The application of barcode DNA rbcL gene for identification of medicinal plants: red jabon and gofasa

Sundari, Sundari; Khadijah, Khadijah; Jayali, Ahmad Muchsin; Sukamto, N. H.

doi:10.1088/1742-6596/1146/1/012030

Cited by 5 publications

(6 citation statements)

References 8 publications

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“…It is currently gaining popularity among plant scientists due to its simplicity and high accuracy in reviewing genetic diversity, species discrimination and phylogeny. Molecular barcoding is the best technique to screen for adulteration in medicinal plants (Sundari et al, 2019). DNA barcoding loci are important modern tools for unfolding the genetic relationships among plant species (Shawkat, 2019).…”

Section: Background Studymentioning

confidence: 99%

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Dna Barcoding: Efficiency of Rbcl Gene for Sequence Characterisation of Cyperus Esculentus in Nigeria

Bello

Ojokoh

Babalola³

et al. 2023

Preprint

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Background Plants have been classified based on morphological traits. However, there are biases associated with this classification. The limitation can be prevented by using DNA barcoding. Therefore, the efficiency of the Ribulose -bisphosphate carboxylase (rbcL) marker was investigated to identify Tiger Nut (Cyperus esculentus), which belongs to the family of Cyperaceae. In this study, C. esculentus samples were collected from two villages in northern Nigeria. For DNA barcoding, the rbcL region of C. esculentus samples were amplified, sequenced in both directions, and subsequently analysed. The amplified sequences' biological sequence homology, sequence divergence, and phylogenetic tree construction were studied using Basic Local Alignment Tool (BLAST), Codon Code Aligner and MEGA X respectively. Results A 100% identity of rbcL locus with several other Cyperus species was obtained from BLAST result. The region seems highly conserved among several Cyperus species as variation within this marker locus’s sequence is minimal. However, a G/T variation at a nucleotide position could differentiate the tested samples from 40% of the other data bank species. The phylogenetic tree analysis clustered the 20 samples and the retrieved sequences based on the very few sequence variations without distinctly separating C. esculentus samples from other Cyperus species. Conclusions These findings showed that rbcL marker could only identify our samples up to genius level. Therefore, other DNA barcoding markers are needed to identify and characterise C. esculentus since the characterization based on rbcL gene sequences conducted in this work could not identify C. esculentus up to the species level.

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Section: Background Studymentioning

confidence: 99%

“…Chloroplast DNA (cpDNA) are DNA barcodes often used in plants. rbcL gene is about 1400bp long, providing many characters for phylogenetic studies (Sundari et al, 2019). In this study, a DNA barcoding approach was used to characterize 20 Tiger nuts samples.…”

Section: Background Studymentioning

confidence: 99%

Dna Barcoding: Efficiency of Rbcl Gene for Sequence Characterisation of Cyperus Esculentus in Nigeria

Bello

Ojokoh

Babalola³

et al. 2023

Preprint

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“…Calculates the total time used to perform the alignment. c. Calculates the identical percentage of the two sequences using Jukes Cantor's model [20,24,31] in equation (2).…”

Section: Genbank Data Retrievalmentioning

confidence: 99%

“…In addition, RNA is also needed for a ribonucleic acid contained in the genetic information flow of organisms in the form of the central dogma of DNA->RNA->protein, namely DNA is transcribed into RNA, and then RNA is translated into protein. [1,2,8,9,17].…”

Section: Introductionmentioning

confidence: 99%

Application of the Smith Waterman and Jukes Cantor Algorithm in the Arrangement of the SARS CoV-2 Virus

Yulianto

Tafrikan

Amalia

et al. 2022

J. Nat. Scien. & Math. Res.

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In early 2020, the world was shocked by an outbreak of a new pneumonia that started in Wuhan, Hubei Province, which then spread rapidly to more than 190 countries and territories. This outbreak was named coronavirus disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The spread of this disease has had a wide social and economic impact. There is still a lot of controversy surrounding this disease, including in the aspects of diagnosis, treatment, and prevention. Therefore, a study was carried out on studies related to COVID-19 that have been widely published since the beginning of 2020 until the end of March 2020.So to overcome this problem, the Smith Waterman Jukes Cantor Algorithm was made to align Covid19 by taking the a pair of DNA and RNA sequencesto align protein sequences. From this alignment, the percentage of identical and mutations will be known. The identical percentage in the genetic code will prove that although the symptoms caused by the disease are almost the same, the protein sequences are not necessarily the same. Based on the simulation results of the distance between sequences that produce a phylogenetic tree using the jukes cantor method, it was obtained that 4 groups of 26 sequences were divided into groups, namely, group 1 consists of 16 sequences, group 2 consists of 6 sequences, group 3 consists of 2 sequences, group 4 consists of 2 sequences. Based on these groups, it turns out that the China Wuhan sequence (sequence MT291826) is located in group 1 and other countries that are almost similar to the sequence in China Wuhan, namely the country of Timoe Leste with the sequence MT641766 also located in group 1.©2022 JNSMR UIN Walisongo. All rights reserved.

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“…[5] Among all the genes matK and rbcL gene sequence are used for the study of plant genomic evaluation. [6,7] The development of DNA barcoding method to recognize these herbs is critically needed for the safety of patients. [8] Maine objective of work genotypic characterization of Flacourtia inermis through DNA sequence of matK and rbcL gene.…”

Section: Introductionmentioning

confidence: 99%

Genomic analysis of chloroplast matK and rbcL gene from Flacourtia inermis Roxb for plant DNA barcoding

Akilabindu

2019

GSC Biol. and Pharm. Sci.

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Identification of medicinally significant plant species is helpful for their utilization as medicine. Flacourtia inermis Roxb are important medicinal plant. Aim: To Genotypic characterization of Flacourtia inermis through DNA sequence of matK and rbcL gene. Flacourtia inermis Roxb DNA was isolated using NucleoSpin® Plant II Kit (Macherey-Nagel gene extraction) Kit. Isolated DNA was amplified by using PCR (matK and rbcL gene primers). Amplified matK and rbcL gene was sequenced by ABI 3500 DNA analyzer and the sequence quality was checked using sequence scanner software v1. The results exposed basic variability of the sequences. The matK and rcbL gene phylogenic tree was constructed using MEGA 6 software. Flacourtia inermis Roxb DNA was successfully isolated using NucleoSpin® Plant II Kit (Macherey-Nagel gene extraction) Kit and confirmed by agarose gel electrophoresis. Isolated matK and rbcL genomic DNA was successfully amplified by using PCR. From the matK sequence, BLASTn analysis result Flacourtia inermis species showed 99.20% relationship with Flacourtia jangomas and rbcL BLASTn analysis result of Flacourtia inermis species showed100% relationship with Flacourtia jangomas at NCBI database. From this study, the result concluded the matK and rcbL genomes can be used for DNA identification of Flacourtia inermis. The information obtained from the study would be helpful for further research involving genotypic identification of Flacourtia sp.

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The application of barcode DNA rbcL gene for identification of medicinal plants: red jabon and gofasa

Cited by 5 publications

References 8 publications

Dna Barcoding: Efficiency of Rbcl Gene for Sequence Characterisation of Cyperus Esculentus in Nigeria

Dna Barcoding: Efficiency of Rbcl Gene for Sequence Characterisation of Cyperus Esculentus in Nigeria

Application of the Smith Waterman and Jukes Cantor Algorithm in the Arrangement of the SARS CoV-2 Virus

Genomic analysis of chloroplast matK and rbcL gene from Flacourtia inermis Roxb for plant DNA barcoding

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