based on noncoding trn regions of chloroplast genome (Master's thesis, Dept. of Biological Sciences, Middle East Technical University, Ankara).
  • Parducci, L. & Szmidt, A. (1999). PCR-RFLP analysis of cpDNA in the genus Abies. TAG Theoretical and Applied Genetics, 98(5), 802-808.
  • Saghai-Maroof, M.A., Soliman, K.M., Jorgensen, R.A. & Allard, R. (1984). Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proceedings of the National Academy of Sciences, 81(24), 8014-8018.
  • Semerikova, S.A., Semerikov, V.L. & Lascoux, M. (2011). Post‐glacial history and introgression in Abies (Pinaceae) species of the Russian Far East inferred from both nuclear and cytoplasmic markers. Journal of Biogeography, 38(2), 326-340.
  • Semerikova, S.A. & Semerikov, V.L. (2014). Molecular phylogenetic analysis of the genus Abies (Pinaceae) based on the nucleotide sequence of chloroplast DNA. Russian Journal of Genetics, 50(1), 7-19.
  • Suyama, Y., Yoshimaru, H. & Tsumura, Y. (2000). Molecular phylogenetic position of Japanese Abies (Pinaceae) based on chloroplast DNA sequences. Molecular Phylogenetics and Evolution, 16(2), 271-277.
  • Şimşek, Y. (1992). Türkiye Orijinli Göknar Türlerinin Genetik Yapıları Üzerine Araştırmalar. Ormancılık Araştırma Enstitüsü, Teknik Bülten Serisi (221).
  • Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30(12), 2725-2729.
  • Tayanç, Y., Çengel, B., Kandemir, G. & Velioğlu, E. (2013). Türkiye’de Yayılış Gösteren Göknar (Abies spp.) Populasyonlarının Genetik Çeşitliliği ve Filogenetik Sınıflandırması. Orman Genel Müdürlüğü Orman Ağaçları ve Tohumları Islah Araştırma Enstitüsü Müdürlüğü Yayınları, (47).
  • Tozkar, C.Ö., Önde, S. & Kaya, Z. (2009). The phylogenetic relationship between populations of marginally and sympatrically located Pinus halepensis Mill. and Pinus brutia Ten. in Turkey, based on the ITS-2 region. Turkish Journal of Agriculture and Forestry, 33(4), 363-373.
  • Wang, X.R., Tsumura, Y., Yoshimaru, H., Nagasaka, K. & Szmidt, A.E. (1999). Phylogenetic relationships of Eurasian pines (Pinus, Pinaceae) based on chloroplast rbcL, matK, rpl20‐rps18 spacer, and trnV intron sequences. American Journal of Botany, 86(12), 1742-1753.
  • Xiang, Q.P., Xiang, Q.Y., Guo, Y.Y. & Zhang, X.C. (2009). Phylogeny of Abies (Pinaceae) inferred from nrITS sequence data. Taxon, 58(1), 141-152.
  • Xiang, Q.P., Xiang, Q.Y., Liston, A. & Zhang, X.C. (2004). Phylogenetic relationships in Abies (Pinaceae): evidence from PCR-RFLP of the nuclear ribosomal DNA internal transcribed spacer region. Botanical Journal of the Linnean Society, 145(4), 425-435.
  • Ziegenhagen, B., Fady, B., Kuhlenkamp, V. & Liepelt, S. (2005). Differentiating groups of Abies species with a simple molecular marker. Silvae Genetica, 54(1-6), 123-126.
There are 30 citations in total.

Details

Primary Language English
Journal Section Articles
Authors

Yasemin Celık Altunoglu This is me 0000-0003-2940-7464

Kerim Güney This is me 0000-0003-2305-790X

Pınar Baloglu This is me 0000-0002-1575-8071

Mehmet Baloglu This is me 0000-0003-2976-7224

Project Number KÜBAP-01/2012-11
Publication Date April 3, 2021
Published in Issue Year 2021 Volume: 21 Issue: 1

Cite

APA Celık Altunoglu, Y., Güney, K., Baloglu, P., Baloglu, M. (2021). Genetic Diversity Analysis of cpDNA in Turkish Abies Taxa. Kastamonu University Journal of Forestry Faculty, 21(1), 41-54. https://doi.org/10.17475/kastorman.908630
AMA Celık Altunoglu Y, Güney K, Baloglu P, Baloglu M. Genetic Diversity Analysis of cpDNA in Turkish Abies Taxa. Kastamonu University Journal of Forestry Faculty. April 2021;21(1):41-54. doi:10.17475/kastorman.908630
Chicago Celık Altunoglu, Yasemin, Kerim Güney, Pınar Baloglu, and Mehmet Baloglu. “Genetic Diversity Analysis of CpDNA in Turkish Abies Taxa”. Kastamonu University Journal of Forestry Faculty 21, no. 1 (April 2021): 41-54. https://doi.org/10.17475/kastorman.908630.
EndNote Celık Altunoglu Y, Güney K, Baloglu P, Baloglu M (April 1, 2021) Genetic Diversity Analysis of cpDNA in Turkish Abies Taxa. Kastamonu University Journal of Forestry Faculty 21 1 41–54.
IEEE Y. Celık Altunoglu, K. Güney, P. Baloglu, and M. Baloglu, “Genetic Diversity Analysis of cpDNA in Turkish Abies Taxa”, Kastamonu University Journal of Forestry Faculty, vol. 21, no. 1, pp. 41–54, 2021, doi: 10.17475/kastorman.908630.
ISNAD Celık Altunoglu, Yasemin et al. “Genetic Diversity Analysis of CpDNA in Turkish Abies Taxa”. Kastamonu University Journal of Forestry Faculty 21/1 (April 2021), 41-54. https://doi.org/10.17475/kastorman.908630.
JAMA Celık Altunoglu Y, Güney K, Baloglu P, Baloglu M. Genetic Diversity Analysis of cpDNA in Turkish Abies Taxa. Kastamonu University Journal of Forestry Faculty. 2021;21:41–54.
MLA Celık Altunoglu, Yasemin et al. “Genetic Diversity Analysis of CpDNA in Turkish Abies Taxa”. Kastamonu University Journal of Forestry Faculty, vol. 21, no. 1, 2021, pp. 41-54, doi:10.17475/kastorman.908630.
Vancouver Celık Altunoglu Y, Güney K, Baloglu P, Baloglu M. Genetic Diversity Analysis of cpDNA in Turkish Abies Taxa. Kastamonu University Journal of Forestry Faculty. 2021;21(1):41-54.

14178  14179       14165           14166           14167            14168