DNA Barcoding in Selected Species and Subspecies of Rye (Secale) Using Three Chloroplast Loci (matK, rbcL, trnH-psbA)

Skuza, Lidia; Szućko, Izabela; Filip, Ewa; Adamczyk, Anastazja

doi:10.15835/nbha47111248

Cited by 9 publications

(7 citation statements)

References 50 publications

(64 reference statements)

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“…Our results showed that the partial region of the matK gene amplified and sequenced gave high polymorphism between all studied species (58.37%). This nearly agreed with Skuza et al (2019) who observed that nucleotide sequences had a high variability within matK and rbcL regions. Polymorphism of the sequences was 2.2% in the rbcL region, while in the matK region was 6.5%.…”

Section: Discussionsupporting

confidence: 91%

DNA barcoding of different Triticum species

Osman

Ramadan

2019

Bull Natl Res Cent

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Background: The genus Triticum L. includes diploid, tetraploid, and hexaploid species. DNA barcoding is a new method to identify plant taxa by using short sequences of DNA and within a short time. In this investigation, we determined a phylogenetic analysis of 20 different Triticum species by partial chloroplast Maturase encoding gene (matK). Materials and methods: Twenty accessions of different Triticum species diploid, tetraploid, and hexaploid were obtained from different countries. Genomic DNA was isolated from young leaves of studied samples and then used as a template for PCR reaction. PCR products were checked by electrophoresis, purified, sequenced, and submitted in the GenBank nucleotide sequence database, the nucleotide sequence was translated into an amino acid sequence. The nucleotide and amino acid sequences were aligned with Clustal W multiple sequence alignment programs to obtain the phylogenetic tree depending on two statistical data analysis such as bootstrapping and pairwise distance from both nucleotide and amino acid sequences. Results: The phylogenetic tree obtained from both nucleotide and amino acid sequences divided the 20 Triticum species into two groups, A and B. Group A represented the diploid Triticum species. Group B was divided into two subgroup, I and II. Subgroup I represented the hexaploid Triticum species and subgroup II represented the tetraploid species. Conclusion: The matK gene sequence has a critical role in discriminating the closely related Triticum species. So these sequences could be used as a DNA barcode for detecting the evolutionary history of Triticum species.

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Section: Discussionsupporting

confidence: 91%

DNA barcoding of different Triticum species

Osman

Ramadan

2019

Bull Natl Res Cent

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“…This causes a significantly reduction of progress in rye breeding that can be enriched with functional traits derived from wild rye species. In the genus, the wild species Secale sylvestre Host ( 1809) is singularized by several genetic peculiarities (Bennett and Smith 1976;Singh and Röbbelen 1977;Shang et al 2006;Zhou et al 2010;Skuza et al 2019a).…”

Section: Introductionmentioning

confidence: 99%

The complete chloroplast genome of Secale sylvestre (Poaceae: Triticeae)

2021

Self Cite

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Secale sylvestre is a wild species of rye, morphologically distinct from domestic species. To draw comparisons between species based on molecular features, it is important to have high-quality sequences, especially in the case of organellar genomes. For such reason, the complete chloroplast genome of Secale sylvestre Host introd. no. 6047 will provide useful data for ecological, agricultural, and phylogenetic purposes. Here we present the complete, annotated chloroplast genome sequence of Secale sylvestre Host introd. no. 6047. The genome is 137116 base pair (bp) long. It is the first complete chloroplast genome that can be used as a reference genome for further analysis. The genome can be accessed on GenBank with the accession number (MW557517).

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“…These markers are highly informative for identifying and differentiating plant species. Recently, the use of DNA barcoding based on the markers rbcl, ITS, and MatK has gained significant traction in the field of plant species authentication . In this study, all three markers were used for the identification of E.…”

Section: Discussionmentioning

confidence: 99%

“…Recently, the use of DNA barcoding based on the markers rbcl, ITS, and MatK has gained significant traction in the field of plant species authentication. 36 In this study, all three markers were used for the identification of E. tithymaloides . The sequence match with rbcl loci showed a match of 98.64 to 99.83% with the top five hits from the BLAST analysis.…”

Section: Discussionmentioning

confidence: 99%

Standardization of Euphorbia tithymaloides (L.) Poit. (Root) by Conventional and DNA Barcoding Methods

Patil,

Imran,

Jaquline

et al. 2023

ACS Omega

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Adulteration and substitution of medicinal plants have become a matter of great concern in recent years. Euphorbia tithymaloides is one such medicinal plant that has gained importance but is often confused with other plants of the same species. In order to address this issue, this study aimed to conduct a conventional and molecular pharmacognostic study for the identification of the root of E. tithymaloides. The root of the plant was studied for the macroscopic observations, and then, the root was ground into coarse powder for microscopic studies and to determine the physiochemical properties. The powder was subjected to extraction with solvents such as ethanol, ethanol/water (1:1), hexane, and ethyl acetate. The extracts were then used for qualitative and quantitative (phenol, alkaloids, and flavonoids) phytochemical analysis. The molecular study was performed with the DNA barcoding technique. The DNA was extracted from the root of the plant, and its purity was examined by gel electrophoresis (1% w/v). The DNA was then amplified using an Applied Biosystems 2720 thermal cycler for the rbcL, matK, and ITS primers. The amplified primers were sequenced with a 3130 Genetic Analyzer, and the generated sequences were searched for similarity in the GenBank Database using the nucleotide BLAST analysis. The micro- and macroscopic studies revealed the morphological and organoleptic characters as well as the presence of medullary rays, fiber, cork, sclereids, parenchymal cells, and scalariform vessels. The physiochemical properties were found within the limit. The phytochemical analysis revealed the presence of terpenoids, flavonoids, saponins, and alkaloids. In addition, the alkaloidal content was high in the ethanol extract (63.04 ± 3.08 mg At E/g), while the phenol content was high in the hexane extract (10.26667 ± 1.77 mg At E/g), and the flavonoid content was high in the ethyl acetate extract (41.458 ± 1.33 mg At E/g). After the BLAST analysis from the GenBank database, the rbcL, ITS, and matK primers showed a similarity percentage of 99.83, 99.84, and 100. The phylogenetic tree for the species closest to each primer was generated using the MEGA 6 software. The matK loci had the highest percentage similar to the rbcL and ITS loci, indicating that the matK loci can be used to identify the root of E. tithymaloides as a standalone. The results from this study can be used to establish a quality standard for E. tithymaloides that will ensure its quality and purity.

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DNA Barcoding in Selected Species and Subspecies of Rye (Secale) Using Three Chloroplast Loci (matK, rbcL, trnH-psbA)

Cited by 9 publications

References 50 publications

DNA barcoding of different Triticum species

DNA barcoding of different Triticum species

The complete chloroplast genome of Secale sylvestre (Poaceae: Triticeae)

Standardization of Euphorbia tithymaloides (L.) Poit. (Root) by Conventional and DNA Barcoding Methods

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