Molecular Genetic Diversity of Prunus armeniaca L. (Rosaceae) Genotypes by RAPD, ISSR-PCR, and Chloroplast DNA (cpDNA) trnL-F Sequences

Sevindik, Emre; Murathan, Zehra Tuğba; Sevindik, Mustafa

doi:10.1080/15538362.2020.1828223

Cited by 13 publications

(6 citation statements)

References 39 publications

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“…The data obtained were aligned using Muscle in MEGA7 [27]. The genetic distance estimation data was analyzed using Pairwise Distance with the Kimura 2-parameter model [28] also in MEGA7. The phylogenetic tree was reconstructed using the Maximum-Likelihood method with 1000 bootstrap replicates [29] with the Kimura 2-Parameter (K2P) model in the MEGA7.…”

Section: Discussionmentioning

confidence: 99%

DNA barcode of Eurycoma longifolia Jack (Simaroubaceae) from Sumatra, Indonesia based on trnL-F plastid sequence.

Yulita

Susilowati

Rachmat

et al. 2020

Proceedings of the 1st International Electronic Conference on Forests — Forests for a Better Future: Sustainability, Innovation

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Eurycoma longifolia (Simaroubaceae) is a popular medicinal plant from the SouthEast Asian rainforest that often used as an aphrodisiac and anti malaria. The main supplies of E. longifolia from Indonesia is Sumatra. The increasing demand of this species for medinical industries has led to illegal export in Indonesia. This study was aimed to identify specific nucleotides as molecular identity of E. longifolia from Sumatra based on DNA sequences of trnL-F plastid gene. Twenty four samples of E. longifolia were collected from three provinces in Sumatra to be sequenced. The aligned sequence of the trnL-F_is 960 bp, and is an A/T rich region (A: 27.2%, T: 39.1%, C: 16.7% and G: 17.1%). The homology search using BLASTn of the genbank NCBI showed that the nucleotide composition of E. longifolia used in this study was similar to partial trnL-F region of E. longifolia MH751519 (100%) and KP995919 (99.76%), Simaba morettii MG599450 (99.76%), and E. apiculata GU593014 (99.76%). Close examination of the gene structure and composition showed that the DNA sequences or E. longifolia from Sumatra have five nucleotides variations that did not possesed by the reference E. longifolia as well other reference taxa used. All variations found were occurred mostly in the trnL intron region. When a phylogenetic analysis was performed, its results confirmed the correct identity of the samples species by their position was at the same clade as the other E. longifolia. The results from this study is expected to assist identification of herbal medicine containing E. longifolia from Sumatra, Indonesia.

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Section: Discussionmentioning

confidence: 99%

DNA barcode of Eurycoma longifolia Jack (Simaroubaceae) from Sumatra, Indonesia based on trnL-F plastid sequence.

Yulita

Susilowati

Rachmat

et al. 2020

Proceedings of the 1st International Electronic Conference on Forests — Forests for a Better Future: Sustainability, Innovation

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“…So that RAPD and ISSR are still preferred markers supplementing DNA barcodes in plant identification (Techen et al 2014;Ramasetty al. 2016) since the capacity of polymorphism of RAPD and ISSR is higher than that of DNA barcodes (Sevindik et al 2020).…”

Section: Combined Rapd and Issr Datamentioning

confidence: 99%

Investigation of the genetic diversity of jewel orchid in Vietnam using RAPD and ISSR markers

Tran

PHAM²,

TRINH³

et al. 2022

Biodiversitas

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Abstract. Tran TKP, Pham MH, Trinh TH, Widiarsih S, Ho VT. 2022. Investigation of the genetic diversity of jewel orchid in Vietnam using RAPD and ISSR markers. Biodiversitas 23: 4816-4825. Jewel orchid is a general name for several genera belonging to the Orchidaceae family, namely Anoectochilus, Doddinia, Goodyera, Ludisia, and Macodes. These plants are generally used as medicinal herbal for common diseases in Vietnam. Due to over-exploitation, the natural resources of jewel orchids are gradually depleted. Therefore, genetic resource research for proper development of this medicinal plant is necessary. This study aimed to investigate the genetic diversity of jewel orchids in Vietnam using RAPD and ISSR markers to provide basic data conservation of genetic resources and the development of this medicinal plant. A total of 20 jewel orchid samples were genetically characterized by using 10 RAPD and 10 ISSR primers. The amplified bands were binary coded and used to construct phylogenetic trees with NTSYSpc 2.1 software. Each RAPD primer produced 5-11 bands with an average of 8.0, and similarity coefficients ranged from 0.52 to 0.81. Each ISSR primer produced 5-10 bands with an average of 7.6, and the similarity coefficients ranged from 0.54 to 0.87. Combined RAPD and ISSR markers produced similarity coefficients ranging from 0.53 to 0.83. Based on the PIC values, the primers used by both markers are highly informative. However, the topology of cluster analysis of 20 jewel orchid accessions does not correspond to the taxa studied. The findings could be potential to employ in future classification, conservation, and development of this plant.

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“…Genetic diversity is a prerequisite for the short and long-term survival of plant species in their natural environment (Verma et al 2017). Morphological, biochemical, and DNA markers are used to determine the genetic diversity of plants (Sevindik et al 2020). DNA-based molecular markers offer many advantages in determining genetic diversity.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and phylogenetic analyses of Vitex agnus castus L. populations using ISSR-PCR and chloroplast DNA trnL intron and trnL-F sequences

Sevindik

2022

Nova Biotechnol. Chim.

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In this study, genetic diversity and phylogenetic analysis of some Vitex agnus-castus L. populations were conducted based on ISSR-PCR and chloroplast DNA trnL intron, and trnL-F sequence analyses. Vitex agnus-castus populations were detected in Aydın province, Turkey. Fresh leaf samples from the populations were collected and brought to the laboratory for genomic DNA isolation. 15 ISSR primers were used to determine the genetic diversity ofe Vitex agnus-castus populations. A total of 138 bands were obtained in ISSR analysis, 85 of which were polymorphic and 53 were monomorphic. Polymorphism rate was determined as 61.59 %. trnC, trnD, trnE, and trnF primers were used for PCR amplification of the chloroplast trnL intron and trnL-F region. A total of 138 bands were obtained by ISSR analysis. For trnL intron analyses, nucleotide lengths of 13 populations were between 508 and 516. The average nucleotide composition consisted of 38.5 % T, 18.3 % C, 27.5 % A and 15.7 % G. In trnL-F assays, the nucleotide lengths of the 13 populations ranged from 330 to 353. The average nucleotide composition consisted of 29.4 % T, 18.1 % C, 32.9 % A and 19.6 % G. The results of the phylogenetic trees constructed using some trnL intron and trnL-F sequences of Vitex doniana, Vitex trifolia, Vitex triflora, Vitex turczaninowii, Vitex queenslandica, Vitex axillariflora, Vitex rotundifolia and Vitex negundo species obtained from NCBI were compared. As a result of the study, polymorphisms were obtained at a rate of 61.59% from the ISSR analysis. In addition, the phylogenetic relationship between chloroplast trnL intron and trnL-F sequences of Vitex agnus-castus populations along with the other species was revealed.

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Molecular Genetic Diversity of Prunus armeniaca L. (Rosaceae) Genotypes by RAPD, ISSR-PCR, and Chloroplast DNA (cpDNA) trnL-F Sequences

Cited by 13 publications

References 39 publications

DNA barcode of<em> Eurycoma longifolia</em> Jack (Simaroubaceae) from Sumatra, Indonesia based on <em>trn</em>L-F plastid sequence.

DNA barcode of<em> Eurycoma longifolia</em> Jack (Simaroubaceae) from Sumatra, Indonesia based on <em>trn</em>L-F plastid sequence.

Investigation of the genetic diversity of jewel orchid in Vietnam using RAPD and ISSR markers

Genetic diversity and phylogenetic analyses of Vitex agnus castus L. populations using ISSR-PCR and chloroplast DNA trnL intron and trnL-F sequences

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Molecular Genetic Diversity of Prunus armeniaca L. (Rosaceae) Genotypes by RAPD, ISSR-PCR, and Chloroplast DNA (cpDNA) trnL-F Sequences

Cited by 13 publications

References 39 publications

DNA barcode of&lt;em&gt; Eurycoma longifolia&lt;/em&gt; Jack (Simaroubaceae) from Sumatra, Indonesia based on &lt;em&gt;trn&lt;/em&gt;L-F plastid sequence.

DNA barcode of&lt;em&gt; Eurycoma longifolia&lt;/em&gt; Jack (Simaroubaceae) from Sumatra, Indonesia based on &lt;em&gt;trn&lt;/em&gt;L-F plastid sequence.

Investigation of the genetic diversity of jewel orchid in Vietnam using RAPD and ISSR markers

Genetic diversity and phylogenetic analyses of Vitex agnus castus L. populations using ISSR-PCR and chloroplast DNA trnL intron and trnL-F sequences

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Product

Resources

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DNA barcode of<em> Eurycoma longifolia</em> Jack (Simaroubaceae) from Sumatra, Indonesia based on <em>trn</em>L-F plastid sequence.

DNA barcode of<em> Eurycoma longifolia</em> Jack (Simaroubaceae) from Sumatra, Indonesia based on <em>trn</em>L-F plastid sequence.