Assessment of DNA Barcoding for the Identification of Chenopodium murale L. (Chenopodiaceae)

Bafeel, Sameera O.; Arif, Ibrahim A.; Al-Homaidan, Ali A.; Khan, Haseeb A.; Ahamed, A. Jafar; Bakir, Mohammad Abdul

doi:10.5539/ijb.v4n4p66

Cited by 10 publications

(8 citation statements)

References 31 publications

(31 reference statements)

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“…Consequently, the missing species in the database cannot be identified and the method may assign the query sequence to an incorrect species [25]. Similar result was previously reported on Chenopodium murale [26]. Their study reported that when using BLAST, the specimen was identified as Chenopodium murale for both matK and rbcL gene with 100% sequence similarity.…”

Section: Species Identificationsupporting

confidence: 73%

Comparison of matK and rbcL DNA barcodes for genetic classification of jewel orchid accessions in Vietnam

Tran

Widiarsih

2021

Journal of Genetic Engineering and Biotechnology

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Background Jewel orchid is the common name of several orchid species which can be alike in morphological characteristics, but variable in medicinal properties. At present, two DNA barcode loci, namely, maturase K (matK) and ribulose 1,5-biphosphate carboxylase (rbcL), are intensively utilized for plant identification. However, the discrimination effectiveness of these loci is variable among plant species. This study was carried out to compare the identifying efficacy of these two loci on jewel orchid population collected throughout Vietnam. Results The results revealed that 21 jewel orchid accessions studied were segregated into four different species with significant variations. The discrimination power of matK and rbcL markers in this jewel orchid study displayed different efficiency level. The rbcL gene has higher distinguishing potential than either matK gene alone or the combination of both genes. Conclusion The findings of this project could provide valuable information that is necessary for classification, plant origin identification, breeding, and conservation program of jewel orchid in Vietnam.

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Section: Species Identificationsupporting

confidence: 73%

Comparison of matK and rbcL DNA barcodes for genetic classification of jewel orchid accessions in Vietnam

Tran

Widiarsih

2021

Journal of Genetic Engineering and Biotechnology

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“…They concluded that rbcL sequences identified 92% of the samples at the genus level but only 17% at the species level. In another study, Bafeel et al (2012a) performed molecular characterization of Chenopodium murale , an invasive herbaceous weed species in Saudi Arabia with negative allelopathic effects to enhance the morphological identification system. Amplification of the barcoding genes rbcL and matK in C. murale’s plastid region indicated that matK possesses high discrimination efficiency and the lowest average pairwise sequence similarity in comparison to rbcL , as well as the fact that the combination of rbcL and matK could yield high resolutions.…”

Section: Plant Dna Barcoding: An Emerging Approachmentioning

confidence: 99%

The Promise of Molecular and Genomic Techniques for Biodiversity Research and DNA Barcoding of the Arabian Peninsula Flora

et al. 2019

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The Arabian Peninsula is known to have a comprehensive and rich endowment of unique and genetically diverse plant genetic resources. Analysis and conservation of biological diversity is a crucial issue to the whole Arabian Peninsula. The rapid and accurate delimitation and identification of a species is crucial to genetic diversity analysis and the first critical step in the assessment of distribution, population abundance and threats related to a particular target species. During the last two decades, classical strategies of evaluating genetic variability, such as morphology and physiology, have been greatly complemented by phylogenetic, taxonomic, genetic diversity and breeding research molecular studies. At present, initiatives are taking place around the world to generate DNA barcode libraries for vascular plant flora and to make these data available in order to better understand, conserve and utilize biodiversity. The number of herbarium collection-based plant evolutionary genetics and genomics studies being conducted has been increasing worldwide. The herbaria provide a rich resource of already preserved and identified material, and these as well as freshly collected samples from the wild can be used for creating a reference DNA barcode library for the vascular plant flora of a region. This review discusses the main molecular and genomic techniques used in plant identification and biodiversity analysis. Hence, we highlight studies emphasizing various molecular techniques undertaken during the last 10 years to study the plant biodiversity of the Arabian Peninsula. Special emphasis on the role of DNA barcoding as a powerful tool for plant biodiversity analysis is provided, along with the crucial role of herbaria in creating a DNA barcode library.

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“…There are several studies from Peninsular Arabia reporting the use of core barcode markers (rbcL and matK) (Figure 1), along with multi-locus markers for the identification and discrimination of plant taxa. For example, Al Qurainy et al [23][24][25][26][27] used supportive markers (ITS, rpoB, rpoC1, PSBA-trnH, and rps16) as well as the core DNA barcode markers (rbcL and matK) on SA plant resources. Bafeel et al [23][24][25] efficiently used rbcL and matK markers for studying arid plants.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Arabian Vascular Plant Barcodes (rbcL and matK): Precision of Unsupervised and Supervised Learning Methods towards Accurate Identification

Jamdade¹,

Upadhyay²,

Shaer³

et al. 2021

Plants

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Arabia is the largest peninsula in the world, with >3000 species of vascular plants. Not much effort has been made to generate a multi-locus marker barcode library to identify and discriminate the recorded plant species. This study aimed to determine the reliability of the available Arabian plant barcodes (>1500; rbcL and matK) at the public repository (NCBI GenBank) using the unsupervised and supervised methods. Comparative analysis was carried out with the standard dataset (FINBOL) to assess the methods and markers’ reliability. Our analysis suggests that from the unsupervised method, TaxonDNA’s All Species Barcode criterion (ASB) exhibits the highest accuracy for rbcL barcodes, followed by the matK barcodes using the aligned dataset (FINBOL). However, for the Arabian plant barcode dataset (GBMA), the supervised method performed better than the unsupervised method, where the Random Forest and K-Nearest Neighbor (gappy kernel) classifiers were robust enough. These classifiers successfully recognized true species from both barcode markers belonging to the aligned and alignment-free datasets, respectively. The multi-class classifier showed high species resolution following the two classifiers, though its performance declined when employed to recognize true species. Similar results were observed for the FINBOL dataset through the supervised learning approach; overall, matK marker showed higher accuracy than rbcL. However, the lower rate of species identification in matK in GBMA data could be due to the higher evolutionary rate or gaps and missing data, as observed for the ASB criterion in the FINBOL dataset. Further, a lower number of sequences and singletons could also affect the rate of species resolution, as observed in the GBMA dataset. The GBMA dataset lacks sufficient species membership. We would encourage the taxonomists from the Arabian Peninsula to join our campaign on the Arabian Barcode of Life at the Barcode of Life Data (BOLD) systems. Our efforts together could help improve the rate of species identification for the Arabian Vascular plants.

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Assessment of DNA Barcoding for the Identification of Chenopodium murale L. (Chenopodiaceae)

Cited by 10 publications

References 31 publications

Comparison of matK and rbcL DNA barcodes for genetic classification of jewel orchid accessions in Vietnam

Comparison of matK and rbcL DNA barcodes for genetic classification of jewel orchid accessions in Vietnam

The Promise of Molecular and Genomic Techniques for Biodiversity Research and DNA Barcoding of the Arabian Peninsula Flora

Evaluation of Arabian Vascular Plant Barcodes (rbcL and matK): Precision of Unsupervised and Supervised Learning Methods towards Accurate Identification

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