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Species resolution success at the family, genus and species levels for single regions and combinations, based on Neighbor-Joining Tree analysis of all the species (samples ≥ 2), collected from the four plots (BB, JJYL, GGYL and LSL) of Xishuangbanna Nature Reserve in southwest China. (R, M, T, S represent rbcL, matK, trnH–psbA and ITS respectively.)
Source publication
Within a regional floristic context, DNA barcoding is more useful to manage plant diversity inventories on a large scale and develop valuable conservation strategies. However, there are no DNA barcode studies from tropical areas of China, which represents one of the biodiversity hotspots around the world.
A DNA barcoding database of an Asian tropic...
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Large-scale DNA barcoding provides a new technique for species identification and evaluation of relationships across various levels (populations and species) and may reveal fundamental processes in recently diverged species. Here, we analysed DNA sequence variation in the recently diverged legumes from the Psoraleeae (Fabaceae) occurring in the Cap...
This study aims at developing fast and accurate species identification methods for the plants of Mussaenda L. In the present study, DNA barcoding analysis was carried out on 89 individuals representing 20 species of Mussaenda in order to evaluate the performance of the four candidate barcoding loci (matK, rbcL, trnH-psbA, and ITS) and ITS2 region....
Citations
... These markers are now available in databases and used for practical applications. Researchers employ them to identify traits in wheat samples (Bakhadirov US. 2024; Parmentier 2013), investigate valuable economic characteristics (Pei N 2011), and assess genetic diversity based on geographic origin (Huang XC 2015). ...
... Contrary to the present study, Feng [10] reported 100% PCR amplification and sequencing success rate of the ITS region in Physalis species. The amplification and sequencing success rate of ITS2 has been shown in other studies to be much lower compared to other barcoding genes such as rbcL, matK and psbA-trnH [30,32]. The ITS2 phylogenetic tree based on Bayesian inference revealed that the Physalis accessions were closely clustered together with the sequences of P. cordata, P. peruviana and P. purpurea chosen from the BLASTn search. ...
Background
The genus Physalis belongs to the Solanaceae family and has different species with important nutritional and medicinal values. Species within this genus have limited morphological differences, a characteristic that hinders accurate identification, safe utilization and genetic conservation of promising genotypes. In addition, to prevent the perceived loss of Physalis diversity due to habitat destruction, species delimitation needs attention. In this study, we used the sequence and structural information of the internal transcribed spacer 2 (ITS2) barcode to efficiently identify and discriminate Physalis species from a collection of 34 Physalis accessions.
Methodology
Physalis plant samples were collected from eight Counties in Kenya based on the availability of the germplasm. The voucher specimens were identified using the botanical taxonomy method and were deposited in the University of Nairobi herbarium. A total of 34 Physalis accessions were identified and accessed for diversity based on the ITS2 barcode region. The sequence similarity of the ITS2 genes was analyzed through the Basic Local Alignment Search Tool (BLAST), the nearest Kimura-2-parameter (K2P) genetic distances were calculated and a phylogenetic tree was constructed using the Bayesian inference (BI) method in MrBayes 3.2.7a software. The differences in the ITS2 secondary structure between the species were analyzed.
Results
The success rate of PCR amplification and sequencing was 75% and 67%, respectively. The analyzed ITS2 sequences displayed significant inter-specific divergences, clear DNA barcoding gaps and high species identification efficiency. Based on the constructed phylogenetic tree, three Physalis species (Physalis peruviana, Physalis purpurea and Physalis cordata) were identified and were clustered in a homogenized distribution. High genetic diversity (0.36923) and genetic distance (0.703) were observed between Physalis peruviana and Physalis cordata. The highest genetic nucleotide diversity (0.26324) and distance (0.46) within species was obtained for Physalis peruviana. The differences in the secondary structures generated from this study discriminated between the Physalis species.
Conclusions
Our study demonstrated that ITS2 is a potential DNA barcode for effective identification and discrimination of Physalis species. The results of this study provide insights into the scientific basis of species identification, safe utilization, genetic conservation and future breeding strategies for this important nutritional and medicinal plant species.
... Investigations on wood-forming plant species showed a higher amplification rate of the cpDNA markers. The ITS in turn showed a higher species resolution for most wood species studied so far and thus a better differentiation between closely related species (Aubriot et al. 2013;Bolson et al. 2015;Chen et al. 2010;Duminil et al. 2012;Hartvig et al. 2015;Huang et al. 2015;Jiao et al. 2014;Liu et al. 2022;Muellner et al. 2011;Pang et al. 2010;Phong et al. 2014;Tripathi et al. 2013). Therefore, the ITS was used for identification in this study. ...
The control authorities of timber trade lack quick and easy methods to verify the legality of the traded product. This includes the clear identification of the timber species. In this study, a simple genetic method, the macroarray technique, was modified and optimised for this purpose. The internal transcribed spacer (ITS) was used as barcode region. Specific probes were designed and tested using this barcode of trade-relevant, CITES protected wood species and their look-alikes. The results reveal that 61 of these probes are suitable for identification purposes. Hence, 32 of the 50 investigated species can be clearly identified using the developed macroarray. Additional 15 species are represented by probes in groups of two to three species, which enables a delimitation of the species present. For four species, no identification was possible applying the probes created. The findings indicate the potential of time and cost savings compared to currently established methods in species control in the timber trade.
... In another study, rbcL showed lower (24.7-28.5%) species discrimination power among tropical trees from Xishuangbanna Nature Reserve in China [57]. In contrast, ITS DNA barcode which had maximum aligned sequence length (450 bases) among individual DNA barcodes showed the best level of species discrimination. ...
... In another study, rbcL showed lower (24.7-28.5%) species discrimination power among tropical trees from Xishuangbanna Nature Reserve in China [57]. In contrast, ITS DNA barcode which had maximum aligned sequence length (450 bases) among individual DNA barcodes showed the best level of species discrimination. ...
Background
Aconitum species, belonging to Ranunculaceae, have high medicinal importance but due to their overexploitation come under IUCN (International Union for Conservation of Nature) red list. The precise identification of the Aconitum species is equally important because they are used in herbal formulations. The present study aimed to develop an efficient DNA barcode system for the authentic identification of Aconitum species.
Methods and results
A set of 92 barcode gene sequences (including 12 developed during the present study and 80 retrieved from NCBI) of 5 Aconitum species (A. heterophyllum, A. vialoceum, A. japonicum, A. napellus, and A. stapfianum) were analyzed using three methods (tree-based, distance-based, and similarity-based) for species discrimination. The PWG-distance method was found most effective for species discrimination. The discrimination rate of PWG- distance ranged from 33.3% (rbcL + trnH-psbA) to 100% (ITS, rbcL + ITS, ITS + trnH-psbA and rbcL + ITS + trnH-psbA). Among DNA barcodes and their combinations, the ITS marker had the highest degree of species discrimination (NJ-40%, PWG-100% and BLAST-40%), followed by trnH-psbA (NJ-20%, PWG-60% and BLAST-20%). ITS also had higher barcoding gap as compared to other individual barcodes and their combinations. Further, we also analyzed six Aconitum species (A. balfourii, A. ferox, A. heterophyllum, A. rotundifolium, A. soongaricum and A. violaceum) existing in Western Himalaya. These species were distinguished clearly through tree-based method using the ITS barcode gene with 100% species resolution.
Conclusion
ITS showed the best species discrimination power and was used to develop species-specific barcodes for Aconitum species. DNA barcodes developed during the present study can be used to identify Aconitum species.
... Studies on C. murale obtained similar results using the matK and rbcL genes, showing 100% match with C. murale using BLAST, while, in BOLD, the rbcL gene showed a high degree of similarity with several taxa, including C. ambrosioides, C. album, and C. fcifolium, ranging from 96.3 to 100% [11]. Research by Huang et al. [34] showed that the combination of the rbcL and matK genes separated 40% of the sampled species in the combined data set for the family Apiaceae. Terefore, these two regions, matK and rbcL, have been shown to be ideal for species identifcation. ...
Chenopodium quinoa is an Andean species of great interest because of its excellent nutritional quality and great adaptability to different environmental conditions. In addition, the high phenotypic diversity has caused difficulties in the correct taxonomic identification, and there are few studies on the phylogenetic relationships of quinoa in Colombia. Therefore, the objective of this research was to determine the phylogenetic relationships of quinoa with the matK and rcbL chloroplastid genes to characterize the genetic diversity in Colombian quinoa. Evolutionary analyses were performed using nucleotide substitution rates, pattern, base composition, and phylogeny construction. The rbcL gene presented approximately 1344 bp, and matK had 646 bp, which were translated into 434 and 215 amino acids, respectively. The nucleotide composition of the genes showed high percentages of similarity and identity with the Chenopodium quinoa sequences registered in GenBank and BOLD. Similar phylogenetic trees were obtained with the rbcL and matK genes, and both concatenated sequences grouped the accessions into clades. The results showed that Colombian quinoa has low rates of genetic differentiation that may be due to the domestication processes of the species, the lack of certified seeds, and the constant exchange of seeds between farmers in the principal producing areas of the Andean region.
... While rbcL and matK had the lowest resolution for the data set with abundant species, ITS performed best for the four single barcodes using the three methods (71.68%/72.66%, 58.05%, and 61.33% for BM/BCM, the barcoding gap, and tree-based method, respectively) ( Table 2), which is consistent with previous DNA barcode studies (e.g., Hu et al. 38 ; Liu et al. 43 ; Gill et al. 33 ; Huang et al. 2 ). Moreover, we observed significant improvements in node supports for the plastid genome tree compared to the standard barcode tree, particularly for species-rich families (Fig. 2, Table 3). ...
The application of DNA barcoding has been significantly limited by the scarcity of reliable specimens and inadequate coverage and replication across all species. The deficiency of DNA barcode reference coverage is particularly striking for highly biodiverse subtropical and tropical regions. In this study, we present a comprehensive barcode library for woody plants in tropical and subtropical China. Our dataset includes a standard barcode library comprising the four most widely used barcodes (rbcL, matK, ITS, and ITS2) for 2,520 species from 4,654 samples across 49 orders, 144 families, and 693 genera, along with 79 samples identified at the genus level. This dataset also provides a super-barcode library consisting of 1,239 samples from 1,139 species, 411 genera, 113 families, and 40 orders. This newly developed library will serve as a valuable resource for DNA barcoding research in tropical and subtropical China and bordering countries, enable more accurate species identification, and contribute to the conservation and management of tropical and subtropical forests.
... The rbcL region of Physalis in this study was amplified more effectively compared to the ITS2 region. This concurs with previous studies, which showed higher amplification and sequencing success rate for rbcL compared to ITS2 [30,50]. The high success rate of rbcL amplification is attributed to the high conservation of the gene and its low frequency rates of mutation [30]. ...
... This indicates the inefficiency of using rbcL in discriminating plant species, and thus we consider this region to offer little information relevant to the taxonomic classification of Physalis. The inefficiency of rbcL in discriminating plant species compared to other barcodes has also been noted in other studies [30,50,55]. Similar results were presented in other studies, where the phylogenetic tree-based method could not effectively identify species of plants based on rbcL sequences [50]. ...
... The inefficiency of rbcL in discriminating plant species compared to other barcodes has also been noted in other studies [30,50,55]. Similar results were presented in other studies, where the phylogenetic tree-based method could not effectively identify species of plants based on rbcL sequences [50]. A study that used over 10,000 rbcL sequences from the GenBank to identify plant species also came up with similar conclusions to this study-that rbcL can only discriminate at the genus level [56]. ...
Plants of the genus Physalis are of economic interest because of their fleshy edible fruits with high nutritional value. Some species have high medicinal value with a long history of ethno-medicinal use to treat diverse diseases. There is therefore a need to correctly discriminate the different species of Physalis for proper utilization. Although most Physalis species have unique morphologies, their vegetative stages are identical, making it difficult to accurately identify them based on morphological characteristics. DNA barcoding has the potential to discriminate species accurately. In this study, ribulose bisphosphate carboxylase large (rbcL) and internal transcribed spacer 2 (ITS2) regions were used to discriminate Physalis species and to reveal their phylogenetic relationships and genetic diversity. Physalis plant samples were collected from seven counties in Kenya based on the availability of the germplasm. The voucher specimens were identified using the botanical taxonomy method and were deposited in the University of Nairobi herbarium. Genomic DNA was isolated from leaf samples of 64 Physalis accessions and used for PCR amplification and the sequencing of rbcL and ITS2 barcode regions. The discriminatory ability of the barcodes was based on BLASTn comparison, phylogenetic reconstruction and cluster analysis, and the determination of inter- and intra-specific distances. The nucleotide polymorphism, genetic diversity and distance of the identified Physalis species were determined using DnaSP and MEGA 11.0 software. Species discrimination was more robust using ITS2 sequences. The species identified and discriminated by ITS2 sequences were Physalis purpurea, Physalis peruviana and Physalis cordata. The rbcL sequences were only able to identify Physalis to the genus level. There was high interspecific and low intraspecific divergence within the identified Physalis species based on ITS2 sequences. The ITS2 barcode is an ideal DNA barcode for use in the discrimination of species, as well as in genetic diversity studies of Physalis accessions in Kenya.
... DNA barcoding has been recognized as an important approach in molecular systematics, emphasizing the diversity of groups in terms of taxonomic features, due to its independence from environmental and geographical conditions, its time-saving nature, and its feasibility in handling of a very large number of plants. The feasibility of DNA barcoding for molecular taxonomy has been recently validated, especially with the revolution in metagenomics and next-generation high-throughput sequencing technologies, achieving a high degree of accuracy and reproducibility (Huang et al., 2015). Traditional morphometric taxonomy is labor-intensive and time-consuming because it is dependent on the organism's developmental stage (Costion et al., 2011;Huang et al., 2015). ...
... The feasibility of DNA barcoding for molecular taxonomy has been recently validated, especially with the revolution in metagenomics and next-generation high-throughput sequencing technologies, achieving a high degree of accuracy and reproducibility (Huang et al., 2015). Traditional morphometric taxonomy is labor-intensive and time-consuming because it is dependent on the organism's developmental stage (Costion et al., 2011;Huang et al., 2015). Thus, integrative approaches for plant taxonomic studies have become critical technologies for plant identification, especially given the scientific reductionism of traditional taxonomy (Crisci et al., 2020). ...
... Estimation of volatile chemical compounds by GC-MS for plant differentiation has been recognized as one of the key technological tools for metabolic profiling and taxonomic analysis that can be used to confirm traditional taxonomic features. Traditional morphometric taxonomy is time-consuming due to its dependence on the plant's developmental stage and involves labor-intensive work based on predetermined categories (Costion et al., 2011;Huang et al., 2015). GC-MS metabolic profiling has been frequently used for taxonomic purposes in Convolvulaceae (Schimming et al., 2005), the tree fern Cyathea (Cyatheaceae) (Janakiraman and Johnson, 2016), Solanum Each entry shows the probability of substitution (r) from one base (row) to another base (column). ...
Among the 70–80 species of the genus Lycium (family Solanaceae) disjunctly distributed around the world, only three are frequently distributed in different locations in Egypt. Due to the morphological similarities between these three species, there is a need for alternative tools to distinguish them. Thus, the objective of this study was to revise the taxonomic features of Lycium europaeum L., Lycium shawii Roem. & Schult., and Lycium schweinfurthii var. aschersonii (Dammer) Feinbrun in consideration of their anatomical, metabolic, molecular, and ecological characteristics. In addition to analysis of their anatomical and ecological features, DNA barcoding was performed for molecular characterization through internal transcribed spacer (ITS) sequencing and start codon targeted (SCoT) markers. Furthermore, metabolic profiling of the studied species was conducted based on gas chromatography–mass spectrometry (GC-MS). The observed anatomical features of the adaxial and abaxial epidermal layers, type of mesophyll, crystals, number of palisade and spongy layers, and the vascular system showed variations between the studied species. Beyond this, the anatomy of the leaves showed an isobilateral structure in the studied species, without distinct differences. Species were molecularly identified in terms of ITS sequences and SCoT markers. The ITS sequences were deposited in GenBank with accession numbers ON149839.1, OP597546.1, and ON521125.1 for L. europaeum L., L. shawii, and L. schweinfurthii var. aschersonii, respectively. The sequences showed variations in GC content between the studied species; this was 63.6% in L. europaeum, 61.53% in L. shawii, and 63.55% in L. schweinfurthii var. aschersonii. A total of 62 amplified fragments, including 44 polymorphic fragments with a ratio of 70.97%, were obtained in the SCoT analysis, as well as unique amplicons in L. europaeum L., shawii, and L. schweinfurthii var. aschersonii of 5, 11, and 4 fragments, respectively. Through GC-MS profiling, 38 compounds were identified with clear fluctuations in the extracts of each species. Of these, 23 were distinguishing chemicals that could help in chemical identification of the extracts of the studied species. The present study succeeds in identifying alternative clear and diverse characteristics that can be used to distinguish between L. europaeum, L. shawii, and L. schweinfurthii var. aschersonii.
... If the process of study and research in the taxonomic field and knowledge of the identity of species and genera is done in a traditional way, this matter takes a long time because it depends primarily on the basic stages of the growth of the organism. Thus, these studies are very stressful and arduous because they also depend on the results of previous classifications, (Costion et al., 2011& Huang et al., 2015. Taking into account that the taxonomic experience has begun to erode and decline due to modern mechanisms of scientific reduction. ...
The DNA barcoding technique is considered one of the most successful scientific leaps in the field of genetic engineering, especially in molecular genetics. Where this technique was able to decipher the puzzles and many blades that were not known to human beings in the past. This technology has also provided many positive paths in many fields and different branches of science. This technique was developed mainly to identify the different life species present in a specific ecological area, and therefore it is a very important method in studying the biodiversity of living organisms in general and this is the main objective of this research. Also, one of the most important uses of DNA barcoding is preserving the endangered species of various plants and animals after studying their biodiversity, preserving their sequencing in the gene bank and making decisions according to their optimal use in the future, which brings positive benefits to humans.
