Discriminatory power of rbcL barcode locus for authentication of some of United Arab Emirates (UAE) native plants

Maloukh, Lina; Kumarappan, Alagappan; Jarrar, Mohammad; Salehi, Jawad; El-wakil, Houssam; Lakshmi, T

doi:10.1007/s13205-017-0746-1

Cited by 40 publications

(26 citation statements)

References 37 publications

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“…This may possibly be linked to sample contamination or a deficiency on the part of the rbcL resolution. The identified genetic distances (0.5000 ± 0.4770 -5.0560 ± 2.5760) based on K2P model regarding the inter-groups were in agreement with the previous works of other researchers in yams [24] [54] and in authentication of native plants [60]. High genetic diversity indices were obtained from between group calculations, producing 5.0560 ± 2.5760 with the highest in two combined groups (groups VI and VII) and this demonstrates higher interspecific diversity than intraspecific one within the yam accessions as obtained in an earlier report involving ornamental plants with interspecific value of 3.080 [61].…”

Section: Discussionsupporting

confidence: 90%

Genetic Diversity and DNA Barcoding of Yam Accessions from Southern Nigeria

Ude¹,

Igwe²,

McCormick³

et al. 2019

AJPS

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Knowledge of genetic diversity and barcoding of yam is lacking in Enugu and Ebonyi States of southern Nigeria. Therefore, DNA barcoding was used to facilitate identification and biodiversity studies of yam species from Southern Nigeria. Seventy five yam accessions were collected from Enugu and Ebonyi States, including International Institute of Tropical Agriculture for DNA extraction and amplification using a chloroplast DNA (cpDNA) ribulose-1,5bisphosphate carboxylase (rbcL) marker. There was high level of similarity among the accessions and presence of 534 conserved and 7 variable sites. A transversional mutation of G/T at a consensus position of 335 was identified followed by transitions at 362 (A/G), 368 (A/G), 371 (C/T) and 391 (C/T) within the accessions. Phylogeny resolved the yam accessions into ten major groups with their bootstrap values ranging from 0 -100. Phylogenetic diversity was highest in group X, followed by VII, VI and IX. The inter-group genetic distance based on Kimura 2-parameter model ranged from 0.5000 ± 0.4770 -5.0560 ± 2.5760, while the intra-group had 0.5250 ± 0.5000 -2.0103 ± 1.2579. The mean genetic diversity within the entire population was 0.7970 ± 0.06910. BLAST analysis of total bit score, query coverage, and percentage identity were in the ranges of 411 -1011, 99% -100% and 97% -100%, respectively. However, the rbcL could not resolve the yam accessions well following the comparative assessment of some discrepancies in the detected number of species from phylogenetic groupings, genetic diversity indices and NCBI BLAST hits, thereby, exposing the inefficiency of this marker in dis-How to cite this paper: Ude, G.N., Igwe, et al.criminating the yam accessions. It was demonstrated that rbcL is not an effective marker; therefore, it should not be recommended as a standard-alone marker of choice for DNA barcoding of yam accessions, especially, when accurate identification, discrimination and estimation of genetic diversity of this vital crop are of paramount importance for crop improvement and germplasm conservation.

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Section: Discussionsupporting

confidence: 90%

Genetic Diversity and DNA Barcoding of Yam Accessions from Southern Nigeria

Ude¹,

Igwe²,

McCormick³

et al. 2019

AJPS

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“…The NJ method in reconstructing kinship relationships based on the proximity of the evolutionary distance that occurs, indicated by the value of the kinship distance matrix among individuals. The evolutionary distance can be considered as genetic distance which shows the evolutionary rate is different for each cultivar (Maloukh et al, 2017). The lower the matrx value the closer kinship relationship and vice versa, the higher kinship matrix value, the farther the kinship distance between the two cultivars in the cladogram.…”

Section: Results Rbcl Sequence Analysismentioning

confidence: 99%

VARIASI INFRASPESIES MACANG (Mangifera foetida) BERDASARKAN SEKUEN GEN rbcL

Rafidah¹,

Fitmawati²,

Juliantari³

et al. 2019

Al-Kauniyah J. Biol.

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AbstrakMacang (Mangifera foetida) adalah jenis mangga kosmopolit dengan vigoritas yang kuat. Macang banyak ditemukan di perkarangan dan kebun dan bersifat semi liar. Penurunan luas lahan seperti deforestasi dapat mengakibatkan keanekaragaman kultivar macang juga mengalami penurunan secara cepat. Penelitian ini bertujuan untuk menganalisis dan merekonstruksi hubungan kekerabatan antar kultivar macang menggunakan sekuen gen rbcL. Sampel berasal dari koleksi hasil eksplorasi mangga Sumatera bagian Selatan, yaitu Provinsi Bengkulu, Lampung dan Sumatera Selatan. Ekstraksi DNA dilakukan dengan menggunakan metode CTAB yang dimodifikasi, kemudian DNA diamplifikasi dengan menggunakan primer spesifik rbcL forward dan reverse, dan dilakukan sekuensing serta analisis filogenetik. Rekontruksi pohon filogenetik menggunakan program PAUP* versi 4.0b10 dengan metode Maximum Parsimony (MP) dan Neighbor Joining (NJ). Kladogram dengan MP diperoleh dua klad, yaitu pada klad I terdiri dari kultivar Macang lonjong dan Macang lado, sedangkan klad II terdiri dari kultivar Macang bulat. Berdasarkan metode NJ, diperoleh Macang bulat memiliki jarak genetik lebih panjang sehingga dianggap sebagai individu yang lebih primitif daripada kultivar yang lain. Dengan demikian, dari penelitian ini diperoleh informasi dan bukti dari status taksonomi kultivar macang.Abstract Mangifera foetida is a species of cosmopolitan mango with strong vigor. Some M. foetida are found in some front houses and gardens and has a character of semi-wild in its cultivation. Decreases in land area, such as deforestation, can lead to a rapid decline in their diversity of cultivars. This study aimed to analyze and reconstructs the phylogenetic relationship among M. foetida cultivars using the rbcL gene sequences. Samples were collected from the exploration within the area of South Sumatra, such as Provinces of Bengkulu, Lampung and South Sumatra. The DNA extraction was carried out using the modified CTAB method, followed by DNA amplification using rbcL-specific primers, sequencing, and phylogenetic analysis. The phylogenetic trees were reconstructed using the PAUP* version 4.0b10 by using the method of Maximum Parsimony (MP) and Neighbor Joining (NJ). Cladogram of the MP tree showed two clades that the clad I consisted of M. foetida (Macang lonjong) and M. foetida (Macang lado) cultivars, whereas clad II consisted of M. foetida (Macang bulat) cultivar. The NJ tree showed that M. foetida (Macang bulat) has a longer genetic distance so it is considered as a more primitive cultivar than others. Therefore, information and evidences from the taxonomic status of the M. foetida cultivars were obtained from this study.

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“…This finding was contrary to previous studies that suggested using the rbcL barcode for the identification of rare desert plants. For example, Maloukh et al (2017) used rbcL and matK loci for a group of 51 native plants (belonging to 22 families) from the United Arab Emirates. Our results are consistent with those of Guo et al (2016), as these authors mentioned the failure of the chloroplast genes rbcL and matK in plant specimens identification.…”

Section: Discussionmentioning

confidence: 99%

“…PCRs of rbcL and matK markers for the chloroplast genome were amplified following the method described by Maloukh et al (2017), using a total volume of 50 µL, including 25 µL of Taq PCR Master Mix, 22 µL of distilled water, 1 µL of forward primer, 1 µL of reverse primer and 1 µL of the DNA template (50 -80 ng/µL). Amplification was performed in a Veriti 96-Well Fast Thermal Cycler (Applied Biosystems, CA, USA), with an initial denaturation at 94°C for 3 min.…”

Section: Dna Amplification and Sequencingmentioning

confidence: 99%

Research Article Evaluation of the capacity of the DNA barcode ITS2 for identifying and discriminating dryland plants

Al-Juhani¹

2019

Genet. Mol. Res.

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Many of the plants that grow in arid and semi-arid regions under harsh conditions (drought, salinity and misuse) are of medical importance. Desert plants also provide other benefits; so conservation efforts should be strengthened in these areas. In this study, three DNA barcodes-chloroplast maturase-K (matK), ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL) and secondary internal transcribed spacer (ITS2)-were tested in order to determine the ability of these markers to distinguish between various species. A total of 93 fresh and dry samples belonging to 30 plant families were examined. These are native to the arid lands around Makkah in the Kingdom of Saudi Arabia. Various tools and tests were used to evaluate the efficiency of the barcode markers; these included the basic local alignment search tool (BLAST), as well as the use of inter-and intraspecific distances, barcode gap, prediction of the secondary structure of the ITS2 and phylogenetic methods. The results confirmed the efficiency and superiority of the ITS2 loci over two chloroplast genes: matK and rbcL. ITS2 had a 97% success rate with amplification and a 95% success rate with sequencing, showing 100% identification at the family level, 77% identification at the genus level and 70% species resolution. A clear barcode gap was observed between inter-and intraspecific distances. Identification was achieved even in cases of degraded samples or old herbarium ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 18 (1): gmr18133 W.S. Al-Juhani 2 specimens. This study contributes to DNA barcode data by adding 224 DNA sequences of desert plants to the National Center for Biotechnology Information NCBI database. The results of this study are important and useful for application in each of the following fields: validation of medicinal plant identity, conservation, and taxonomic and evolutionary studies.

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Discriminatory power of rbcL barcode locus for authentication of some of United Arab Emirates (UAE) native plants

Cited by 40 publications

References 37 publications

Genetic Diversity and DNA Barcoding of Yam Accessions from Southern Nigeria

Genetic Diversity and DNA Barcoding of Yam Accessions from Southern Nigeria

VARIASI INFRASPESIES MACANG (Mangifera foetida) BERDASARKAN SEKUEN GEN rbcL

Research Article Evaluation of the capacity of the DNA barcode ITS2 for identifying and discriminating dryland plants

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