Endorsement and Phylogenetic Analysis of some Fabaceae Plants based on DNA Barcoding gene MatK (original) (raw)
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Phylogenetic analysis of chloroplast matK gene from Zingiberaceae for plant DNA barcoding
MaturaseK gene (MatK) of chloroplast is highly conserved in plant systematics which is involved in Group II intron splicing. The size of the gene is 1500 bp in length, located with in the intron of trnK. In the present study, matK gene from Zingiberaceae was taken for the analysis of variants, parsimony site, patterns, transition/tranversion rates and phylogeny. The family of Zingiberaceae comprises 47 genera with medicinal values. The matK gene sequence have been obtained from genbank and used for the analysis. The sequence alignments were performed by Clustal X, transition/transversion rates were predicted by MEGA and phylogenetic analyses were carried out by PHYLIP package. The result indicates that the Zingiberaceae genus Afromonum, Alpinia, Globba, Curcuma and Zingiber shows polyphylogeny. The overall variants between the species are 24% and transition/transversion rate is 1.54. Phylogenetic tree was designed to identify the ideal regions that could be used for defining the inter and intera-generic relationships. From this study it could be concluded that the matK gene is a good candidate for DNA barcoding of plant family Zingiberaceae.
Molecular taxonomy via DNA barcodes for species identification in selected genera of Fabaceae
Jurnal Pengelolaan Sumberdaya Alam dan Lingkungan (Journal of Natural Resources and Environmental Management)
Fabaceae is an invaluable plant family with considerable ecological and economic importances for example as food sources, bio-fertilizer, and medicinal plants. However, Fabaceae has been overexploited in Indonesia and several species belong to this family are critically endangered. Due to morphological similarity, rapid and accurate identification of Fabaceae species is essential to support its conservation efforts. Nowadays, species identification through DNA barcoding has become an effective taxonomic classification tool. This study was aimed to evaluate the effectiveness of chloroplast markers, matK and rbcL and the combination (matK+rbcL), as DNA barcodes for the identification of seleted genera in Fabaceae. The result showed that matK+rbcL and matK had the highest level of identification (90% and 82.05%) of the investigated genera, respectively. Additionally, matK had the highest mean of interspesific distance (0.134) and intraspecific distance (0.003). The combined barcode mat...
BMC Research Notes, 2012
Background Based on the testing of several loci, predominantly against floristic backgrounds, individual or different combinations of loci have been suggested as possible universal DNA barcodes for plants. The present investigation was undertaken to check the applicability of the recommended locus/loci for congeneric species with Dendrobium species as an illustrative example. Results Six loci, matK, rbcL, rpoB, rpoC1, trnH-psbA spacer from the chloroplast genome and ITS, from the nuclear genome, were compared for their amplification, sequencing and species discrimination success rates among multiple accessions of 36 Dendrobium species. The trnH-psbA spacer could not be considered for analysis as good quality sequences were not obtained with its forward primer. Among the tested loci, ITS, recommended by some as a possible barcode for plants, provided 100% species identification. Another locus, matK, also recommended as a universal barcode for plants, resolved 80.56% species. ITS rema...
Utility of DNA Barcoding for Plant Biodiversity Conservation
Plant Breeding and Biotechnology, 2013
DNA barcoding is a technique that provides rapid identification of species without using morphological cues. The method employs relatively small-standardized DNA fragments as tags to define or discover species. In plants, the mitochondrial genome evolves much more slowly than in animals. There is currently no consensus on which candidate markers comprise the best plant DNA barcoding region; however, DNA barcodes such as rbcL, matK, psbA-trnH and ITS have been proposed for the plant kingdom. And also very recently the chloroplast intergenic spacer (IGS) like trnE-trnT, trnT-psbD, ndhF-rpl32 and rpl14-rpl16 were also employed for discriminating the cultivar species. The region ITS2 showed better intra-species variation, followed by psbA-trnH. Several analyses reveal that the ITS2 region is able to distinguish all tested species of the plant kingdom, but evaluations of DNA barcodes have to be conducted for more species covering many genera to confirm the above results. In this review we discussed the current view of DNA barcoding.
PLoS ONE, 2013
Background: DNA barcoding as a tool for species identification has been successful in animals and other organisms, including certain groups of plants. The exploration of this new tool for species identification, particularly in tree species, is very scanty from biodiversity-rich countries like India. rbcL and matK are standard barcode loci while ITS, and trnH-psbA are considered as supplementary loci for plants. Methodology and Principal Findings: Plant barcode loci, namely, rbcL, matK, ITS, trnH-psbA, and the recently proposed ITS2, were tested for their efficacy as barcode loci using 300 accessions of tropical tree species. We tested these loci for PCR, sequencing success, and species discrimination ability using three methods. rbcL was the best locus as far as PCR and sequencing success rate were concerned, but not for the species discrimination ability of tropical tree species. ITS and trnH-psbA were the second best loci in PCR and sequencing success, respectively. The species discrimination ability of ITS ranged from 24.4 percent to 74.3 percent and that of trnH-psbA was 25.6 percent to 67.7 percent, depending upon the data set and the method used. matK provided the least PCR success, followed by ITS2 (59. 0%). Species resolution by ITS2 and rbcL ranged from 9.0 percent to 48.7 percent and 13.2 percent to 43.6 percent, respectively. Further, we observed that the NCBI nucleotide database is poorly represented by the sequences of barcode loci studied here for tree species. Conclusion: Although a conservative approach of a success rate of 60-70 percent by both ITS and trnH-psbA may not be considered as highly successful but would certainly help in large-scale biodiversity inventorization, particularly for tropical tree species, considering the standard success rate of plant DNA barcode program reported so far. The recommended matK and rbcL primers combination may not work in tropical tree species as barcode markers.
Shneyer RJG 2009-DNA barcoding in plants
DNA barcoding was proposed as a method for recognition and identification of eukaryotic species through comparison of sequences of a standard short DNA fragment-DNA barcode-from an unknown specimen to a library of reference sequences from known species. This allows identifying an organism at any stage of development from a very small tissue sample, fresh or conserved many years ago. Molecular identification of plant samples can be used in various scientific and applied fields. It would also help to find new species, which is particularly important for cryptogamic plants. An optimal DNA barcode region is a small fragment presented in all species of a major taxonomic group, having invariable nucleotide sequence in all members of the same species, but with sufficient variation to discriminate among the species. This fragment should be flanked by low-variable regions for use of universal primers in PCR for amplification and sequencing. The DNA barcode that is well established in animals is a sequence of a fragment of the mitochondrial cytochrome c oxidase gene CO1. However, searching for DNA barcode in plants proved to be a more challenging task. No DNA region universally suitable for all plants and meeting all of the necessary criteria has been found. Apparently, a multilocus or two-stage approach should be applied for this purpose. Several fragments of the chloroplast genome ( trnH-psbA, matK, rpoC, rpoB, rbcL ) in combinations of two or three regions were suggested as candidate regions with highest potential, but more representative samples should be examined to choose the best candidate. The possibility is discussed to use as DNA barcode internal transcribed spacers (ITS) of nuclear rRNA genes, which are highly variable, widely employed in molecular phylogenetic studies at the species level, but also have some limitations.
DNA Barcoding in Plants and Current Molecular Issues
Scholars International Journal of Biochemistry, 2020
DNA barcoding especially used in the field of molecular biology that uses primers with 500-700 segments to classify various species at molecular and genetic level. This review focuses on the role of DNA barcoding in conservation of biodiversity and current applications for the discovery of species. Some species of plants and animals remain unidentified at molecular level. DNA barcoding uses molecular tools for the discovery of species found in natural ecosystem and playing important role in biodiversity conservation. Genetic barcoding mainly focuses on conservation strategies on populations due to differences found in the mitochondrial DNA. The most commonly used DNA barcodes for the plant species are ITS, rbcL, psbA-trnH and matK. DNA barcodes has several applications for the detection of plants species by providing specific information about the taxa. There is need to use DNA barcoding in combinations with other sciences such as ecology and taxonomy methods for conservation of biodiversity. There is also need to use databases for appropriate storage of data about species to conserve biodiversity.
Evolutionary Analysis based on DNA Barcoding of Certain Aquatic Plants using rbcL Gene Sequences
DNA barcoding is currently gaining popularity due to its simplicity and high accuracy as compared to the complexity and subjective biases associated with morphology-based identification of taxa. The standard chloroplast DNA barcode for land plants is normally recommended by the Consortium for the Barcode of Life (CBOL) plant working group that needs to be evaluated for a wide range of plant species. In Vadodara district of Gujarat, there are many natural and manmade seasonal wetlands that serve as important gateways for the migratory waterfowl. Hence these wetlands contribute significantly towards balancing of ecosystem. Many researchers had identified plant species of these wetlands by traditional methods but the aspect of identification of plants through barcoding has largely been ignored. We therefore, tested the potential of the rbcL marker for the identification of aquatic plants belonging to diverse families of some wetlands of Vadodara. This had been carried out by 2-locus combination of rbcL and matK as the standard plant barcode Maximum likelihood tree analysis was also performed to evaluate the discriminatory power of the rbcL gene. The classical taxonomic classification was then compared with the classification obtained through DNA Barcode tree. For evolutionary analysis, Tajima's D Test, Substitutional Matrix and Nucleotide substitution model analysis were performed. Our findings showed that using rbcL gene sequences, majority of the samples, i.e. (90%) were identified at genus level but at species level only 10% identification was possible.
Searching for DNA barcodes in plants
American-Eurasian Journal of Agricultural and Environmental Science, 2015
The utility of large scale standardized DNA sequencing and bioinformatics tools are now increasing in the area of plant systematics and evolution while a short DNA segment can be effectively used for the identification of species. However the consensus is still lacked about the precise DNA segments that are to be used for identification. DNA barcoding was proposed as a technique for recognizing and identifying a eukaryotic species through comparison of sequences of a standard short DNA fragment referred as a DNA barcode from an unknown specimen to a library of reference sequences from known species. An optimal DNA barcode region is a small fragment which is present in all representatives of the major taxonomic group which is accompanied by invariable nucleotide sequence in all members of the same species, but with enough variation to discriminate among the species. DNA barcoding is accomplished in animals in which Cytochrome c oxidase gene [CO1] is utilized as a barcode but finding a barcode in plants is proved to be a challenge. Several fragments of DNA [rbcL, matK, rpoB, rpoC, trnh-psbA etc] or combination of these segments have been proposed for identification of plants and systematic studies. Internal transcribed spacer region of nuclear ribosomal DNA are also evolving as a potential barcode for the major plant groups. With no doubts DNA barcoding will be reshaped in the future. The present review highlights the potential of DNA barcoding for the characterization of land plants and future prospects.