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Ordu İli Rubus Türlerinin Moleküler Tanısı ve Filogenisi

Year 2018, Volume: 21 Issue: 2, 39 - 46, 29.12.2018

Abstract

Bu çalışmanın amacı, Doğu Karadeniz Bölgesi Ordu ilinin fındık ve boş alanlarında yaygın olarak bulunan yabancı ot
türlerinden biri olan Rubus spp.’nin filogenetik farklılıklarını Ribozomal RNA (rRNA) Internal Transcribed Spacer (ITS)
gen bölgelerini kullanarak belirlemektir. Çalışma için, Ordu ilinden 30 Rubus spp. örnekleri toplanmıştır. DNA izolasyon
prosedürü olan Haymes (1996) CTAB (hexadecyl-trimethyl-ammonium bromide) protokolü modifiye edilerek
uygulanmıştır. Ribozomal RNA (rRNA) ITS gen bölgesi için, GenBankasından temin edilen referans sekans dizileri ile
çalışmada elde edilen sekans sonuçları karşılaştırılmıştır. Dizilerin genetik uzaklıkları MEGA6 paket programı kullanılarak
hesaplanmış ve bu veri setleri ile filogeni ağaçlarının çizimi yapılmıştır. Örnekler arasından (Fatsa 3-F3, Fatsa 6-F6,
Perşembe 2-P2, Perşembe 5-P5, Çamaş 3-CM3, Ordu 1-O1, Saraycık 1-S1, Çatalpınar 1-CT1, Çatalpınar 2-CT2 ve
Çatalpınar 3-CT3) on Rubus türü tespit edilmiştir. Örneklerimizden 6 tane haplotip sonucu çıkmıştır. Bunlardan; Haplotip 1
(F3), Haplotip 3 (P2), Haplotip 4 (P5), Haplotip 5 (CM3, S1) ve Haplotip 6 (O1, CT1, CT2, CT3) %100 nükleotid dizisi
benzerliği bakımından sırasıyla R. sanctus (KM037599), Rubus sp. (KM037207), R. divaricatus (KM037293), R.
conothyrsoides (KM037285) ve R. capricollensis (KM037256) ile yakın akraba olarak belirlenmiştir. Haplotip 2 (F6) ise,
%99,8 nükleotid dizisi benzerliği bakımından R. silvativus (KM037557) ile yakın akraba olarak görülmüştür.

References

  • Ağaoğlu YS. (1986). Üzümsü Meyveler. Ankara Üniversitesi Ziraat Fakültesi Yayınları No: 984 Ders Kitabı No: 290, 377s.
  • Bothmer RV., Jacobsen N., Baden C., Jbrgensen RB., Linde-Laursen I. (1991). An ecogeographical study of the genus Hordeum. Systematic and Ecogeographic Studies on Crop Genepools 7, IBPGR, Rome, 126 pp.
  • Brouat C., Gielly L., Mckey D. (2001). Phylogenetic relationships in the genus Leonardoxa (Leguminosae: Caesalpinioideae) inferred from chloroplast trnL intron and trnL-trnF intergenic spacer sequences. American Journal of Botany, 88: 143- 149.
  • Eck RV., Dayhoff MO. (1966). Atlas of protein sequence and structure. National Biomedical Research Foundation, Silver Spring.
  • Eriksson T., Hibbs MS., Donoghues MJ. (1998). Phylogenetic analysis of Potentilla using DNA sequences of nuclear ribosomal internal transcribed spacers (ITS), and implications for the classification of Rosoideae (Rosaceae). Plant Systematics and Evolution, 211: 155-179.
  • Eriksson T., Hibbs MS., Yoder AD., Delwiche CF., Donoghues MJ. (2003). The Phylogeny of Rosoideae (Rosaceae) based on sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA and the trnL/F region of choloroplast DNA. International Journal of Plant Sciences, 164(2): 197–211.
  • Fitch W. (1977). On the problem of discovering the most parsimonious tree. American Naturalist, 111: 223-257.
  • Hall TA. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symposium Series, 41: 95-98.
  • Haymes KM. (1996). Mini-prep method suitable for a plant breeding program. Plant Molecular Biology Reporter, 14 (3): 280-284.
  • Karakoç D. (2011). Orta ve Doğu Karadeniz Bölgesi Doğal Florasındaki Böğürtlen Genotipleri Arasındaki Biyoçeşitliliğin Moleküler Belirteçlerle Saptanması. Gaziosmanpaşa Üniversitesi Fen Bilimleri Enstitüsü Yüksek Lisans Tezi, Tokat.
  • Longhi S., Giongo L., Buti M., Surbanovski N., Viola R., Velasco R., Ward JA., Sargent DJ. (2014). Molecular genetics and genomics of the Rosoideae: state of theart and future perspectives. Horticulture Research, 1, 2052-7276/14.
  • Onur C. (2006). Üzümsü meyveler ıslah programından sempozyumlara. II. Ulusal Üzümsü Meyveler Sempozyumu, 14-16 Eylül 2006, Tokat.
  • Potter D., Eriksson T., Evans RC., Oh S., Smedmark JEE., Morgan DR., Kerr M., Robertson KR., Arsenault M., Dickinson TA.,
  • Campbell, CS. (2007). Phylogeny and classification of Rosaceae. Plant Systematics and Evolution, 266: 5-43.
  • Saitou N., Nei M. (1987). The Neighbor-Joining method: a new method for reconstructing phylogenetic trees. Molecular Biology Evolution, 4: 406-425.
  • Sochor M., Vasut RJ., Sharbel TF., Travnicek B. (2015). How just a few makes a lot: speciation via reticulation and Apomixis on example of European Brambles (Rubus subgen. Rubus, Rosaceae). Molecular Phylogenetics and Evolution, 89: 13-27.
  • Soejima A., Nagamasu H. (2004). Phylogenetic analysis of Asian Symplocos (Symplocaceae) based on nuclear and chloroplast DNA sequences. Journal of Plant Research, 117(3):199-207.
  • Tamura K., Stecher G., Peterson, D. Filipski A., Kumar S. (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology Evolution, 30: 2725-2729.
  • Thompson JD., Gibson TJ., Plewniak F., Jeanmougin F., Higgins DG. (1997). The clustal x-windows interface: flexible strategies formul tiple sequence alignmentaided by quality analysis tools. Nucleic Acids Research, 25: 4876-4882.

Molecular Diagnosis and Phylogeny of the Rubus Species of Ordu Province

Year 2018, Volume: 21 Issue: 2, 39 - 46, 29.12.2018

Abstract

The aim of this study; identify phylogenetic differences of Rubus spp., which are one of the most common weed species in
the hazelnut and untreated areas of Ordu province in the Eastern Black Sea Region of Turkey, by ITS intergenic spacer. For
this study, 30 population samples were collected from the hazelnut gardens and untreated areas in the Ordu province. DNA
extraction was made by modifying the CTAB (hexadecyl-trimethyl-ammonium bromide) protocol as described by Haymes
(1996). The sequence results in this study were compared with reference sequences from GenBank for the ribosomal RNA
ITS intergenic spacer. Genetic distances for sequences were calculated using MEGA6 packet program and phylogeny trees
were drawn using this date sets. We determined ten Rubus species among our samples (Fatsa 3-F3, Fatsa 6-F6, Persembe 2-
P2, Persembe 5-P5, Camas 3-CM3, Ordu 1-O1, Saraycik 1-S1, Catalpinar 1-CT1, Catalpinar 2-CT2 ve Catalpinar 3-CT3).
Six haplotype were determined. Haplotype I (F3), Haplotype III (P2), Haplotype IV (P5), Haplotype V (CM3, S1) ve
Haplotype VI (O1, CT1, CT2, CT3) appeared as sister R. sanctus (KM037599), Rubus sp. (KM037207), R. divaricatus
(KM037293), R. conothyrsoides (KM037285) and R. capricollensis (KM037256) with 100% nucleotide sequence
similarity. The nucleotide sequence similarity between Haplotype II (F6) with R. capricollensis (KM037256) were 100%.

References

  • Ağaoğlu YS. (1986). Üzümsü Meyveler. Ankara Üniversitesi Ziraat Fakültesi Yayınları No: 984 Ders Kitabı No: 290, 377s.
  • Bothmer RV., Jacobsen N., Baden C., Jbrgensen RB., Linde-Laursen I. (1991). An ecogeographical study of the genus Hordeum. Systematic and Ecogeographic Studies on Crop Genepools 7, IBPGR, Rome, 126 pp.
  • Brouat C., Gielly L., Mckey D. (2001). Phylogenetic relationships in the genus Leonardoxa (Leguminosae: Caesalpinioideae) inferred from chloroplast trnL intron and trnL-trnF intergenic spacer sequences. American Journal of Botany, 88: 143- 149.
  • Eck RV., Dayhoff MO. (1966). Atlas of protein sequence and structure. National Biomedical Research Foundation, Silver Spring.
  • Eriksson T., Hibbs MS., Donoghues MJ. (1998). Phylogenetic analysis of Potentilla using DNA sequences of nuclear ribosomal internal transcribed spacers (ITS), and implications for the classification of Rosoideae (Rosaceae). Plant Systematics and Evolution, 211: 155-179.
  • Eriksson T., Hibbs MS., Yoder AD., Delwiche CF., Donoghues MJ. (2003). The Phylogeny of Rosoideae (Rosaceae) based on sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA and the trnL/F region of choloroplast DNA. International Journal of Plant Sciences, 164(2): 197–211.
  • Fitch W. (1977). On the problem of discovering the most parsimonious tree. American Naturalist, 111: 223-257.
  • Hall TA. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symposium Series, 41: 95-98.
  • Haymes KM. (1996). Mini-prep method suitable for a plant breeding program. Plant Molecular Biology Reporter, 14 (3): 280-284.
  • Karakoç D. (2011). Orta ve Doğu Karadeniz Bölgesi Doğal Florasındaki Böğürtlen Genotipleri Arasındaki Biyoçeşitliliğin Moleküler Belirteçlerle Saptanması. Gaziosmanpaşa Üniversitesi Fen Bilimleri Enstitüsü Yüksek Lisans Tezi, Tokat.
  • Longhi S., Giongo L., Buti M., Surbanovski N., Viola R., Velasco R., Ward JA., Sargent DJ. (2014). Molecular genetics and genomics of the Rosoideae: state of theart and future perspectives. Horticulture Research, 1, 2052-7276/14.
  • Onur C. (2006). Üzümsü meyveler ıslah programından sempozyumlara. II. Ulusal Üzümsü Meyveler Sempozyumu, 14-16 Eylül 2006, Tokat.
  • Potter D., Eriksson T., Evans RC., Oh S., Smedmark JEE., Morgan DR., Kerr M., Robertson KR., Arsenault M., Dickinson TA.,
  • Campbell, CS. (2007). Phylogeny and classification of Rosaceae. Plant Systematics and Evolution, 266: 5-43.
  • Saitou N., Nei M. (1987). The Neighbor-Joining method: a new method for reconstructing phylogenetic trees. Molecular Biology Evolution, 4: 406-425.
  • Sochor M., Vasut RJ., Sharbel TF., Travnicek B. (2015). How just a few makes a lot: speciation via reticulation and Apomixis on example of European Brambles (Rubus subgen. Rubus, Rosaceae). Molecular Phylogenetics and Evolution, 89: 13-27.
  • Soejima A., Nagamasu H. (2004). Phylogenetic analysis of Asian Symplocos (Symplocaceae) based on nuclear and chloroplast DNA sequences. Journal of Plant Research, 117(3):199-207.
  • Tamura K., Stecher G., Peterson, D. Filipski A., Kumar S. (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology Evolution, 30: 2725-2729.
  • Thompson JD., Gibson TJ., Plewniak F., Jeanmougin F., Higgins DG. (1997). The clustal x-windows interface: flexible strategies formul tiple sequence alignmentaided by quality analysis tools. Nucleic Acids Research, 25: 4876-4882.
There are 19 citations in total.

Details

Primary Language Turkish
Journal Section Research Article
Authors

Onur Kolören This is me

Seçil Eker

Publication Date December 29, 2018
Acceptance Date November 29, 2018
Published in Issue Year 2018 Volume: 21 Issue: 2

Cite

APA Kolören, O., & Eker, S. (2018). Ordu İli Rubus Türlerinin Moleküler Tanısı ve Filogenisi. Turkish Journal of Weed Science, 21(2), 39-46.

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