Analysis of the Variations Within Quercus ilex L. and the Evaluation of Morphological Types Based on Chloroplast and Nuclear DNA Sequences

Aykut Yılmaz

doi:10.18016/ksutarimdoga.vi.1478950

EN TR

Analysis of the Variations Within Quercus ilex L. and the Evaluation of Morphological Types Based on Chloroplast and Nuclear DNA Sequences

Abstract

Quercus ilex, evaluated within evergreen oaks, has a wide geographic distribution in the Mediterranean basin. Hybridization and gene flow are effective and frequently observed mechanisms in Q. ilex. Additionally, weak reproductive barriers between closely related taxa in zones of geographical contact further increase genetic diversity and subsequent taxonomic problems. Two morphological types, known as rotundifolia and ilex, are defined based on the variations between Q. ilex populations appearing as a result of all these factors. However, it is still controversial whether morphological types: ilex and rotundifolia are subspecies of Q. ilex or two separate species. In this study, short DNA sequences that consist of matK gene-partial trnK gene intron of chloroplast DNA and ITS1-5.8S rRNA gene-ITS2 of nuclear DNA were used to overcome such difficulties and to reveal the variations between Q. ilex populations. All Q. ilex populations based on both barcoding regions were determined and examined using the Molecular Evolutionary Genetics Analysis (MEGA 11). The analysis such as base substitutions, variable and parsim-info sites, transitional and transversional base substitution ranges (%), and nucleotide frequencies (%) was performed and transitional substitutions according to the transversional substitutions for both barcoding regions were observed in the high-value. Furthermore, the sequences belonging to nuclear DNA in comparison to other barcoding regions exhibited higher variable and parsim-info sites. Finally, Maximum Parsimony (MP) dendrograms for both barcoding regions were drawn to evaluate the populations belonging to Q. ilex in terms of their variations, phylogenetic-evolutionary relationships, and taxonomic status. Although both barcoding regions support the separation of Q. ilex populations based on different morphological types, matK gene-partial trnK gene intron sequences exhibited clearer and more informative results than ITS1-5.8S rRNA gene-ITS2 sequences.

Keywords

Quercus ilex L. Içerisindeki Varyasyonlarin Analizi ve Kloroplast ve Nükleer DNA Sekanslari Temelinde Morfolojik Tiplerin Değerlendirmesi

Öz

Herdem yeşil meşeler içerisinde değerlendirilen Quercus ilex, Akdeniz temelinde geniş coğrafik dağılıma sahiptir. Hibridizasyon ve gen akışı Q. ilex’de etkili ve sıklıkla gözlenen mekanizmalardır. Ayrıca, coğrafik olarak temaslı bölgelerde, yakın ilişkili taksonlar arasında zayıf üreme bariyerleri, Q. ilex içerisindeki genetik çeşitliliği ve sonrasında taksonomik problemleri arttıran diğer bir önemli durumdur. Rotundifolia ve ilex olarak bilinen iki morfolojik tip, tüm bu faktörlerin sonucu olarak ortaya çıkan, Q. ilex populasyonları arasındaki varyasyonlar temelinde tanımlanır. Ancak, morfolojik tipler: ilex ve rotundifolia nın Q. ilex’in alttürlerimi yoksa iki ayrı türmü olup olmadığı hala tartışmalı durumdur. Bu çalışmada, kloroplast DNA’ya ait matK geni-kısmi trnK gen intronu ve nükleer DNA’ya ait ITS1-5.8S rRNA geni-ITS2 den oluşan kısa DNA sekansları, bu tarz zorlukların üstesinden gelmek ve Q. ilex populasyonları arasındaki varyasyonları ortaya çıkarmak için kullanıldı. Q. ilex’e ait tüm populasyonlar heriki barkodlama bölgesi temelinde belirlendi ve Molecular Evolutionary Genetics Analysis (MEGA 11) kullanarak incelendi. Baz değişimleri, varyasyonlu ve parsim info bölgeler, transisyonel ve transversiyonel baz değişim oranları (%) ve nükleotid frekansları (%) gibi analizler gerçekleştirildi ve her iki barkodlama bölgesi için transisyonel baz değişimlerinin transversiyonel değişimlere göre daha yüksek değerde olduğu gözlemlendi. Ayrıca, nükleer DNA’ya ait sekanslar diğer barkodlama bölgesi ile karşılaştırmada daha yüksek varyasyonlu ve parsim info bölgeler sergiledi. Son olarak her iki barkodlama bölgesi için Maximum Parsimony (MP) dendrogramlar, varyasyonlar, filogenetik-evrimsel ilişkiler ve taksonomik statüler açısından Q. ilex’e ait populasyonları değerlendirmek için çizildi. Her iki barkodlama bölgesi, Q. ilex populasyonlarının farklı morfolojik tipler temelinde ayrımını desteklemesine rağmen, özellikle matK geni-kısmi trnK gen intron sekansları, ITS1-5.8S rRNA geni-ITS2 sekanslarından daha açık ve bilgilendirici sonuçlar sergiledi.

Anahtar Kelimeler

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Details

Primary Language

English

Subjects

Plant Cell and Molecular Biology

Journal Section

Research Article

Authors

Aykut Yılmaz ^*
0000-0002-0327-8388
Türkiye

Early Pub Date

January 30, 2025

Publication Date

February 12, 2025

Submission Date

May 5, 2024

Acceptance Date

November 8, 2024

Published in Issue

Year 2025 Volume: 28 Number: 1

DOI

https://doi.org/10.18016/ksutarimdoga.vi.1478950

IZ

https://izlik.org/JA93GE68SN

Cite

RIS / Bibtex

APA

Yılmaz, A. (2025). Analysis of the Variations Within Quercus ilex L. and the Evaluation of Morphological Types Based on Chloroplast and Nuclear DNA Sequences. Kahramanmaraş Sütçü İmam Üniversitesi Tarım Ve Doğa Dergisi, 28(1), 36-46. https://doi.org/10.18016/ksutarimdoga.vi.1478950

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