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Evaluating DNA barcoding using cpDNA matK and rbcL for species identification and phylogenetic analysis of Prunus armeniaca L. (Rosaceae) genotypes

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Abstract

In this study, DNA barcoding and phylogenetic analysis of five Prunus armeniaca L. genotypes (Cataloglu, Hacihaliloglu, Hasanbey, Hudayi, and Kabaasi) grown in Malatya/Türkiye were conducted using chloroplast DNA (cpDNA) matK and rbcL regions. The cpDNA matK region was amplified using matK472F and matK1248R primers, while the rbcL region was amplified with rbcLaF and rbcLaR primers. The matK and rbcL sequences were utilized to assess nucleotide ratios, genetic distance, and nucleotide diversity (π). The neighbor- joining (NJ) tree including other Prunus species from NCBI was created. In addition, physiochemical and 3-D analysis of matK and rbcL proteins were performed. As a result, π = 0.000549 for matK sequence and π = 0.002657 for rbcL sequence were determined. NJ (neighbor joining) phylogenetic trees formed with both matK and rbcL sequences were found to be compatible with each other. The matK and rbcL gene regions were found to be suitable for phylogenetic analysis.

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Authors and Affiliations

  1. Department of Agricultural Biotechnology, Faculty of Agriculture, Aydın Adnan Menderes University, South Campus, Cakmar, Aydın, Türkiye

    Emre Sevindik

  2. Department of Plant Protection, Faculty of Agriculture, Aydın Adnan Menderes University, Aydın, Türkiye

    Yunus Korkom

  3. Battalgazi Vocational School, Malatya Turgut Özal University, Malatya, Battalgazi, Türkiye

    Zehra TuÄŸba Murathan

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  1. Emre Sevindik
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  2. Yunus Korkom
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  3. Zehra TuÄŸba Murathan
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ZTM collected plant specimens. Molecular and data analyses were done by ES and YK. The manuscript was drafted by ES, YK, ZTM and reviewed by all of the authors before submission. All authors read and approved the final manuscript.

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Correspondence to Emre Sevindik.

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Sevindik, E., Korkom, Y. & Murathan, Z.T. Evaluating DNA barcoding using cpDNA matK and rbcL for species identification and phylogenetic analysis of Prunus armeniaca L. (Rosaceae) genotypes. Genet Resour Crop Evol 71, 1825–1835 (2024). https://doi.org/10.1007/s10722-023-01748-9

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