Phylogenetic analysis of Prunus genus using nuclear and chloroplast gene markers as a bioorganic structure profiling

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dc.authoridDurna Dastan, Sevgi/0000-0003-4946-5602
dc.authoridSelamoglu, Zeliha/0000-0001-9056-6435
dc.contributor.authorAbdulrahman, Shamiran Salih
dc.contributor.authorDastan, Sevgi Durna
dc.contributor.authorShahbaz, Saleem Esmael
dc.contributor.authorSelamoglu, Zeliha
dc.date.accessioned2024-11-07T13:34:37Z
dc.date.available2024-11-07T13:34:37Z
dc.date.issued2023
dc.departmentNiğde Ömer Halisdemir Üniversitesi
dc.description.abstractPrunus species are known as model species for the family Rosaceae and other woody plants with their small genome size and relatively small life cycle as woody plants. Also Prunus species are economically important plants in the subfamily Amygdaloideae of the Rosaceae have a controversial taxonomic history due to the lack of a phylogenetic framework. Therefore, mapping, classification, determination the ge-netic structure and characterization of genes as a spesific chemical and fuctional units of nucleic acids and making phylogenetic analysis in these species have important implications. The aim of this study to find any gene markers as a bioorganic - chemical structure profiling to determine genetic diversity of dif-ferent Prunus species from Iraq by using nuclear and chloroplast DNA markers to evaluate the phylogeny of Prunus. A total of 12 species Prunus subgenus amygdalus were collected from Iraq. Ten gene region markers on both nuclear DNA and chloroplast DNA have been tested to evaluate the genetic variation at their molecular levels by using multiplex PCR with 10 gene region primers and sequence analysis for matK. The name of the gene regions using in this study are ITS (ITS1 + ITS2 + 5.8S coding region), rbcL, matK, rpl16, trnL-trnF, atpB-rbcL, rp136-infA-rps8, trnK-rps16, pbsM-trnD, psbA-trnH. As a result, five dif-ferent phylogenetic trees were obtained from the gene sequences of the samples and the base sequences were close to each other. The estimated value of the shape parameter for the discrete Gamma Distribu-tion is 0.05. The nucleotide frequencies are A = 29.41%, T/U = 37.37%, C = 17.52%, and G = 15.67%. The nucleotide diversity of the sequence was low with the 0.004113 value. There were 14 different informa-tive base site between the samples. The polymorphism observed was less in agreement with higher level of conservation of the gene regions. The Prunus species from Iraq region were grouped on two closed clusters on the phylogenetic trees.(c) 2023 Elsevier B.V. All rights reserved.
dc.identifier.doi10.1016/j.molstruc.2023.135300
dc.identifier.issn0022-2860
dc.identifier.issn1872-8014
dc.identifier.scopus2-s2.0-85150463365
dc.identifier.scopusqualityQ2
dc.identifier.urihttps://doi.org/10.1016/j.molstruc.2023.135300
dc.identifier.urihttps://hdl.handle.net/11480/16062
dc.identifier.volume1284
dc.identifier.wosWOS:000967389000001
dc.identifier.wosqualityQ2
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.language.isoen
dc.publisherElsevier
dc.relation.ispartofJournal of Molecular Structure
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/closedAccess
dc.snmzKA_20241106
dc.subjectChemical structure profiling
dc.subjectFunctional chemistry
dc.subjectMatK
dc.subjectNucleotide chemistry
dc.subjectPrunus
dc.titlePhylogenetic analysis of Prunus genus using nuclear and chloroplast gene markers as a bioorganic structure profiling
dc.typeArticle

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