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Background: Cinnamomum parthenoxylon is an important component of tropical Vietnam and has major ecological and economic significance, which has been threatened in recent decades due to the destruction of its habitat and overexploitation. Methods: In the present study, first, three chloroplast DNA (cpDNA) regions (matK, rbcL, and trnH-psbA) were initially examined to identify C. parthenoxylon species using Maximum Likelihood (ML). Then, genetic diversity analysis of C. parthenoxylon species in the Song Hinh protection forest, Phu Yen Province, Vietnam. Results: The nucleotide sequences of matK, rbcL, and trnH-psbA were determined to be 786bp, 513bp, and 464bp, respectively. The novel sequences have been deposited in Genbank with matK (PQ106670-PQ106689), rbcL (PQ106690-PQ106709), and trnH-psbA (PQ1066710-PQ106729). The analysis revealed that the mean base compositions of matK, rbcL, and trnH-psbA were nucleotide T (34.8%, 28.3%, and 30.4%), C (19.4%, 22.5%, and 15.1%), A (29.1%, 26.6%, and 39.8%), and G (16.7%, 22.7%, and 14.7%), respectively. In each of the three cpDNA regions, the GC content was discovered to be significantly lower than the AT content. According to ML phylogenetic analyses, all samples in the Song Hinh protection forest are closely related to C. parthenoxylon in GenBank, with robust supporting values. Moreover, only 0.25% (2 haplotypes) of the sequences showed polymorphism in the matK region, whereas 0.78% (4 haplotypes) in the rbcL region. The most variable trnH-psbA (3.44%) (16 haplotypes) intergenic region was the most useful genetic diversity analysis of C. parthenoxylon. The genetic variations in C. parthenoxylon were moderate, with an average number of nucleotide differences (Kt = 1.042–4.984), haplotype diversity (Hd = 0.521–0.916), and nucleotide diversity (Pi = 1.33–10.74 × 10–3). Conclusions: The results of this study have the potential to provide valuable information that is essential for the classification, and identification of the plant’s origin, propagation, and conservation program of C. parthenoxylon in Vietnam.

The article "Exploring biodiversity of Uruguayan vascular plants through DNA barcoding" published in Frontiers in Genetics on October 15, 2024, discusses the use of DNA barcoding to study the biodiversity of Uruguayan vascular plants. The study aims to address the decline in biodiversity in Uruguay by establishing a DNA barcode national network. By analyzing 171 sequences from four loci for 50 vascular plant species, the researchers identified suitable markers for plant DNA barcoding and contributed to the Uruguayan Barcode of Life Initiative. The study highlights the importance of creating a comprehensive public database for species identification and biodiversity research. [Extracted from the article]

Background: Cinnamomum parthenoxylon is an important component of tropical Vietnam and has major ecological and economic significance, which has been threatened in recent decades due to the destruction of its habitat and overexploitation. Methods: In the present study, first, three chloroplast DNA (cpDNA) regions (matK, rbcL , and trnH-psbA) were initially examined to identify C. parthenoxylon species using Maximum Likelihood (ML). Then, genetic diversity analysis of C. parthenoxylon species in the Song Hinh protection forest, Phu Yen Province, Vietnam. Results: The nucleotide sequences of matK, rbcL , and trnH-psbA were determined to be 786bp, 513bp, and 464bp, respectively. The novel sequences have been deposited in Genbank with matK (PQ106670-PQ106689), rbcL (PQ106690-PQ106709), and trnH-psbA (PQ1066710-PQ106729). The analysis revealed that the mean base compositions of matK, rbcL , and trnH-psbA were nucleotide T (34.8%, 28.3%, and 30.4%), C (19.4%, 22.5%, and 15.1%), A (29.1%, 26.6%, and 39.8%), and G (16.7%, 22.7%, and 14.7%), respectively. In each of the three cpDNA regions, the GC content was discovered to be significantly lower than the AT content. According to ML phylogenetic analyses, all samples in the Song Hinh protection forest are closely related to C. parthenoxylon in GenBank, with robust supporting values. Moreover, only 0.25% (2 haplotypes) of the sequences showed polymorphism in the matK region, whereas 0.78% (4 haplotypes) in the rbcL region. The most variable trnH-psbA (3.44%) (16 haplotypes) intergenic region was the most useful genetic diversity analysis of C. parthenoxylon. The genetic variations in C. parthenoxylon were moderate, with an average number of nucleotide differences (Kt = 1.042–4.984), haplotype diversity (Hd = 0.521–0.916), and nucleotide diversity (Pi = 1.33–10.74 × 10–3). Conclusions: The results of this study have the potential to provide valuable information that is essential for the classification, and identification of the plant's origin, propagation, and conservation program of C. parthenoxylon in Vietnam. [ABSTRACT FROM AUTHOR]

Obtaining reliable species identification of the legume genus Caragana has been challenging. Until now, species identification was mostly carried out utilizing diagnostic morphological characteristics, in addition to some successful applications of secondary chemical compounds. This study was designed to establish a DNA barcoding protocol enabling unambiguous identification of 238 accessions belonging to 67 species of Caragana. The performance of four DNA barcoding regions nrITS, trnH‐psbA, matK, and rbcL was explored using three analytical approaches, Pairwise Genetic Distance, Sequence Similarity and Phylogenetic Tree method. The chloroplast regions rbcL and matK showed lower discriminatory power compared with the nuclear region internal transcribed spacer (ITS) and the chloroplast region trnH‐psbA. The nrITS outperformed the other regions in the resolution rate. The present study brings forth an efficient barcode locus for Caragana. A barcode based either on a single‐locus nrITS or the combination of nrITS and trnH‐psbA was found to be most suitable for species discrimination with distinctive barcoding gaps. An attempt has also been made to resolve taxonomic issues in the Caragana opulens complex. DNA barcoding tools when complemented with alpha taxonomic evidence can aid in solving complex systematic problems, especially when taxa are characterized by overlapping traits, such as species belonging to the Fabaceae family. [ABSTRACT FROM AUTHOR]

Abstract Background Dalbergia odorifera is a precious tree species with unique economic and medicinal values, which is difficult to distinguish from Dalbergia tonkinensis by traditional identification methods such as morphological characteristics and wood structure characteristics. It has been demonstrated that the identification of tree species can be effectively achieved using DNA barcoding, but there is a lack of study of the combined sequences used as DNA barcodes in the two tree species. In this study, 10 single sequences and 4 combined sequences were selected for analysis, and the identification effect of each sequence was evaluated by the distance-based method, BLAST-based search, character-based method, and tree-based method. Results Among the single sequences and the combined sequences, the interspecies distance of trnH-psbA and ITS2 + trnH-psbA was greater than the intraspecies distance, and there was no overlap in their frequency distribution plots. The results of the Wilcoxon signed-rank test for the interspecies distance of each sequence showed that the interspecies differences of the single sequences except trnL-trnF, trnH-psbA, and ycf3 were significantly smaller than those of the combined sequences. The results of BLAST analysis showed that trnH-psbA could accurately identify D. odorifera and D. tonkinensis at the species level. In the character-based method, single sequences of trnL-trnF, trnH-psbA with all the combined sequences can be used for the identification of D. odorifera and D. tonkinensis. In addition, the neighbor-joining (NJ) trees constructed based on trnH-psbA and ITS2 + trnH-psbA were able to cluster D. odorifera and D. tonkinensis on two clades. Conclusions The results showed that the character-based method with the BLOG algorithm was the most effective among all the evaluation methods, and the combined sequences can improve the ability to identify tree species compared with single sequences. Finally, the trnH-psbA and ITS2 + trnH-psbA were proposed as DNA barcodes to identify D. odorifera and D. tonkinensis.

With the rapid growth of the fruit industry worldwide, it is important to assess adulteration to ensure the authenticity and the safety of fruit products. The DNA barcoding approach offers a quick and accurate way of identifying and authenticating species. In this study, we developed reference DNA barcodes (rbcL, ITS2, and trnH-psbA) for 70 cultivated and wild tropical fruit species, representing 43 genera and 26 families. In terms of species recoverability, rbcL has a greater recoverability (100%) than ITS2 (95.7%) and trnH-psbA (88.6%). We evaluated the performance of these barcodes in species discrimination using similarity BLAST, phylogenetic tree, and barcoding gap analyses. The efficiency of rbcL, ITS2, and trnH-psbA in discriminating species was 80%, 100%, and 93.6%, respectively. We employed a multigene-tiered approach for species identification, with the rbcL region used for primary differentiation and ITS2 or trnH-psbA used for secondary differentiation. The two-locus barcodes rbcL + ITS2 and rbcL + trnH-psbA demonstrated robustness, achieving species discrimination rates of 100% and 94.3% respectively. Beyond the conventional species identification method based on plant morphology, the developed reference barcodes will aid the fruit agroindustry and trade, by making fruit-based product authentication possible. [ABSTRACT FROM AUTHOR]

Background: Dalbergia odorifera is a precious tree species with unique economic and medicinal values, which is difficult to distinguish from Dalbergia tonkinensis by traditional identification methods such as morphological characteristics and wood structure characteristics. It has been demonstrated that the identification of tree species can be effectively achieved using DNA barcoding, but there is a lack of study of the combined sequences used as DNA barcodes in the two tree species. In this study, 10 single sequences and 4 combined sequences were selected for analysis, and the identification effect of each sequence was evaluated by the distance-based method, BLAST-based search, character-based method, and tree-based method. Results: Among the single sequences and the combined sequences, the interspecies distance of trnH-psbA and ITS2 + trnH-psbA was greater than the intraspecies distance, and there was no overlap in their frequency distribution plots. The results of the Wilcoxon signed-rank test for the interspecies distance of each sequence showed that the interspecies differences of the single sequences except trnL-trnF, trnH-psbA, and ycf3 were significantly smaller than those of the combined sequences. The results of BLAST analysis showed that trnH-psbA could accurately identify D. odorifera and D. tonkinensis at the species level. In the character-based method, single sequences of trnL-trnF, trnH-psbA with all the combined sequences can be used for the identification of D. odorifera and D. tonkinensis. In addition, the neighbor-joining (NJ) trees constructed based on trnH-psbA and ITS2 + trnH-psbA were able to cluster D. odorifera and D. tonkinensis on two clades. Conclusions: The results showed that the character-based method with the BLOG algorithm was the most effective among all the evaluation methods, and the combined sequences can improve the ability to identify tree species compared with single sequences. Finally, the trnH-psbA and ITS2 + trnH-psbA were proposed as DNA barcodes to identify D. odorifera and D. tonkinensis. [ABSTRACT FROM AUTHOR]

Despite many efforts to determine the phylogenetic relationship between Barbeyaceae and other families of Rosales, the sister relationship of this family has remained unclear. Barbeya oleoides, which is currently the only species in the family Barbeyaceae, and native to Somalia, Ethiopia, and the Arabian Peninsula were collected from Wadi Turbah Zahran northwestern of Al-Baha City, southwestern Saudi Arabia (20°14’N, 41°15’E). To study the sister relationship of Barbeyaceae and the other families of Rosales, the complete chloroplast sequences were used for phylogenetic analysis. In addition, four standard DNA barcodes (the internal transcribed spacer 2 (ITS2), ribulose 1,5-biphosphate carboxylase (rbcL), maturase K (matk), the intergenic spacer region (trnH-psbA)) were used to test for their quality in identifying phylogenetic relationship of the studied families. Sequence analysis of the complete chloroplast sequences showed that Rosales clade has two subclades and clearly discriminated all families within this order. This is the first report of a partial ITS2 locus sequence in B. oleoides. The partial ITS2, rbcL, matk, and gene sequences discriminate B. oleoides of the Barbeyaceae family from the closely related plant families: Cannabaceae, Rosaceae, Rhamnaceae, Urticaceae, Moraceae, Elaeagnaceae, Dirachmaceae, and Ulmaceae. In contrast, the partial trnH-psbA sequence of B. oleoides did not show any homology to the available DNA sequence of plant families in GenBank, suggesting that it is more suitable as DNA barcode for variations within one species.

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Camellia is a large genus in the tea family of Theaceae. In this genus, several species serve different purposes, such as, medicinal and ornamental plants and beverage production. Thus, country-wide cultivation of various species of Camellia genus sought to alleviate poverty and promote economic development in many regions. However, studies on evaluating its genetic resources as a foundation for the conservation and development of this plant are yet to start. Currently, using DNA barcoding often serves as a highly reliable approach to identifying and characterizing numerous plants. In the presented study, a total of 10 Camellia accessions collected from Dong Bua village, Tam Quan commune, District Tam Dao, and Vinh Phuc province, Vietnam, underwent study during 2020-2022 at Ho Chi Minh City University of Food Industry, Vietnam. Evaluation of two DNA barcoding regions, namely, rbcL and trnH-psbA, transpired for their ability to distinguish the Camellia accessions belonging to different species in Vietnam. The results revealed a significant difference in the DNA sequences of the rbcL and trnH-psbA regions among the Camellia species. In addition, the trnH-psbA barcode region also showed higher effectiveness versus the rbcL region in recognizing various species of Camellia. The results authenticated the potential of DNA barcoding in the management, conservation, and development of the genetic resources of Camellia in Vietnam. [ABSTRACT FROM AUTHOR]

This study proposes the use of genetic analysis as a complementary method for species identification in the genus Pinus, particularly in cases where anatomical identification is challenging. Pinus species were grouped based on anatomical similarities, and the efficacy of using ycf1b, which is the most variable for Pinus species identification, and rbcL, which is a suggested DNA barcode for land plants, was evaluated within each group. Sequences for each species were obtained from the National Center for Biotechnology Information database and were used to perform phylogenetic analysis. Among the species in Group 1 (P. echinata, P. elliottii, P. ponderosa, P. radiata, P. rigida, P. taeda, and P. virginiana), rbcL was only effective in identifying P. radiata and P. ponderosa, while ycf1b classified five species. An additional DNA barcode, trnH-psbA, was needed to identify P. radiata and P. taeda. In Group 2 (P. densiflora, P. sylvestris, and P. thunbergii), most species were identified using both rbcL and ycf1b, with the exception of possible hybrids of P. densiflora and P. sylvestris. In Group 3 (P. koraiensis and P. strobus), two species were identified using rbcL and ycf1b. Combining genetic species identification with anatomical identification can accurately identify species of the genus Pinus. [ABSTRACT FROM AUTHOR]

A new species, Nitraria iliensis sp. nov., is described from the Ili basin, Almaty region, Kazakhstan. It belongs to section Nitraria ser. Sibiricae and is morphologically similar to N. sibirica Pall. An integrative taxonomic approach based on molecular, biochemical and morphological analyses, along with palynological data, was used to delimit this new species. The studied species of the genus are illustrated, and photographs of authentic specimens of the new species, as well as a distribution map of the new species and segregate taxa, are provided. Morphological characters were investigated, more important traits for identification were found, and a new key to distinguish between all species of the genus was prepared. [ABSTRACT FROM AUTHOR]

Solanum is the largest and most diverse genus of the Solanaceae family. The genus includes around 1,400 species, and almost a third belong to subgenus Leptostemonum. The species in this subgenus are commonly known as the spiny solanums, and include economically important species such as brinjal eggplant, naranjilla/lulo, and cocona. This study investigates the feasibility of using standard DNA barcoding markers for molecular identification in this subgenus, using sequence similarity (barcoding gap and best close match) and tree‐based (maximum likelihood tree) methods. The molecular framework uses 189 matK, 112 trnH-psbA and 222 nrITS sequences, corresponding to 37, 29 and 51 species, respectively. From them, 164 sequences were newly generated for this study and 359 were obtained from NCBI GenBank. Sequence divergence analysis shows that nrITS is the most variable region with the greatest nucleotide divergence between species, followed by trnH-psbA and matK. Using tree‐based methods nrITS region discriminates 69% of the 51 included species, matK discriminates 76% of 37 species. Discrimination of the closely related species S. quitoense—S. pseudolulo—S. candidum was possible with nrITS, whereas this was not possible using matK or trnH-psbA. The main drawback of nrITS was primer universality and amplification success with a sequencing rate of only 51%. Subgenus specific universal primers for nrITS could overcome this limitation, and make this a high resolution molecular identifier for the Leptostemonum group. In conclusion this study recommends that the standard matK coding region barcode is supplemented with nrITS in Solanum subgenus Leptostemonum, especially when matK has limited discriminatory power. [ABSTRACT FROM AUTHOR]

Tulsi (Holy basil, Ocimum tenuiflorum L., Lamiaceae), native to Asia, has become globalised as the cultural, cosmetic, and medicinal uses of the herb have been popularised. DNA barcoding, a molecular technique used to identify species based on short regions of DNA, can discriminate between different species and identify contaminants and adulterants. This study aimed to explore the values associated with Tulsi in the United Kingdom (UK) and authenticate samples using DNA barcoding. A mixed methods approach was used, incorporating social research (i.e., structured interviews) and DNA barcoding of Ocimum samples using the ITS and trnH-psbA barcode regions. Interviews revealed the cultural significance of Tulsi: including origins, knowledge exchange, religious connotations, and medicinal uses. With migration, sharing of plants and seeds has been seen as Tulsi plants are widely grown in South Asian (SA) households across the UK. Vouchered Ocimum specimens (n = 33) were obtained to create reference DNA barcodes which were not available in databases. A potential species substitution of O. gratissimum instead of O. tenuiflorum amongst SA participants was uncovered. Commercial samples (n = 47) were difficult to authenticate, potentially due to DNA degradation during manufacturing processes. This study highlights the cultural significance of Tulsi, despite a potential species substitution, the plant holds a prestigious place amongst SA families in the UK. DNA barcoding was a reliable way to authenticate Ocimum species. [ABSTRACT FROM AUTHOR]

Abstract Background Mangrove ecosystems have been the focus of global attention for their crucial role in sheltering coastal communities and retarding global climate change by sequestering ‘blue carbon’. China is relatively rich in mangrove diversity, with one-third of the ca. 70 true mangrove species and a number of mangrove associate species occurring naturally along the country’s coasts. Mangrove ecosystems, however, are widely threatened by intensifying human disturbances and rising sea levels. DNA barcoding technology may help protect mangrove ecosystems by providing rapid species identification. Results To investigate this potential, 898 plant specimens were collected from 33 major mangrove sites in China. Based on the morphologic diagnosis, the specimens were assigned to 72 species, including all 28 true mangrove species and all 12 mangrove associate species recorded in China. Three chloroplast DNA markers rbcL, trnH-psbA, matK, and one nuclear marker ITS2 were chosen to investigate the utility of using barcoding to identify these species. According to the criteria of barcoding gaps in genetic distance, sequence similarity, and phylogenetic monophyly, we propose that a single marker, ITS2, is sufficient to barcode the species of mangroves and their associates in China. Furthermore, rbcL or trnH-psbA can also be used to gather supplement confirming data. In using these barcodes, we revealed a very low level of genetic variation among geographic locations in the mangrove species, which is an alert to their vulnerability to climate and anthropogenic disturbances. Conclusion We suggest using ITS2 to barcode mangrove species and terrestrial coastal plants in South China. The DNA barcode sequences we obtained would be valuable in monitoring biodiversity and the restoration of ecosystems, which are essential for mangrove conservation.

Epimedium elatum (Morren & Decne) belonging to the family Berberidaceae is a rare medicinal plant endemic to the Western Himalayas and is being rare species, it is an ideal case for DNA barcoding. The present study was aimed at molecular identification, authentication, and development of reference DNA barcodes for Epimedium elatum collected from the Western Himalayas of Pakistan. We investigated four reference DNA barcode markers namely, rbcL, matK, trnH-psbA, and ITS for molecular analysis of Epimedium elatum. Three out of the four DNA barcode markers showed 100% amplification and sequencing success rate; matK was the only exception. The nucleotide sequence data were analyzed using Sequencher, BLAST, Muscle alignment, BioEdit, and MEGA6 software. The ITS and TrnH-psbA sequences showed significant similarity to a related species of the genus Epimedium, while rbcL showed low discriminatory power. Further analysis revealed that all barcodes could clearly distinguish Epimedium elatum from its closely related species. We concluded that all three barcodes are powerful tools for the identification of Epimedium elatum. [ABSTRACT FROM AUTHOR]

Anemone and Gladiolus are economically important geophyte genera due to their usage as ornamental plants. However, species identification is still under debate. Recently, DNA barcoding has become an efficient alternative tool for species identification. Here, candidate DNA barcode regions, rbcL, rpoB, and trnH-psbA were analyzed as potential DNA barcodes in 248 accessions of these geophyte genera using pair-wise distance-based, sequence similarity (best match and best close match) and tree-based (neighbor joining, maximum likelihood, and Bayesian tree) methods. Among all barcoding single or combination loci, trnH-psbA had the highest interspecific genetic variation in Anemone, and the region was the most promising candidate for barcoding gap analysis. However, none of the barcode regions showed a clear barcode gap for identification. The internal spacer, trnH-psbA, also showed the highest correct identification rate in Anemone, while rbcL showed the best performance in Gladiolus using the sequence similarity method. In the single barcode approach, rpoB had the best discrimination rate for both genera when using tree-based methods. Therefore, we recommend a tree-based method because it was clear that all tested loci had specific performance degrees depending on the methods. This is the first application of rpoB in terms of DNA barcoding criteria in geophyte taxa. [ABSTRACT FROM AUTHOR]

Recent divergence can obscure species boundaries among closely related taxa. Silene section Italicae (Caryophyllaceae) has been taxonomically controversial, with about 30 species described. We investigate species delimitation within this section using 500 specimens sequenced for one nuclear and two plastid markers. Despite the use of a small number of genes, the large number of sequenced samples allowed confident delimitation of 50% of the species. The delimitation of other species (e.g., Silene nemoralis, S. nodulosa and S. andryalifolia) was more challenging. We confirmed that seven of the ten chasmophyte species in the section are not related to each other but are, instead, genetically closer to geographically nearby species belonging to Italicae yet growing in open habitats. Adaptation to chasmophytic habitats therefore appears to have occurred independently, as a result of convergent evolution within the group. Species from the Western Mediterranean Basin showed more conflicting species boundaries than species from the Eastern Mediterranean Basin, where there are fewer but better-delimited species. Significant positive correlations were found between an estimation of the effective population size of the taxa and their extent of occurrence (EOO) or area of occupancy (AOO), and negative but non-significant correlations between the former and the posterior probability (PP) of the corresponding clades. These correlations might suggest a lower impact of incomplete lineage sorting in species with low effective population sizes and small distributional ranges compared with that in species inhabiting large areas. Finally, we confirmed that S. italica and S. nemoralis are distinct species, that S. nemoralis might furthermore include two different species and that S. velutina from Corsica and S. hicesiae from the Lipari Islands are sister species. [ABSTRACT FROM AUTHOR]

A species-level phylogeny of the Odontarrhena section in the Urals was estimated for the first time. Alyssum obovatum (C.A. Mey.) Turcz., A. tortousum Willd. and A. litvinovii Knjaz. are known for their heavy metal hemi- and hyperaccumulating ability. A total of 15 haplotypes were found based on the genetic diversity of the two chloroplast DNA markers. There are only a few species-specific haplotypes observed in the A. obovatum and A. tortuosum populations, while geographically close populations of both species share the most part of closely related haplotypes. Thus, the species form a geographically structured pattern of haplotype distribution. The Ural endemic A. litvinovii turned out to be monomorphic and genetically close to the other species. [ABSTRACT FROM AUTHOR]

Recent divergence can obscure species boundaries among closely related taxa. Silene section Italicae (Caryophyllaceae) has been taxonomically controversial, with about 30 species described. We investigate species delimitation within this section using 500 specimens sequenced for one nuclear and two plastid markers. Despite the use of a small number of genes, the large number of sequenced samples allowed confident delimitation of 50% of the species. The delimitation of other species (e.g., Silene nemoralis, S. nodulosa and S. andryalifolia) was more challenging. We confirmed that seven of the ten chasmophyte species in the section are not related to each other but are, instead, genetically closer to geographically nearby species belonging to Italicae yet growing in open habitats. Adaptation to chasmophytic habitats therefore appears to have occurred independently, as a result of convergent evolution within the group. Species from the Western Mediterranean Basin showed more conflicting species boundaries than species from the Eastern Mediterranean Basin, where there are fewer but better-delimited species. Significant positive correlations were found between an estimation of the effective population size of the taxa and their extent of occurrence (EOO) or area of occupancy (AOO), and negative but non-significant correlations between the former and the posterior probability (PP) of the corresponding clades. These correlations might suggest a lower impact of incomplete lineage sorting in species with low effective population sizes and small distributional ranges compared with that in species inhabiting large areas. Finally, we confirmed that S. italica and S. nemoralis are distinct species, that S. nemoralis might furthermore include two different species and that S. velutina from Corsica and S. hicesiae from the Lipari Islands are sister species.

In the present study, two chloroplast DNA markers (trnH-psbA, TabCD) were used to analyze genetic differentiation of six populations of Rhododendron adamsii from Sakhalin, Yakutia, Buryatia, Western Sayan, and Magadan oblast and two populations of Rhododendron parvifolium from Buryatia and Khabarovsk krai. A total of six haplotypes were found. While R. parvifolium with a single unique haplotype did not possess any genetic variability, R. adamsii exhibited a geographically determined distribution of cpDNA haplotypes. The samples from Buryatia were grouped into one homogeneous clade and the samples from the Far Eastern part of the range were grouped into another, showing a moderate genetic diversity within populations. Analysis of molecular variance (AMOVA) detected high genetic differentiation among R. adamsii populations (FST = 0.98, p < 0.001). GenBank sequences of closely related species were obtained for the estimation of the phylogenetic relationships of these species. We suggest that trnH-psbA and TabCD markers may be applicable for the species identification and for the elucidation of the population structure of rare R. adamsii. [ABSTRACT FROM AUTHOR]

Background: Mangrove ecosystems have been the focus of global attention for their crucial role in sheltering coastal communities and retarding global climate change by sequestering 'blue carbon'. China is relatively rich in mangrove diversity, with one-third of the ca. 70 true mangrove species and a number of mangrove associate species occurring naturally along the country's coasts. Mangrove ecosystems, however, are widely threatened by intensifying human disturbances and rising sea levels. DNA barcoding technology may help protect mangrove ecosystems by providing rapid species identification. Results: To investigate this potential, 898 plant specimens were collected from 33 major mangrove sites in China. Based on the morphologic diagnosis, the specimens were assigned to 72 species, including all 28 true mangrove species and all 12 mangrove associate species recorded in China. Three chloroplast DNA markers rbcL, trnH-psbA, matK, and one nuclear marker ITS2 were chosen to investigate the utility of using barcoding to identify these species. According to the criteria of barcoding gaps in genetic distance, sequence similarity, and phylogenetic monophyly, we propose that a single marker, ITS2, is sufficient to barcode the species of mangroves and their associates in China. Furthermore, rbcL or trnH-psbA can also be used to gather supplement confirming data. In using these barcodes, we revealed a very low level of genetic variation among geographic locations in the mangrove species, which is an alert to their vulnerability to climate and anthropogenic disturbances. Conclusion: We suggest using ITS2 to barcode mangrove species and terrestrial coastal plants in South China. The DNA barcode sequences we obtained would be valuable in monitoring biodiversity and the restoration of ecosystems, which are essential for mangrove conservation. [ABSTRACT FROM AUTHOR]

Garcinia L. is a pantropically distributed genus with high species richness in South East Asia. It is a tropical evergreen plant with distinct morphological characteristics and has a high degree of endemism. Outstanding features of the Garcinia L. genus are monopodial growth, leafy texture, oil cavities containing yellow or light-colored resins present on all parts of the plant and polygamodioecious reproductive behavior. The current study was conducted to develop barcodes for different species of the genus Garcinia L., distributed widely in the Western Ghats of India. We assess the discrimination power of the plant DNA barcode (rbcL, matK, trnH-psbA, rpoB-trnCGAR and ITS), across major Garcinia L. species. Our results clearly demonstrate the value of plastid barcode data, previously unavailable for Garcinia L. species. Ten Garcinia L. species and three outgroup taxa selected from the Western Ghats of India for evaluation using four regions in the plastid genome (rbcL matK, trnH-psbA, rpoB-trnCGAR) and nuclear-transcribed spacer (nrITS) in order to discriminate them at the species level. A characteristic feature of all barcodes, maximum likelihood analysis, and Wilcoxon signed-rank test were used for species discrimination. The number of conserved sites were more using matK primer whereas more variables and informative sites found in rpoB-trnCGAR loci. For internal branches of species-specific clusters, maximum likelihood analysis showed a more resolved topology. Wilcoxon signed-rank test indicated a higher divergence for coding and non-coding regions. DNA barcoding was found to be a practical and rapid method for identifying more endemic species. These findings will potentially be helpful in delineating the various species of Garcinia L. [ABSTRACT FROM AUTHOR]

Contemporary mangrove forest areas took shape historically and their genetic connectivity depends on sea-faring propagules, subsequent settlement, and persistence in suitable environments. Mangrove species world-wide may experience genetic breaks caused by major land barriers or opposing ocean currents influencing their population genetic structure. For Malay Peninsula, several aquatic species showed strong genetic differentiation between East and West coast regions due to the Sunda shelf flooding since the Last Glacial Maximum. In this study genetic diversity and structure of Avicennia marina populations in Malay Peninsula were assessed using nuclear microsatellite markers and chloroplast sequences. Even though all populations showed identical morphological features of A. marina, three evolutionary significant units were obtained with nuclear and cytoplasmic markers. Avicennia marina along a 586 km stretch of the West coast differed strongly from populations along an 80 km stretch of the East coast featuring chloroplast capture of Avicennia alba in an introgressive A. marina. Over and above this expected East-West division, an intra-regional subdivision was detected among A. marina populations in the narrowest region of the Strait of Malacca. The latter genetic break was supported by an amova, structure, and barrier analysis whereas RST > FST indicated an evolutionary signal of long-lasting divergence. Two different haplotypes along the Western coast showed phylogeographic relationship with either a northern or a putative southern lineage, thereby assuming two Avicennia sources facing each other during Holocene occupation with prolonged separation in the Strait of Malacca. Migrate-n model testing supported a northward unidirectional stepping-stone migration route, although with an unclear directionality at the genetic break position, most likely due to weak oceanic currents. Low levels of genetic diversity and southward connectivity was detected for East coast Avicennia populations. We compared the fine-scale spatial genetic structure (FSGS) of Avicennia populations along the exposed coast in the East vs. the sheltered coast in the West. A majority of transects from both coastlines revealed no within-site kinship-based FSGS, although the remoteness of the open sea is important for Avicennia patches to maintain a neighborhood. The results provide new insights for mangrove researchers and managers for future in-depth ecological-genetic-based species conservation efforts in Malay Peninsula.

Members of the genus Pandanus are popularly known for their variety of uses, yet there is difficulty identifying its species since discrimination is dependent on its seasonal reproductive parts. DNA barcoding was utilized to establish an ideal locus for the rapid identification and authentication of six Pandanus species in the Philippines. A total of 17 samples representing six species with three endemic taxa were collected and analyzed. Genomic DNA was extracted from leaf samples and was used as a template to generate the DNA barcodes. The BLAST (Basic Local Alignment Search Tool) method, divergence, and NJ (neighbor-joining) analyses were conducted to determine the efficiency of each barcode. The internal transcribed spacer, a nuclear region, was initially assessed in this study; however, plastid markers showed more universality with better amplification and sequencing success rates. In terms of discriminatory power, trnH-psbA revealed a significantly higher interspecific divergence compared to its intraspecific divergence. Phylogenetic analyses using the NJ approach exhibited that trnH-psbA has a better ability to resolve species identity and exclusive lineages than matK. The concatenated gene trnH-psbA + matK was able to generate better species resolution compared to the single barcodes analyzed. In general, rbcL performed poorly in the NJ analysis and has the lowest species discrimination based on its interspecific and intraspecific distances with close values. We provisionally recommend trnH-psbA as the most efficient single candidate barcode for the molecular authentication of Philippine Pandanus species and the combination of trnH-psbA + matK for a better discriminatory ability. [ABSTRACT FROM AUTHOR]

While plant species identification in forensics can be useful in cases involving poisonous, psychoactive, or endangered plant species, it can also become quite challenging, especially, when dealing with processed, decaying, colonized or infected material of plant origin. The Animal Plant and Soil Traces expert working group of the European Network of Forensic Science Institutes in their best practice manual has recommended several markers for plant species identification. Current study is a part of implementation of method in a forensic laboratory and its aim is to evaluate four of the recommended markers (ITS , matK , rbcL , and trnH-psbA) for species identification of forensically important plant species including medicinal, poisonous, psychoactive, and other plants. Such parameters as PCR and sequencing success, sequence length, species resolution rate and species cover in GenBank were analysed. Blind testing was performed to evaluate use of the markers for identification of forensically more complicated samples. According to results, a combination of ITS , matK and trnH-psbA is the best choice for plant species identification. The best results with fresh plant material can be achieved with ITS, trnH-psbA, and matK , while ITS and matK are the best choice when working with low quality plant material. rbcL due to its low species discrimination rate can be used only as an indicative marker. • Markers ITS , matK , rbcL , and trnH-psbA were tested for plant species identification. • With fresh plant material best results were gained by combination of ITS , trnH-psbA and matK. • In blind test with old and dried plant material best results were achieved with ITS and matK. • rbcL has low species resolution rate and can be used only as an indicative marker. [ABSTRACT FROM AUTHOR]

Berberidaceae contains 17 genera and nearly 650 species, in which the genus Berberis and the genus Mahonia are sisters with a very close relationship and share many similar characteristics. In the past, the two genera were merged into the genus Berberis. At present, the Berberidaceae is at risk and is prioritized for conservation, especially the species of Mahonia and Berberis. In the fact, identification for the Berberidaceae species based on the morphology of parts for sale (such as roots, stems, leaves) without reproductive organs (flowers and fruits) is impossible. In recent years, molecular biology techniques are being applied widely and effectively in research on the evolution, classification and genetic diversity of populations. Study based on DNA has highly accurate and particularly useful for closely related species which morphological observations are not sufficient to distinguish. Results from DNA analysis allow authentic species, populations or individuals from un-intact specimens accurately and especially, it is not affected by objective factors such as the environment or human. In this study, we assessed the taxonomy ability of three commonly DNA barcoding regions used for classification including rbcL, trnH-psbA and ITS2 on 12 samples of the Berberidaceae family, in which 7 samples are genus Mahonia, 4 samples are genus Berberis and one sample of Epimedium was used as the control sample. The results of the study will contribute to the selection of suitable DNA barcode for the identification of Mahonia and Berberis samples. The results demonstrated that the rbcL region showed the most obvious ability to distinguish the 12 Berberidaceae species. The ITS2 sequences of Berberis julianeae and Mahonia bealei of Vietnam were submitted to GenBank with accession numbers MT073031 and MT008067, respectively. The sequence of rbcL of Mahonia bealei was also submitted to GenBank with accession number MT457415.1. [ABSTRACT FROM AUTHOR]

Ruppia cf. maritima is one of the few native Hawaiian brackish water flowering plants, but its identity has never been examined using genetic analysis. The ability of this seagrass to tolerate a wide range of salinities and temperatures is reflected in its morphological variability among locations worldwide. Three populations on the island of Hawai'i were sampled, and molecular analyses of the nuclear gene ITS and two chloroplast genes trnH-psbA and rbcL were used to examine the identity of Hawaiian Ruppia. Concatenated analyses showed that the populations contained little intra- or interpopulation variability, and indicated greatest genetic similarity to specimens from Japan, India, Vietnam, and Africa. Slight variations in tree topologies were present among the individual nuclear and two plastid markers; however, all Hawaiian specimens nested within other sequences reported as R. maritima. Molecular phylogenetic analyses demonstrate that there are multiple clades of samples from around the world labeled as R. maritima, and that the Hawaiian samples are allied with one of these clades. The geographic isolation and geologic age of each Hawaiian island, as well as the disjunct distribution of Ruppia populations among islands and within each island suggest a multiplex biogeography and evolutionary history of Hawaiian Ruppia. [ABSTRACT FROM AUTHOR]

Background: DNA barcoding is a relatively new method of identifying plant species using short sequences of chloroplast DNA. Although there is a large number of studies using barcoding on various plant species, there are no such studies in the genus Nelumbo. Method: Three chloroplast DNA regions (rbcL, matK, trnH-psbA) were tested for their suitability as DNA barcoding regions of thirty three lotus samples which were collected in Thua Thien Hue province, Vietnam. Universal primers were used and sequenced products were analyzed using Minimum Evolution method in the MEGA 7.0 program. Result: We did not observe high variability in nucleotide sequences within the rbcL region (0.135%). White Nelumbo, while, the most encoding matK (8.013%) and variable trnH-psbA (with different number of repeating regions TAAAA) intergenic regions was the most useful for Nelumbo barcoding. Individual application of the studied regions did not provide the expected results. None of the regions used in the study allowed the division of white and pink lotus varieties of N. nucifera specie according to the adopted classification of the genus Nelumbo. The results confirm that the use of matK, rbcL and trnH-psbA or combine all three regions together is insufficient for DNA barcoding in white and pink lotus varieties of N. nucifera specie and better discrimination within the genus Nelumbo. Our results also indicate the necessity of using a different region. All of the new sequences have been deposited in GeneBank under the following accession numbers: rbcL (MN011708 to MN068956); matK (MN011719 to MN068978) and trnH-psbA (MN011730 to MN086252). [ABSTRACT FROM AUTHOR]

Several species of the Lamiaceae family are the primary source of bioactive aromatic oils and secondary metabolites, having broader applications in the cosmetics, pharmaceuticals, food, confectionery and liquor industries. Due to the scarcity of raw materials and high costs of this family's economically vital species, its products often adulterated to cater to the market's high demand. The present study provides a DNA based approach for identifying different species of this family. Henceforth, the performance of three already proposed barcode loci (matK, trnH-psbA and trnL) was examined for their PCR amplification and species recognition efficacy on various Lamiaceae species and cultivars using three different approaches such as pairwise genetic distance method, BLASTn and phylogenetic tree based on maximum likelihood (ML) analysis. Results illustrate that among all the DNA barcoding loci, matK locus can accurately and efficiently distinguish all the studied species followed by trnH-psbA and trnL. Present investigation may help diminish the illegal trade and events of adulteration of medicinally important plants species in genus Mentha, Ocimum and Plectranthus. This investigation will also help fulfil the scarcity of sequences of barcode loci of these species in the NCBI database. Apart from providing a molecular level reference for identifying processed herbal products, this technique also offers a convenient method for species identification and germplasm conservation of the Lamiaceae family. [ABSTRACT FROM AUTHOR]

• In this study, the morphological, molecular and elemental compositions of three endemic Lathyrus L. species in Turkey were investigated. • In genetically, chloroplast intergenic spacer trnH-psbA was used to reveal the genetic diversity and phylogenetic relationship Lathyrus species. • Additionally, the concentration of some elements such as Ni, Fe, Cu, Cd, Cr, Mn, Mg, Zn, Na and K were also determined. • L. belinensis , which is included in the Lathyrus section, shows close similarity to L. lycicus and L. phaselitanus in the Cicercula section. In this study, the morphological, genetical (molecular) and elemental compositions of morphologically similar three endemic Lathyrus L. species such as L. phaselitanus Hub.-Mor. & Davis , L. lycicus Boiss. and L. belinensis N. Maxted & D. J. Goyder belong to genus Lathyrus in Turkey were investigated. In the morphological part, some important parameters such as stem shape, plant height, leaflet number, leaflet length, leaflet width, stipule shape, stipule length, stipule width, fruit length, fruit width, fruit shape, number of flowers and standard were investigated. In the genetical part of the study, chloroplast intergenic spacer trnH-psbA was used to reveal the genetic diversity and phylogenetic relationship among the three endemic Lathyrus species to decide whether they were systematically similar or not. Additionally, the concentration of some elements such as Nickel (Ni), Iron (Fe), Copper(Cu), Cadmium (Cd), Chromium (Cr), Manganese (Mn), Magnesium (Mg), Zinc (Zn), Sodium (Na) and Potassium (K) were also determined by flame atomic absorption spectrometry to observe the similarities and/or differences among these three endemic Lathyrus species based on elemental composition. The results revealed that there was also a genetic similarity of 99% between morphologically similar L. belinensis and L. lycicus species but they were previously placed in different sections. [ABSTRACT FROM AUTHOR]

The analysis of variability of three intergenic spacers of chloroplast DNA in 47 samples of Rhododendron camtschaticum on the Kamchatka Peninsula and the Commander Islands was performed. The analysis of molecular variation (AMOVA) revealed that about 99% of genetic diversity occurs in interpopulation differences (FST = 0.99, p < 0.001). Two genetic lines have been identified, probably due to the northern and southern migration routes. Samples from central and northern Kamchatka form a separate cluster and demonstrate high homogeneity, which supports the taxonomic independence of the subspecies R. camtschaticum ssp. glandulosum. In samples from the southern part of the peninsula, polymorphism was revealed; together with samples from the Commander Islands, they correspond to R. camtschaticum ssp. camtschaticum. [ABSTRACT FROM AUTHOR]

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Honey is a natural and sweet product produced from Apis mellifera L. It can be classified as monofloral and polyfloral. DNA barcoding of pollen in honey can be used to identify the source of honey with high efficiency. Three polyfloral honey samples were used in the study. The trnH-psbA barcode was found to be an effective marker as source of additional date in identifying of the botanical origin of honey samples with high level of confidence. The purpose of this study was first to assess the efficiency of trnH-psbA marker as a DNA barcode for botanical identification and to compare the data with the obtained results for rbcL marker as a complex approach for botanical identification of polyfloral honey samples. [ABSTRACT FROM AUTHOR]

Since floras of oceanic islands are distinct from those of the closest continents, islands can serve as useful systems for understanding the evolution of host specificity during speciation of parasitic plants. Orobanche boninsimae (Orobanchaceae) is a holoparasitic plant species endemic to the isolated Bonin (Ogasawara) Islands; previous observations suggested several possible host species for O. boninsimae. In this study we sought to provide more definitive identification of O. boninsimae host plants through DNA analyses of host plant roots. We investigated nine populations of O. boninsimae from Chichijima and Hahajima Islands and determined their hosts by DNA barcoding of the chloroplast trnH-psbA region. We determined that three endemic woody species, Ochrosia nakaiana (Apocynaceae), Melicope grisea (Rutaceae), and Melicope nishimurae (Rutaceae), and one exotic tree, Bischofia javanica (Phyllanthaceae), were host species of O. boninsimae. These three families are newly recorded as hosts for the genus Orobanche , suggesting that O. boninsimae might have developed these unique host specificities in the islands. In addition, we established that O. boninsimae parasitizes completely different species between the islands, even though all available host species of O. boninsimae execpt for M. nishimurae were commonly distributed throughout these islands. This result suggests that intraspecific differentiation for host preference and possibly cryptic speciation has occurred between isolated islands. [ABSTRACT FROM AUTHOR]

Vicia L. is an invaluable genus with considerable agricultural and economic importance due to its high value as feed, green manure, and medicine. However, most of this genus is not well known and remains underutilized. Due to the imprecise circumscription and delineation of Vicia species, the taxonomic history of this genus is controversial, which has hindered the identification of species with high economic potential. Therefore, rapid and accurate identification of Vicia species is essential. Simultaneously, species identification through DNA barcoding has become an effective taxonomic classification tool. Here, the species‐discrimination abilities of matK, rbcL, trnH‐psbA, trnL‐trnF, ITS1, and ITS2 were tested in 161 Vicia species with both sequence similarity (nearest neighbor, best match, and best close match) and tree‐based (maximum likelihood tree) methods. Among the single barcode sites, trnH‐psbA had the highest level of polymorphism (52.4% variable sites; nucleotide diversity, 0.1338). Additionally, trnH‐psbA had the highest mean interspecific distance (0.1352) and intraspecific distance (0.0071). The combined barcode matK+trnH‐psbA had the highest correct identification rate by the sequence similarity method. Both trnH‐psbA (75.38%) and matK (70.73%) showed higher species discrimination rates than the other barcodes when using the tree‐based method. Based on overall performance, matK and trnH‐psbA, alone or in combination, were the best barcodes for Vicia. Internal transcribed spacer (ITS1) also showed good performance and provided essential information regarding nuclear DNA, so this site is also recommended as a backup barcode for Vicia. These Vicia barcodes can be used to identify species and to evaluate germplasm resource collections. [ABSTRACT FROM AUTHOR]

DNA barcoding is gaining importance in food authenticity studies due to its sensitivity, reliability and accuracy in identification of adulterant species from pure food commodity. In the present study, three barcoding loci viz., rbcL, trnH-psbA and ITS were explored to test their potential in detection of adulteration of black gram flour and its products with refined wheat flour (maida) and white pea flour. All three loci exhibited 100% success rate of PCR amplification and sequencing. Amplicons of band size 600 bp, 380 bp and 680 bp were obtained for rbcL, trnH-psbA and ITS, respectively. The method was validated on simulated samples of black gram flour (variety TPU-4) adulterated with 5% each of refined wheat flour and white pea flour. Sequence analysis and BLAST searches of the model blends revealed the presence of these two potential adulterants, thereby making the method sensitive enough to detect adulteration at 5% level. Among the 3 loci studied, loci rbcL and trnH-psbA, served as ideal candidates for detection of refined wheat flour adulteration in black gram flour. Eleven market samples of black gram products such as flour, papad, instant medu vada mix and papad atta of different brands were analysed using DNA barcoding. The method could successfully detect the presence of refined wheat flour in one of the papad samples. Therefore, molecular identification of black gram flour products and its adulterants can be done using the developed DNA barcoding method based on rbcL and trnH-psbA sequences. • Loci rbcL, trnH-psbA and ITS showed 100% PCR and amplification success. • Loci rbcL and trnH-psbA served as ideal candidates for detection of adulteration. • The method was sensitive at 5% level of adulteration. • Presence of refined wheat flour in black gram papad could be successfully identified. [ABSTRACT FROM AUTHOR]

Annona cherimola is a woody perennial species in the Annonaceae family that produces edible fruits and has economic importance in several regions of the world with subtropical climates. Together with other 10‐12 species, A. cherimola belongs to the section Atta of the Annona genus with a center of origin in Central America and the Caribbean. Species of the section Atta produce soft skin ripe fruits with raised areoles bounded by recessed furrows. Annona cherimola is the only species of the section naturally found in the Andean region of South America. Currently, no information is available at the molecular level on the phylogenetic relationships of most of the species of Atta and closely related sections in Annona. In order to fill this gap, in this work a phylogenetic approach was performed using five coding and non‐coding plastid DNA regions, to determine the phylogenetic relationships between A. cherimola and other related species included in Atta and other sections of the genus. The results obtained support recent studies that demonstrated the likely Mesoamerican origin of A. cherimola based on biogeographical analysis with SSR markers, rather than the previously considered South American origin hypothesis. In addition, the species belonging to the Atta section did not show monophyly. Finally, A. cherimola and A. pruinosa seem to be phylogenetically close species and additional studies are needed to discern the relations between them. [ABSTRACT FROM AUTHOR]

Amorphophallus is widely distributed in Southeast Asia, Africa, and other places, with more than 170 species. Amorphophallus has high medicinal value and is commonly used in medicine. However, the current classification based on morphology is challenging in with regard to Amorphophallus and closely related species. This study used six barcodes, namely ITS2, matK, rcbL, nad1, trnH-psbA, and trnL-trnF, to evaluate their identification ability for three important Amorphophallus species, including A. konjac, A. albus, and A. muelleri. We recommend that trnH-psbA can be applied to the Amorphophallus trade, quickly identify the purity of A. konjac and A. albus and distinguish A. muelleri from its related species for A. konjac and A. albus genetic improvement.

Dendrobium has been widely used not only as ornamental plants but also as food and medicines. The identification and evaluation of the genetic diversity of Dendrobium species support the conservation of genetic resources of endemic Dendrobium species. Uniquely identifying Dendrobium species used as medicines helps avoid misuse of medicinal herbs. However, it is challenging to identify Dendrobium species morphologically during their immature stage. Based on the DNA barcoding method, it is now possible to efficiently identify species in a shorter time. In this study, the genetic diversity of 76 Dendrobium samples from Southern Vietnam was investigated based on the ITS (Internal transcribed spacer), ITS2, matK (Maturase_K), rbcL (ribulose-bisphosphate carboxylase large subunit) and trnH-psbA (the internal space of the gene coding histidine transfer RNA (trnH) and gene coding protein D1, a polypeptide of the photosystem I reaction center (psaB)) regions. The ITS region was found to have the best identification potential. Nineteen out of 24 Dendrobium species were identified based on phylogenetic tree and Indel information of this region. Among these, seven identified species were used as medicinal herbs. The results of this research contributed to the conservation, propagation, and hybridization of indigenous Dendrobium species in Southern Vietnam.