Sürdürülebilir Kalkınma Amaçları
Yayınlar
- DüzeltmeAçık Erişim2026Scopus SJRQ3Erratum to: Sequence Analysis and Genetic Diversity of ndhF of the Chloroplast DNA (cpDNA) of Chrysophthalmum (Asteraceae) Species in Türkiye
Sevindik, Emre; Gelir, Seda Nur; Demircan, Şelale; Çiftçi, İbrahim; Paksoy, Mehmet Yavuz
The article number was incorrectly given as 30 but should have been 29.
- MakaleYalnız künye2026Scopus SJRQ3Sequence Analysis and Genetic Diversity of ndhF of the Chloroplast DNA (cpDNA) of Chrysophthalmum (Asteraceae) Species in Türkiye
Sevindik, Emre; Gelir, Seda Nur; Demircan, Şelale; Çiftçi, İbrahim; Paksoy, Mehmet Yavuz
Absract: In this study, chloroplast DNA (cpDNA) ndhF sequence analysis was used to determine the sequence analysis and genetic diversity of Chrysophthalmum Schultz Bip. species distributed in Türkiye. Genomic DNA was isolated from green leaves and cpDNA ndhF region was amplified by PCR. The results of the PCR, the forward and reverse sequences were edited using the Sequencher 5.4.6 programme and the contig sequences were obtained. To determine the phylogenetic relationships between species, MEGA 6.0 was used to construct a maximum likelihood (ML) tree. Using the same program, nucleotide composition, phylogenetic trees, genetic distance matrix, and genetic diversity analyses were performed. In addition, the physicochemical properties and 3D structure of ndhF proteins were determined. From the results of the ndhF analyses, the nucleotide length of Chrysophthalmum species was found to vary between 471 and 625. The genetic matrix value was determined to be between 0.000 and 0.009. In the phylogenetic tree constructed using ndhF sequences from Anvillea DC., Pulicaria Gaertn., Limbarda Adans, Inula L., Carpesium L., Pentanema Cass., Dittrichia Greuter, Rhanteriopsis Rauschert and Telekia Baumg species from NCBI, C. montanum was grouped with Inula, Pentanema and Rhanteriopsis species. C. gueneri was grouped with C. dichotomum and Pentanema alanyense. Previous phylogenetic studies were in agreement with our results. In addition, the ndhF results supported that Chrysophthalmum species are not a monophyletic group.
AtıfWoS1
İncele - MakaleYalnız künye2025Scopus SJRQ2Phylogenetic analysis of the nrDNA ITS and cpDNA rbcL sequences of some endemic Dianthus (Caryophyllaceae) species from Türkiye
Sevindik, Emre; Güner, Özal; Yolcu, Seher; Başköse, İsa; Paksoy, Mehmet Yavuz; Khadivi, Ali; Tunç, Yazgan; Yaman, Mehmet
In this study, the phylogenetic relationship of four species of Dianthus genus which are endemic and distributed in Türkiye, including D. zederbaueri Vierch, D. varankii Hamzaoğlu & Koç, D. halisdemirii Hamzaoğlu & Koç, and D. goekayi Kaynak, was determined using nuclear DNA (nrDNA) internal transcribed spacer (ITS) and chloroplast DNA (cpDNA) rbcL regions. After sampling from the plant, DNA was extracted and the ITS (ITS4-ITS5A) and rbcL (rbcLaF-rbcLaR) primers were used to perform PCR amplification. Sequencer 5.4.6. was used to edit the sequences. MEGA 11 software was used to determine the nucleotide ratios, genetic distance matrix, and π = nucleotide diversity. Some species of Dianthus available in the National Center for Biotechnology Information (NCBI) were used to construct maximum likelihood (ML) phylogenetic trees. As a result, based on the ITS analysis π = nucleotide diversity was determined as: 0.001543, and the result of the rbcL analysis π = nucleotide diversity was determined as: 0.000000. In the ITS results, D. halisdemirii, D. superbus, and D. varankii appeared together, while D. zederbaueri and D. aculeatus appeared together. The rbcL results showed that D. zederbaueri and D. varankii were closely related, but the relationship between D. halisdemirii and D. goekayi could not be determined. Furthermore, in the phylogenetic tree constructed by taking the ITS and rbcL sequences of Dianthus, Gypsophila, Silene, Arenaria, Saponaria, Cerastium, Stellaria, Petrorhagia, Minuartia, Agrostemma, and Polycarpon species from NCBI using ITS and rbcL sequences, our endemic Dianthus species appeared in the same group with Petrorhagia, Gypsophila, and Saponaria species. To conclude, our ITS and rbcL results were consistent in determining the phylogenetic relationships of our Dianthus species with other species.
AtıfScopus1İncele - MakaleYalnız künye2025Scopus SJRQ3Phylogenetic Analysis of Lisaea Boiss. (Apiaceae) Species in Türkiye Based on Chloroplast DNA (cpDNA) trnL-intron, trnL-F, matK and rbcL Sequences
Efe, Fadime; Sevindik, Emre; Sevindik, Mustafa; Paksoy, Mehmet Yavuz
Abstract: In this study, Lisaea heterocarpa,Lisaea papyracea and Lisaea strigosa species belonging to the Lisaea genus distributed in Türkiye phylogenetic analysis was determined chloroplast DNA regions. Plant samples were collected from different provinces of Türkiye and taken to the laboratory for genomic DNA isolation, polymerase chain reaction and bioinformatics analysis. As a result of the study, the lowest π-nucleotide diversity was found in the rbcL analyses (0.000917), while the highest π-nucleotide diversity was found in the trnL-F analysis (0.008700). In the phylogenetic trees constructed using trnL intron, trnL-F,and rbcL sequences, the species L. strigosa and L. papyracea appeared together, while L. heterocarpa appeared close to this group. The matK sequences, L. strigosa and L.heterocarpa appeared together, while L. papyracea appeared close to this group. In addition, the phylogenetic trees constructed using sequences from some Apiaceae species from National Center for Biotechnology Information (NCBI) determined that the genus Lisaea is monophyletic. In the trnL-F and rbcL analyses, Lisaea species appeared together with Torilis,Yabea, Daucus, Cuminum, Pternopetalum and Anthriscus species, while in the matK analysis, Lisaea species appeared in a different group from Anthriscus species.
AtıfScopus1WoS1OpenAlex1İncele - MakaleYalnız künye2024Scopus SJRQ2Phylogenetic analysis of the endemic Bornmuellera Hausskn. spp. (Brassicaceae) in Türkiye based on nuclear ITS and chloroplast trnL intron, trnL-F, rbcL and trnQ-rps16 DNA sequences
Okan, Kemalcan; Sevindik, Emre; Paksoy, Mehmet Yavuz
In this study, phylogenetic analysis of Turkish endemic Bornmuellera (Brassicaceae) species was conducted based on nuclear ribosomal DNA (ITS) and chloroplast DNA (trnL intron, trnL-F, rbcL and trnQ-rps16 DNA) sequences. In addition, the relationships between the sequences of some Brassicaceae family species retrieved from NCBI, and Bornmuellera species were documented. All of the plant specimens were collected from different regions of Türkiye, and brought to the laboratory. Total genomic DNA was extracted using the GeneMark kit. After polymerase chain reaction (PCR) analyses, DNA sequences obtained were then edited using Sequencher 5.4, Bioedit 7.2.3 and FinchTV 1.4.0, and analyzed using MEGA 6.0 software. Maximum likelihood (ML) and bootstrap trees were constructed in order to identify the relationships among Bornmuellera species. In the study, the highest nucleotide diversity was detected by rps16-trnQ (0.039146) sequence analysis, while the lowest was detected by rbcL (0.004186) sequence analysis. In addition, according to the phylogenetic analysis results obtained with other Brassicaceae species, it is revealed that the Turkish endemic Bornmuellera genus is monophyletic.
AtıfScopus5WoS4OpenAlex5İncele - MakaleYalnız künye2023Scopus SJRQ3MOLECULAR CHARACTERIZATION OF Dittrichia viscosa (L.) GREUTER (ASTERACEAE) POPULATIONS REVEALED BY ISSR MARKERS AND CHLOROPLAST (cpDNA) trnL INTRON SEQUENCES; [MOLEKULARNA KARAKTERIZACIJA POPULACIJA Dittrichia viscosa (L.) GREUTER (ASTERACEAE) POMOĆU ISSR MARKERA I HLOROPLAST (cpDNA) trnL INTRONSKIH SEKVENCI]
Sevindik, Emre; Bozkurt, Makbule; Yilmaz, Mehmet; Şenyüz, Ezginur; Paksoy, Mehmet Yavuz
In this study, molecular characterization of Dittrichia viscosa (L.) Greuter populations collected from Aydın province was carried out based on ISSR technique and chloroplast DNA trnL intron sequences. 10 ISSR primers were used to determine the molecular characterization among the populations. For cpDNA trnL intron amplification, trnC and trnD primers were used. In ISSR analysis, a total of 70 bands were obtained. The polymorphism rate was determined to be approximately 94.28%. According to the ISSR analysis, the UPGMA dendrogram consisted of three groups. For cpDNA trnL intron sequences, phylogenetic analyses were obtained along with genetic distances. For populations, cpDNA trnL intron sequences were determined between 454 and 472 bases. The maximum likelihood phylogenetic tree consist of two clades. In addition, cpDNA trnL intron sequences of some species (Chrysophthalmum Pulicaria Inula Jasonia Stenachaenium Carpesium Blumea Iphiona Limbarda Rhanterium Lifago Duhaldea Chiliadenus) of Asteraceae family from NCBI with Dittrichia viscosa populations phylogenetic tree was constructed. As a result of the study, it was determined that the polymorphism rate of Dittrichia viscosa populations obtained by ISSR-PCR was higher than the results obtained from trnL intron sequences.
AtıfScopus3WoS4İncele - MakaleAçık Erişim2022Genetic Relationship of Seven Endemic Inula L. (Asteraceae) Species Grown in\rTurkey
Paksoy, Mehmet Yavuz; Sevindik, Mustafa; Sevindik, Emre
In this study, genetic relationship of ISSR markers of seven endemic Inula species distributed in\rTurkey was carried out. Plant samples were collected from different regions of Turkey in 2013 and\rgDNA was obtained by DNA isolation from green leaves. Genetic relationship between species was\rdetermined using 12 ISSR primers. PCR products were run on agarose gel electrophoresis and\rvisualized under UV light. All gel images were examined and the presence and absence of\rpolymorphic bands were scored as 0 and 1. A total of 85 bands were obtained from the primers. Of\rthese, 74 polymorphic and 11 monomorphic bands were obtained. The total polymorphism rate was\rfound to be approximately 87.05%. The phylogenetic tree and genetic distances between species\rwere calculated using the PAUP 0 4.0b10 analysis program. According to the distance matrix, the\rgenetic distance was found between the closest Inula helenium subsp. orgyalis and Inula helenium\rsubsp. vanensis (0.29851), while the farthest between Inula sarana and Inula macrocephala\r(0.56000) species. The phylogenetic tree was obtained using the UPGMA algorithm, and the tree\rconsisted of two groups. The results were compared with the morphological, palynological nrDNA\rand cpDNA results of the past. Our findings supported previous studies
AtıfOpenAlex2
İncele - MakaleAçık Erişim2021Phylogenetic analysis of the genus conringia heist. Ex fabr. (brassicaceae) in turkey based on nuclear (nrits) and chloroplast ((trnl-f)) dna sequences
Sevindik, Emre; Aydogan, Melike; Paksoy, Mehmet Y.
In this study, phylogenetic analysis of Turkish Conringia (Brassicaceae) species was conducted based on nuclear ribosomal DNA (nrITS) and chloroplast DNA (trnL-F) sequences. In addition, the relationships between the sequences of some Brassicaceae family species retrieved from NCBI, and Conringia species were documented. All of the plant specimens were collected at their flowering and vegetation periods from different regions of Turkey, and brought to the laboratory. Total genomic DNA was extracted using the GeneMark kit. In PCR analyses, ITS4 and ITS5A primers were used for the amplification of the nrITS region, while the trnLe and trnLf primers were used for the cpDNA trnL-F region. The DNA sequences obtained were then edited using BioEdit and FinchTV, and analyzed using MEGA 6.0 software. Neighbor joining (NJ) and bootstrap trees were constructed in order to identify the relationships among Conringia taxa. The nrITS sequences ranged between 573 and 672 nucleotides, while the trnL-F sequences ranged between 346 and 764 nucleotides. The divergence values of nrITS sequences differed between 0.177 and 0.00 and divergence values of trnL-F sequences differed between 0.902 and 0.00. NJ tree generated using nrITS and trnL-F sequences consisted of two clades. In trees generated with both the nrITS and trnL-F sequences, C. orientalis, C. grandiflora and C. austriaca appeared within the same group. In addition, according to the phylogenetic analysis results obtained with other Brassicaceae species, it is revealed that the Conringia genus is polyphyletic.
AtıfScopus1İncele - MakaleAçık Erişim2020Scopus SJRQ3ANTI-UREASE, TOTAL PHENOLIC CONTENT AND ANTIOXIDANT ACTIVITIES OF SOME Inula L. (ASTERACEAE) TAXA IN TURKEY
Sevindik, Emre; Aydin, Sinem; Paksoy, Mehmet Yavuz; Sokmen, Bahar Bilgin
The genus Inula belongs to family Asteraceae and it is medicinally important because it possesses cytotoxic, anticancer, hepatoprotective, antibacterial and anti-inflammatory properties. The aim of this research was to explore antioxidant and anti-urease activities of fifteen Inula taxa in Turkey. Ethanol extracts of Inula taxa were obtained by Soxhlet extraction. Antioxidant activity was determined through total antioxidant activity, total phenolic content and copper reducing antioxidant capacity (CUPRAC) analyses. The highest total phenolic content and total antioxidant capacity were found in I. orientalis (158.54±0.002 µg GAE/mL) and I. macrocephala (189.16±0.002 µg AAE/mL). CUPRAC activity increases with the increasing concentration of the extracts and the standard. Moreover, all the tested plants exhibited better anti-urease activity than standard thiourea except for I. anatolica and I. thapsoides subsp. thapsoides. Results obtained from this study demonstrate that Inula species might be utilized as a probable natural source in the pharmaceutical and food industries but further and more specific studies are needed to determine active antioxidative and anti-urease compounds in the extracts.
AtıfScopus8WoS7OpenAlex10İncele - MakaleYalnız künye2019Genetic Diversity Analysis of Aydın/Turkey Dittrichia viscosa (L). Greuter (Asteraceae) Populations Using RAPD Markers
Paksoy, Mehmet Yavuz; Sevindik, Emre; Uzun, Sefa
In this study, we performed a genetic diversity using RAPD markers for some Dittrichia viscosa populations grown in the Aydın region of Turkey. Total genomic DNA isolation from the leaves of Dittrichia viscosa was performed using commercial kit. eight RAPD primers were used to determine genetic diversity among populations. Polymerase Chain Reaction (PCR) was performed with all DNA samples and primers with ability of scoreing band. PCR products were run in agarose gel and visualized under UV light. They scored as there were bands (1) and no bands (0) at all gel images and their files were created. A total of 50 characters were obtained from the primers. Phylogenetic relationships and genetic distances between the cultivars were calculated by using the PAUP* 4.0b10 analysis program. According to the PAUP data, the closest genetic distance was determined 0.20000 and between Central and İncirliova populations, the most distant genetic distance were determined 0.36842 between İncirliova and Koçarlı populations. In the phylogenetic analysis has been obtained using UPGMA algorithms and phylogenetic tree consist of two clades. The results also propose that RAPD markers are useful tools for indicating genetic relationships among Dittrichia viscosa populations.
- MakaleAçık Erişim2019Phylogenetic Analysis of Chrysochamela (Fenzl) Boiss. (Brassicaceae) Taxa Growing in Turkey
Paksoy, Mehmet Yavuz; Sevindik, Emre; Topseçer, Feyzanur; Aydoğan, Melike
In this study, we performed a genetic diversity analysis using RAPD (Random AmplifiedPolymorphic DNA) and ISSR (Inter simple sequence repeat) markers for some Chrysochamelaspecies growing in Turkey. PCR was performed using RAPD and ISSR primers and genomic DNAsamples from each specimen, and the resulting bands were scored. Phylogenetic relationships andgenetic distances between the studied taxa were calculated using the PAUP analysis program.According to the RAPD analysis, the closest genetic distance was found to be 0.20000 between C.noeana populations, while the most distant values were found as 0.60000 between C. noeana and C.elliptica. The ISSR analysis also revealed the closest genetic distance as 0.34043 between C. noeanapopulations, while the most distant values were found to be 0.55319 between C. noeana and C.elliptica. UPGMA (unweighted pair group method with arithmetic mean) dendrogram generated forboth RAPD and ISSR analyses consisted of two groups. As a result, it was found that RAPD datawere more appropriate for comparison with the previous anatomical and morphological data of the studied taxa.
AtıfOpenAlex1TR Dizin1İncele - MakaleYalnız künye2017Aydın/Türkiye’de Yayılış Gösteren Dittrichia L. (Asteraceae) Cinsinin Kimyasal Kompozisyonunun Değerlendirilmesi
Paksoy, Mehmet Yavuz; Sevindik, Emre
Küçük bir cins olarak Greuter tarafından tanımlanan Dittrichia (Asteraceae) cinsi, önceden Inula’nın bir bölümü olarak biliniyordu ve Atlantik Avrupa ülkelerinde, Ortadoğu ve Akdeniz bölgesinde yayılış göstermektedir. Bu çalışma da Dittrichia cinsine ait bitkilerden elde edilen uçucu yağların kimyasal bileşimi incelenmiştir. Çalışma materyali Dittrichia viscosa (L). Greuter ve Dittrichia graveolens (L.) Greuter Eylül-Ekim 2015 tarihinde Batı Anadolu (Aydın/Türkiye) ekolojik koşullarında toplanmıştır. Yaprakların uçucu yağları Clevenger cihazıyla ekstrakte edildi. Esansiyel yağ bileşimleri Gaz Kromatografisi-Kütle Spektrometresi (GC-MS) cihazı ile belirlendi. Gaz kromatografisi-kütle spektrometresi analizinin sonuçları, D. graveolens bitkisinden elde edilen uçucu yağda levo-bornyl acetate en yüksek düzeyde (% 25.23) olduğunu gösterdi. D. viscosa bitkisinde ise 2,4-diokso-3-metil6-izopropil pirido [2,3-b]- [1,4] pirazin en yüksek düzeyde (% 29.02) olduğu belirlendi.
AtıfTR Dizin1İncele