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In 1865, Müller Argoviensis proposed Acalypha fallax based on specimens from Peninsula Indiae orientalis, which is now considered synonymous with A. lanceolata Willd. A recent study conducted in Tamil Nadu, India, from 2019 to 2022 thoroughly examined Acalypha species using multiple criteria: leaf epidermal characteristics, seed morphology, pollen features observed via scanning electron microscopy (SEM), and sequencing of the ITS, rbcL and matK spacer regions. This work identified distinctions between A. fallax and A. lanceolata, such as longer peduncles, obovate bracts in male flowers, and stems with two types of trichomes: strigose and hirsute. Moreover, the study proposed a new species, A. brittoi, which is described here as distinguishable from A. fallax by its larger leaf blades with 13–14‐toothed margins (compared to smaller blades with 8–9‐toothed margins in A. fallax), and by the ovate perianth of its male flowers (versus orbicular perianth in A. fallax). Unique patterns of leaf epidermal crystals and granules on seed surfaces further aided in distinguishing A. fallax from A. brittoi. Molecular analysis additionally confirmed genetic differences among these three species. [ABSTRACT FROM AUTHOR]

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]

Endemic taxa are critical constituents in the flora of most parts of the world. Recently, most of these taxa have become exposed to extinction. This study aims to increase understanding of four monocot Mediterranean threatened endemic taxa in Egypt (Allium mareoticum Bornm. & Gauba, Bromus aegyptiacus Tausch, Muscari salah-eidii (Täckh. & Boulos) Hosni, Pancratium arabicum Sickenb.) by description of their pollen and seed and authentication of DNA barcoding using rbcL and matK genes. Twenty field visits were conducted from March 2017 till April 2023 including different localities through Mediterranean area for covering the presence of these species. Characterization of pollen grains and seeds were examined using a light (LM) and scanning electron microscopes (SEM). DNA barcoding was carried out for documentation of the four species. Maturase K (matK) and ribulose-bisphosphate carboxylase (rbcL) were used as primers for PCR amplification and gene sequencing. The two genes were successful in identifying Allium mareoticum, Bromus aegyptiacus, and Muscari salah-eidii at the genus level and Pancratium arabicum at both species and genus levels for rbcL marker, and the genus level for matK marker. This study is considered a leading study for new barcodes of (A) mareoticum, (B) aegyptiacus, and M. salah-eidii which were initially made available to the NCBI. [ABSTRACT FROM AUTHOR]

Background and aims - Bulbophyllum, the largest genus in Orchidaceae, exhibits a diverse morphology in both reproductive and vegetative characters. While trait diversity and evolution has been extensively studied in Malagasy species and within the Cirrhopetalum alliance clade, the evolution of reproductive and vegetative characters at the whole level of the Asian clade remains largely unexplored. Material and methods - We reconstructed the phylogeny of approximately 11% of all Asian Bulbophyllum species using Bayesian inference and maximum likelihood estimation based on nuclear (ITS) and chloroplast (matK, psbA-trnH) DNA sequence data. This phylogenetic framework allowed us to examine the evolution of two vegetative and four floral characters through ancestral state reconstruction. Key results and conclusion - The ancestral character states of the Asian clade of Bulbophyllum include a single leaf, distinct pseudobulbs, multiple-flowered inflorescences, and lateral and dorsal sepals similar in length. One-leaved pseudobulbs evolved into two-leaved pseudobulbs multiple times. Distinct pseudobulbs gave rise to indistinct pseudobulbs twice. Multiple-flowered inflorescences shifted to solitary flowers and 2-3-flowered inflorescences multiple times, with some instances of evolutionary reversal. Lateral sepal elongation also presents a convergent evolutionary scenario. [ABSTRACT FROM AUTHOR]

A new species of Chlorophytum is described and illustrated in this article. Morphological, root anatomical, pollen and molecular features were compared with its allied species C. laxum R.Br. which has apiculate anther, lanceolate bract, 16–18 nerved flat leaf and ellipsoid pollen with contrast to obtuse anther, ovate bract, 11–13 nerved conduplicate leaf and ovoid pollen. The molecular features complement the differences. [ABSTRACT FROM AUTHOR]

Copyright of Eurasian Journal of Applied Biotechnology is the property of National Center for Biotechnology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Eurasian Journal of Applied Biotechnology is the property of National Center for Biotechnology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The effectiveness of plant-based therapies depends on precise botanical identification. However, tribal communities and practitioners sometimes misclassify medicinal plants due to a lack of scientific understanding. Plants cannot always be identified simply by morphology; the DNA-based approach uses a small segment of genomic DNA to authenticate medicinal plant species. Many tribal communities in Bangladesh have utilized plants for healing purposes for centuries. Therefore, this research used DNA sequences to identify Bangladeshi ethnomedicinal plants. DNA was extracted from the fresh leaves of eight important medicinal plants using the AddPrep Genomic DNA Extraction Kit and stored at − 20 °C. Three important loci (matK, rbcL and psbA-trnH) were amplified using PCR, and the sequences of these regions were analyzed for identification. rbcL and matK showed amplification success rates of 100% and 75% respectively, while for psbA-trnH the level was 50%, which subsequently led to the production of a total of 18 novel sequences. To validate the taxonomic identity of the samples, a MEGABLAST sequence comparison was performed, with nine species-level (50%) and nine genus-level (50%) identifications confirmed. The neighbor-joining method was used to construct four phylogenetic trees. The sequences obtained from the plant (leaf) samples and downloaded sequences from NCBI were employed, with the topologies of the trees being identical. Our findings demonstrate that partial genome sequencing is a viable way of identifying medicinal plants and closely related species utilizing the three plastid loci rbcL, matK and psbA-trnH, which are efficient and feasible DNA markers for plant authenticity. [ABSTRACT FROM AUTHOR]

In this study, DNA barcoding and phylogenetic analysis of five Prunus armeniaca L. genotypes (Cataloglu, Hacihaliloglu, Hasanbey, Hudayi, and Kabaasi) grown in Malatya/Türkiye were conducted using chloroplast DNA (cpDNA) matK and rbcL regions. The cpDNA matK region was amplified using matK472F and matK1248R primers, while the rbcL region was amplified with rbcLaF and rbcLaR primers. The matK and rbcL sequences were utilized to assess nucleotide ratios, genetic distance, and nucleotide diversity (π). The neighbor- joining (NJ) tree including other Prunus species from NCBI was created. In addition, physiochemical and 3-D analysis of matK and rbcL proteins were performed. As a result, π = 0.000549 for matK sequence and π = 0.002657 for rbcL sequence were determined. NJ (neighbor joining) phylogenetic trees formed with both matK and rbcL sequences were found to be compatible with each other. The matK and rbcL gene regions were found to be suitable for phylogenetic analysis. [ABSTRACT FROM AUTHOR]

Background: The species of genus Ageratum (family Asteraceae) are distributed in various parts of the world. Ageratum conyzoides and A. houstonianum are the most commonly occurring species in India. These species are quite similar in their morphology thus creating a challenge in identification during the field survey and taxonomic validation. The accurate identification of the species is highly significant especially when those are of medicinal interest. To overcome the barriers in morphological based identification, DNA barcoding has been employed during the present investigation. Methods and results: Morphological and DNA barcodes matK and ITS genes, were employed to differentiate between Ageratum conyzoides and A. houstonianum. The obtained matK and ITS gene sequences were submitted to GenBank and BOLD system to obtain accession numbers. The DNA sequences were aligned with database sequences using BLAST and phylogenetic trees were constructed through neighbor-joining algorithm in MEGA 11 software. The distinguish features of A. conyzoides include ovate to elliptic-oblong leaves with a cuneate base and inflorescence heads forming domed to flat-topped clusters. However, A. houstonianum has triangular to ovate leaves with a cordate to truncate base, cymose clusters in the inflorescence and stipulate glandular involucre bracts. The matK gene has shown the highest identity percentages (100%) for A. houstonianum and 99.87% for A. conyzoides. The phylogenetic tree analysis has demonstrated a close association of A. conyzoides and A. houstonianum with their respective species, supported by bootstrap values in the matK and ITS trees. Conclusion: This study revealed that morphological and molecular data can be successfully utilized in the identification of A. conyzoides and A. houstonianum. The matK and ITS barcodes provide promising results in the identification of Ageratum species, with their phylogeny supporting classification within the family asteraceae. [ABSTRACT FROM AUTHOR]

Background: Elymus atratus (Nevski) Hand.-Mazz. is perennial hexaploid wheatgrass. It was assigned to the genus Elymus L. sensu stricto based on morphological characters. Its genome constitution has not been disentangled yet. Objective: To identify the genome constitution and origin of E. atratus. Methods: In this study, genomic in situ hybridization and fluorescence in situ hybridization, and phylogenetic analysis based on the Acc1, DMC1 and matK sequences were performed. Results: Genomic in situ hybridization and fluorescence in situ hybridization results reveal that E. atratus 2n = 6x = 42 is composed of 14 St genome chromosomes, 14 H genome chromosomes, and 14 Y genome chromosomes including two H-Y type translocation chromosomes, suggesting that the genome formula of E. atratus is StStYYHH. The phylogenetic analysis based on Acc1 and DMC1 sequences not only shows that the Y genome originated in a separate diploid, but also suggests that Pseudoroegneria (St), Hordeum (H), and a diploid species with Y genome were the potential donors of E. atratus. Data from chloroplast DNA showed that the maternal donor of E. atratus contains the St genome. Conclusion: Elymus atratus is an allohexaploid species with StYH genome, which may have originated through the hybridization between an allotetraploid Roegneria (StY) species as the maternal donor and a diploid Hordeum (H) species as the paternal donor. [ABSTRACT FROM AUTHOR]

Maman is a traditional plant frequently used as food by people in Melayu Rokan of Riau Province. Morphological detection indicates that the scientific name of maman is Cleome gynandra L. The objective of this study is to confirm the taxonomic status of maman from Riau based on matK and trnL-trnL-trnF intergenic spacer (IGS) sequences. Methods utilized in this study included sampling, DNA extraction, PCR, electrophoresis, sequencing, and data analysis. The fresh leaves were picked up from Rokan Hulu Regency, Riau Province. In this study, the matK and trnL-trnL-trnF IGS sequences of maman with a length of 754 bp and 938 bp, respectively, had been obtained. The BLASTn analysis based on both sequences showed that maman had 100% similarity to Gynandropsis gynandra. Cleome gynandra was synonymous with G. gynandra. There were 49 nucleotide variations, 16 critical nucleotides, and there were no indels in matK. Meanwhile, in trnL-trnL-trnF IGS there were 181 nucleotide variations, 13 critical nucleotides, and 61 indels. In conclusion, this study succeeded in confirming the taxonomic status of maman from Riau as C. gynandra syn. G. gynandra. The result enriched the abundance of DNA barcode sequences of this plant in GenBank which is useful for the molecular identification. [ABSTRACT FROM AUTHOR]

Orchids comprise the second-largest family of flowering plants in the world. Most of the Indian orchids are horticulturally and medicinally important because of having exotic flowers and many important phytochemicals and secondary metabolites. Unfortunately, endemic Indian orchids are rare, threatened, and listed in Appendix 1 and 2 of CITES. Hence, having a reliable method for identifying orchids is an immediate need to save them. DNA barcoding is a popular and useful technology for quickly and accurately identifying plant species. The present survey looked to find the best suitable research papers on DNA barcoding of Indian orchids using standard search engines. We explored studies published between 2003 and 2023. A total of 545 appropriate studies were systematically analyzed. We found seven relevant studies on the barcoding of Indian orchids, where researchers deliberated rpoC1, rpoB, rbcL, and matK from the chloroplast genome, trnH-psbA, an intergeneric spacer, and nrITS from the nuclear genome to find best candidate barcode for orchids in India. Our survey concludes that ITS is the most effective candidate barcode for the identification of Indian orchids among single-locus barcoding genes. The matK in combination with ITS is best among multilocus barcodes for accurate identification of orchid species. [ABSTRACT FROM AUTHOR]

Key message: The combination of nuclear and chloroplast barcode regions was very effective for distinguishing pomegranate genotypes. The simultaneous use of molecular, biochemical and morphological markers had a complementary function. Exclusion of similar genotypes regardless of their geographic region based on different markers helps to reduce the size of the collection, especially when building a core collection is the ultimate goal. Accurate identification of genotypes and their relationships is one of the major challenges in the study of plant taxonomy, especially at the subspecies level. For this purpose, molecular, biochemical, and morphological markers are commonly used in different plant species. In the present study, the sequences of three DNA barcode regions, including the ITS, trnl-F, and matK regions, and all their possible combinations were examined in 21 pomegranate (Punica granatum L.) accessions. In addition, 18 morphological and biochemical characteristics of the genotypes were measured simultaneously to confirm the distinctions. The results show that the combination of three barcode regions (ITS + trnl-F + matK) has the highest efficiency due to the highest number of variable sites as well as parsimony informative sites. Considering the phylogenetic trees obtained from the barcode regions and the morpho-biochemical traits, it can be seen that genotype 808 is clearly different from the other genotypes. Of the genotypes studied in this experiment, ten genotypes were classified into close groups based on their geographic origin in both the barcode and morpho-biochemical clusters. However, genotypes 709, 712, and 708, which were grown in different geographical areas, had similar characteristics, so they were grouped in close branches in both dendrograms. This suggests that the simultaneous use of molecular and morphological markers is essential for distinguishing pomegranate genotypes. [ABSTRACT FROM AUTHOR]

Balsa (Ochroma pyramidale) is fast-growing forest plant species introduced to Indonesia with limited genetic information. Genetic information can be obtained through molecular assessment which is now feasible due to sequencing technology development. This is supported by the third-generation sequencer technology, which has been developed using long-read sequencing technology. MinION Oxford Nanopore Technology is one of the long-read sequence-based sequencers with a real-time process and portable. This study aims to generate genomic data and analyze the phylogenetic relationship of balsa (O. pyramidale) based on long-read sequences with MinION Oxford Nanopore Technologies. Balsa long-read sequencing generated a partial chloroplast genome (cpDNA) sequence of 155,430 bp, which can be used for further DNA barcode-based phylogenetic analysis from the chloroplast genome. Phylogenetic analysis showed that the balsa species (O. pyramidale) was genetically grouped in one clade with other O. pyramidale species in phylogeny analysis based on rbcL, matK, and a combination of rbcL and matK genes indicated that those genes were a suitable marker for phylogenetic analysis in balsa species (O. pyramidale). [ABSTRACT FROM AUTHOR]

Olives (Olea europaea L.) are the most well-known trees of the Mediterranean basin. The genetic heritage of olive trees is very rich and characterized by an abundance of varieties, eventually leading to significant genotype mixing. Therefore, the classification and analysis of the genetic diversity of olive cultivars are challenges of high priority. It helps make more efficient use of the olive resources distributed globally and benefits the genetic improvement and breeding of olive varieties. DNA barcoding is a method for evaluating and classifying species that uses short, variable, and uniform DNA regions. This study used DNA sequencing data for the first time for DNA barcoding of Egyptian olive cultivars and assessed the genetic relationship between four local cultivars grown in Egypt and their relation to sequences within the database. PCR amplification and sequence characterization were used to assess the effectiveness of the two barcoding sites, rbcL and matK. Based on multiple alignments of all the sequences obtained from the analyzed regions, matK had the longest sequence (816 bp) and rbcL the shortest (411 bp) of the two barcoding loci. The matK gene region was the least varied, with a variability level of 77%, while the rbcL gene region had the highest amount of variability (98.7%). Because of the presence of unique variable sites, both barcoding loci rbcL and matK efficiencies discriminate the selective Egyptian olive cultivars. The DNA sequences from the individual and combined barcode loci were used in a maximum likelihood tree-based phylogenetic analysis to successfully distinguish the selected olive cultivars. [ABSTRACT FROM AUTHOR]

Typhonium rhizomatosum A.Galloway & P.Schmidt is reported here as a new record to the flora of Vietnam. It is described and illustrated with detailed photographs of key morphological characters. Besides, the sequences of matK and trnL-F regions were also successfully sequenced to confirm its identity. [ABSTRACT FROM AUTHOR]

Rhodomyrtus tomentosa is a source of a novel antibiotic, rhodomyrtone. Because of the increasing industrial demand for this compound, germplasm with a high rhodomyrtone content is the key to sustainable future cultivation. In this study, rhodomyrtone genotypes were verified using the plastid genomic region marker matK and nuclear ribosomal internal transcribed spacer ITS. These two DNA barcodes proved to be useful tools for identifying different rhodomyrtone contents via the SNP haplotypes C569T and A561G, respectively. The results were correlated with rhodomyrtone content determined via HPLC. Subsequently, R. tomentosa samples with high- and low-rhodomyrtone genotypes were collected for de novo transcriptome and gene expression analyses. A total of 83,402 unigenes were classified into 25 KOG classifications, and 74,102 annotated unigenes were obtained. Analysis of differential gene expression between samples or groups using DESeq2 revealed highly expressed levels related to rhodomyrtone content in two genotypes. semiquantitative RT-PCR further revealed that the high rhodomyrtone content in these two genotypes correlated with expression of zinc transporter protein (RtZnT). In addition, we found that expression of RtZnT resulted in increased sensitivity of R. tomentosa under ZnSO4 stress. The findings provide useful information for selection of cultivation sites to achieve high rhodomyrtone yields in R. tomentosa. [ABSTRACT FROM AUTHOR]

A molecular phylogenetic investigation was undertaken for 30 species belonging to 15 genera of the palm family Arecaceae in Bangladesh to infer evolutionary relationships and molecular dating utilizing plastid-based matK and rbcL genes through multifacetedalgorithm driven approaches with Neighbor-Joining, Maximum-Likelihood, and Bayesian Inference methods. The study revealed that matK has better species discrimination efficiency than rbcL gene due to its highly variable nature. Transition/transversion bias test corroborated this finding as matK showed higher bias (2.632) than rbcL (2.235). Nucleotide substitution patterns were visualized via HYPERMUT program, which unveiled higher variability in matK and lower variability in rbcL alignment. Phylogenetic trees constructed with matK revealed monophyletic nature of origin for all the three subfamilies, viz. Arecoideae, Coryphoideae and Calamoideae, while rbcL trees exhibited polyphyly for Coryphoideae and monophyly for Arecoideae and Calamoideae. All the nine tribes belonging to three subfamilies demonstrated monophyletic nature in matK trees. Bootstrap support and Bayesian posterior probability were found to be higher in matK topologies than that of rbcL. The molecular clock test unraveled an equal evolutionary rate for matK and unequal rate for rbcL sequences. Molecular dating approach unveiled Calamoideae to be the most ancient subfamily (65.75 MYA) among the three subfamilies that originated during the Late Cretaceous period in the Mesozoic era, whereas Coryphoideae and Arecoideae were found to have originated in the Cenozoic era. [ABSTRACT FROM AUTHOR]

Backgroud: Twelve taxa of herbaceous Paeonia species were recorded in Türkiye. All definitions were performed morphologically and/or anatomically and there is no study based on DNA barcode sequences. Three barcode regions were sequenced to determine the phylogenetic relationships of Turkish Paeonia taxa. The chemical comparison of roots was also investigated. Methods and results: The taxons were collected between May and June 2021 from nine cities. Leaf materials were used for DNA isolation and ITS, matK and rbcL regions were amplified and sequenced. There was no difference among taxa in terms of rbcL sequences. But the ITS and matK regions distinguished 12 taxa and structured them in two groups. ITS region distinguished P. peregrina, P. arietina, and P. tenuifolia from other taxa, while matK region distinguished P. arietina and P. witmanniana from other taxa. Both barcode sequences actually showed that the registration of P. mascula subsp. arasicola was actually 100% similar to P. arietina. ITS was the most polymorphic region (n = 54) followed by matK (n = 9). These sequences could successfully discriminate Paoenia species from each other and diploid P. tenuifolia. The methanolic root (100 gr) extracts were examined for total phenolic and flavonoid content, and antioxidant activities. Significant variation was found for polyphenolic content, and antioxidant properties (TPC from 204.23 to 2343.89 mg, TFC from 7.73 to 66.16 mg, and FRAP from 523.81 to 4338.62 mg). SC50 values of ABTS and DPPH were ranged from 115.08 to 1115.52 μg/ml and 73.83 to 963.59 μg/ml, respectively. Conclusion: It was concluded that 11 of 12 taxa had differences in terms of ITS and matK sequences and these region must be used for the correct identification of Turkish Paeonia. [ABSTRACT FROM AUTHOR]

The precise identification of plant species is exclusively important in forensic studies and plants of medicinal interest. In addition to conventional methods, DNA barcoding is coming up as a supportive tool in the identification of biological entities, including plant species. DNA barcoding may be useful, especially when plant species are indistinguishable during their vegetative phase of growth. The present study focused on the identification of Calotropisprocera and C. gigantea through morphological characters and DNA barcoding analysis. The markers (rbcL, matK, and ITS) used for DNA barcoding could not differentiate these two species, whereas morphological parameters are distinct enough to establish their identity. The BLAST analysis has shown 100% similarity for C. procera and C. gigantea with rbcL, matK, and ITS markers. [ABSTRACT FROM AUTHOR]

Hybridization and polyploidy are key evolutionary forces in plant diversification, and their co-occurrence in the context of allopolyploid speciation is often associated with increased ability to colonize new environments and invasiveness. In the genus Ulex (Fabaceae), the European gorse (Ulex europaeus subsp. europaeus) is the only invasive and the only polyploid that has recently spread in different eco-geographical regions across the world. Understanding what confers such ecological advantages to this species, compared to its diploid and polyploid congeners, first requires clarification of the ecogeographical and evolutionary context of its formation. To achieve this, the geographical distributions of all Ulex spp. were estimated from species occurrence records, and phylogenetic analyses including all Ulex spp. were performed based on four nuclear (ITS and ETS nrDNA) and plastid (rps12 intron and trnK - matK) regions. The resulting trees were dated using a secondary calibration. Patterns of DNA sequence variation and dated phylogenetic trees were then interpreted in light of previous knowledge of chromosome numbers in Ulex to infer past events of polyploid speciation in the genus. We show that: (1) most current Ulex spp. radiated in the Iberian Peninsula during the past 1–2 Myr; (2) the history of Ulex was punctuated by multiple whole-genome duplication events; and (3) U. europaeus subsp. europaeus is the only gorse taxon that was formed by hybridization of two well-differentiated lineages (which separated c. 5 Mya) with wide climatic ranges (currently represented by Ulex minor and Ulex europaeus subsp. latebracteatus), possibly contributing to the invasive nature and wider climatic range of U. europaeus subsp. europaeus. These findings provide a much-needed evolutionary framework in which to explore the adaptive consequences of genome mergers and duplication in Ulex. [ABSTRACT FROM AUTHOR]

Step-wise analysis of core variability in centers of origin and distribution can resolve conflicts over the taxonomic status of any plant species. Ash gourd [Benincasa hispida (Thunb.) Cogn.] and tinda [Praecitrullus fistulosus (Stocks) Pangalo] are vegetables in tropical and subtropical regions of the world. Identification of unique genotypes under Benincasa has led to a situation that requires verifying the monotypic status of this genus. Tinda, also known as round melon, was recommended to be included as a second species in Benincasa. This study tested the hypothesis that Benincasa is monotypic. Morphological evaluation of a mini-core collection comprising 26 ash gourd and 5 tinda entries exhibited variability. Ash gourd and tinda genotypes varied for multiple morphological traits. Cluster analysis differentiated ash gourd and tinda, with nearly 70% dissimilarity. All ash gourd accessions were freely crossable in both directions, ruling out the possibility of any new species. Non-cross-ability of tinda with ash gourd has confirmed its genetic distinctiveness. Nine barcodes distinctly differentiating the genera were identified from the matK and ITS2 loci. With the characteristic morphological traits, non-crossable nature and distinct barcodes that are not shared with any of the members of Praecitrullus, Benincasa should be considered monotypic and a separate genus status retained for Praecitrullus. [ABSTRACT FROM AUTHOR]

Anacardiaceae is well-known for its edible fruits and economically important species in Indonesia. Approximately 3% of Indonesia's endangered and vulnerable species belong to this family. Fast and accurate species identification is crucial to support the conservation efforts for this family, such as employing DNA sequences. Species identification using DNA sequences, known as DNA barcoding, has been widely used in many applied fields. So far, the application of DNA barcoding for Anacardiaceae plant species is limited to several genera only, such as Mangifera and Spondias. This research aimed to enrich the DNA barcode references of Anacardiaceae and to evaluate the most suitable and effective genetic marker as DNA barcodes to identify species of 35 samples representing sixteen species of the Anacardiaceae family using chloroplast markers matK and rbcL as barcode regions. When comparing the morphological identification with the molecular assignments, the barcode accuracy was 62.50% (matK), 60.61% (rbcL), and 73.33% (matK+rbcL) at the genus level. All the markers failed to show a barcoding gap, even though the t-test showed that the intraspecific and interspecific genetic distances were significantly different for matK and rbcL+matK. Among others, Gluta walichii (Hook.f.) Ding Hou and Melanochyla caesia Jack were the only species successfully resolved by all markers. Nevertheless, new DNA barcodes of six Anacardiaceae species were made available by this study, enriching the genetic references of tropical flora diversity. [ABSTRACT FROM AUTHOR]

Background: Averrhoa carambola L. (star fruit) is an underutilized plant in the family Oxalidaceae. The plant has various pharmacological activities and has fleshy juicy fruit with high nutritional value and is rich in vitamins. Objectives: This study aims to authenticate and examine the evolutionary relationships between various Averrhoa taxa. Materials and Methods: The species identification was verified using the well-established DNA barcoding method. For this, a few predetermined loci including rpoB, matK, atpF-atpH, and rbcL were employed. Results: Amplicons were observed with a molecular weight of 450bp, 950bp, 800bp, and 650bp respectively as reported earlier. The sequences of these loci were submitted to NCBI. The sequences were approved with accession numbers MN447319, MN733917, MT195537, and MT195538 respectively. The amplified loci of the species and related taxa of the genus were compared using bioinformatics tools. 204 numbers of SNPs/indels were identified out of which some are unique for the species. K2P analysis showed that the maximum intraspecific distance (1.3%) was lower than the minimum interspecific distance (2.6%). Conclusion: Among the different universal barcoding loci, matK was found to be most informative in terms of the occurrence of SNPs and genetic distance. So, the information can be utilized for species authentication in the family Oxalidaceae. [ABSTRACT FROM AUTHOR]

Phylogenetic analysis for plants can be very helpful in determining species identification or taxonomic status morphologically. rbcL and matK are widely used as genetic markers in constructing seed plant phylogenies. Different identification and new collection during the re-inventory from the previous study were found in two and four types of rare fruits in Sibohe Forest, West Kalimantan. The six types include pisang karok (Musa sp.) and Kandis (Garcinia sp.), as well as nubik (Artocarpus sp.), tehengan (Artocarpus sp.), smallest arok (Ficus sp.), and amok (Alpinia sp.). This study aimed to analyze the phenetic relationship of six rare fruits from Kalimantan based on rbcL and matK genes. DNA samples were obtained from dried body parts of the previous study and amplified by PCR using both forward and reverse primers for rbcL and matK genes. Amplification was observed on electrophoresis gel for rbcL gene of nubik, tehengan, smallest arok, amok, and pisang karok, while only pisang karok in matK gene. However, matK gene sequence was also obtained for amok even though the band was not seen on the gel. Phylogenetic analysis using the two genes confirmed the morphological identification reported in the previous study; however, using matK as a single gene for taxonomic confirmation must be reconsidered. The information of rbcL and matK sequences of six rare fruits from West Kalimantan could be the first information for building the DNA barcodes of the rare fruits in West Kalimantan. [ABSTRACT FROM AUTHOR]

The high diversity and limited floral information in tropical forests often pose a challenge for species identification. However, over the past decade, DNA barcoding has been employed in tropical forests, including Sumatran forests, to enhance floristic surveys. This technique facilitates the discrimination of morphologically similar species and addresses the limitations of conventional species identification, which relies on short‐lived reproductive structures. This study aimed to evaluate the efficiency of matK, rbcL, and the combination of both chloroplast markers for species identification in Burseraceae by employing genetic distance and species tree inference. In this study, we collected 197 specimens representing 20 species from five genera of Burseraceae. The highest percentage of specimens' identification (36%) at the species level was obtained using matK + rbcL, followed by matK (31%), and rbcL (7%). The matK dataset presented the highest interspecific divergence with a mean of 0.008. In addition, a lack of barcode gap was observed in both markers, suggesting potential limitations of the core barcodes for distinguishing Sumatran species within Burseraceae. The monophyly test confirmed five species as monophyletic using Bayesian species tree inferences for matK. Overall, our results demonstrate that matK outperforms rbcL in species identification of Burseraceae, whereas their combination did not enhance species delimitation. To improve the molecular species assignments of this family, future studies may consider including more DNA markers in conjuction with matK, and broadening the availability of reference sequences for species that have not yet been included in the databases. The outcomes of molecular species identification vary depending on the taxonomic group under investigation. Implementation of phylogenomics for species delimitation and diagnostic marker development is strongly recommended for tropical biodiversity assessments, especially for poorly studied clades. [ABSTRACT FROM AUTHOR]

Epilobium and Chamaenerion included 165 and 8 species over the world, respectively. The members of the genera are distributed particularly in moist habitats from subpolar to tropical regions. This paper aims to provide improvements in the phylogeny of the genera Epilobium and Chamaenerion using Internal Transcribed Spacer (ITS) of nuclear DNA and matK gene sequence data evaluation with maximum parsimony, maximum likelihood, and Bayesian inference criterations. A total of 188 individual accessions belonging to 28 taxa were newly generated and 110 sequences imported from GenBank (NCBI) were analysed. The nrDNA and plastid DNA gene trees supported to treat Epilobium and Chamaenerion as separate genera in two well-supported clades. The matK analyses revealed a better resolution than nrDNA ITS within the Chamaenerion clade and supported the inclusion of C. angustifolium in the sect. Chamaenerion. However, most of the examined species mostly fell into the polytomy in both trees excluding E. roseum subsp. consimile which should be considered a distinct species in the Epilobium contrary to morphological treatment in many national flora books. Both phylogenetic trees also support distinguishing E. prionophyllum from E. anatolicum previously treated as a subspecies of E. anatolicum. In conclusion, these preliminary phylogenetic analyses have contributed significantly to the determination of the limits of members belonging to Epilobium and Chamaenerion distributed in Türkiye. [ABSTRACT FROM AUTHOR]

Yams (Dioscorea species) are tuber crops that are grown in tropical regions of Africa, the Caribbean, South America, Asia and South Pacific islands. It is an important food security crop with economic, nutritional and medicinal values. However, many Dioscorea species have similar morphology leading to inaccurate identification, which hinders their conservation and adequate exploitation of the economically important species. The aim of this study was to test the ability of DNA barcoding [ribulose 1, 5-bisphosphate carboxylase/oxygenase (rbcL) and Maturase K (matK)] markers to distinguish species and as an alternative tool for correcting species misidentification. Phylogenetic analysis of rbcL and matK sequences revealed four strongly supported distinct species that included Dioscorea bulbifera, Dioscorea alata, Dioscorea minutiflora and Dioscorea cayennensis. The specific clade of each of the yam accession was informed by the species. The phylogenetic clustering was confirmed by Principal Component Analysis (PCA). DNA polymorphism in the yam species exhibited both synonymous and non-synonymous mutation. RbcL and matK gene sequences had nucleotide diversity of 0.00392 and 0.00632, respectively. There were seven haplotypes within the rbcL gene with a diversity index of 0.800 and variation of 0.00374. For matK gene, there were four haplotypes with a diversity index of 0.745 and variation of 0.00956. This study demonstrates that rbcL and matK are efficient DNA barcoding markers that can be used to identify and discriminate Dioscorea species. The identification and delimitation of Dioscorea species is crucial in utilization, conservation and in designing their breeding strategies. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Agriculture & Nature / Kahramanmaraş Sütçü İmam Üniversitesi Tarım & Doğa Dergisi is the property of Kahramanmaras Sutcu Imam Universitesi and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Theriophonum blumei sp. nov., a new species is described and illustrated from Tamil Nadu, India based on morphological and leaf epidermal features. Although morphologically T. blumei appears to be similar to T. sivaganganum (Ramam. & Sebastine) Bogner having long acuminate spathe, it is different from T. sivaganganum in various aspects such as ellipsoid seed with ridged surface, spinulose and bifid stigma, filiform neuters and berries with purplish strands. T. blumei has echinate pollen sculpture and T. sivaganganum has verrucate sculpture. Added to that, molecular based (rbcL, matK, trnL‐F) phylogenetic analysis also indicate that T. blumei is genetically distinct from T. sivaganganum. [ABSTRACT FROM AUTHOR]

Large-scale soybean [Glycine max (L.) Merr.] cultivation has substantially transformed the Midwestern landscape in recent decades. Floral nectar produced by immense fields of soybeans has the potential to influence foraging ecology and resource accumulation of honey bee (Apis mellifera L.) colonies. In this study, we combined microscopic and molecular pollen analysis of honey samples with waggle dance inference of spatial foraging patterns to demonstrate that honey bees routinely forage on soybeans in Ohio. In analyzing honey samples from across the state, we found ubiquitous presence of soybean pollen in honey collected from agricultural lands during soybean bloom. The abundance of soybean pollen in honey increased with the amount of soybean fields surrounding the apiaries. Honey bee waggle dances recorded during soybean bloom revealed that honey bees preferred soybean fields for foraging over other habitat types. With these results, future research efforts aimed at enhancing mutual interactions between soybeans and honey bees may represent an unexplored pathway for increasing soybean production while supporting honey bees and other pollinators in the surrounding landscape. [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]

A new orchid species, Liparis macrosepala, is illustrated and described from Yunnan Province, China, based on morphological and molecular analyses. This plant is characterised by the ovoid-fusiform, slightly compressed pseudobulbs with 4 or 5 leaves with slightly crisped margins on their apical half, dorsal sepal heart-shaped, lip with a bituberculate basal callus and a thickened folded lateral lobe on each side, centrally with one cavity with slightly raised margins, the column with a single pair of broadly triangular, obtuse wings. Maximum Likelihood and Bayesian Inference analyses of combined nrITS and plastid matK DNA sequences place this species in section Cestichis. [ABSTRACT FROM AUTHOR]

Copyright of Forest Engineering is the property of Forest Engineering Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Jurnal Syntax Admiration is the property of Ridwan Institute and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Camellia is the largest and most important genus in the family Theaceae, with many species being of great economic, ornamental and ecological value. However, the phylogenetic resolution of these species has been difficult due to interspecific hybridization and polyploidy. Consequently, the interspecies relationships of the genus Camellia are still hotly debated. In this study, four chloroplast genomic regions (matK, rbcL, ycf1, trnL-F) were used as markers among 161 species representing all four subgenera within this genus to investigate the phylogeny and interspecies relationship of the genus Camellia. The results showed that the 161 species of the genus Camellia could be grouped into 13 clades (A-M). Clades A and B mainly consisted of sect. Camellia. Clades C and I were made up of sect. Theopsis and sect. Eriandria. Clades D and J were composed of species from sect. Thea. Clade F consisted of the sect. Paracamellia species, whilst Clades G and M included sect. Furfuracea species. Clade H contained sect. Tuberculata and most species of sect. Pseudocamellia, whereas Clades K and L comprised the sect. Chrysantha species. These results supported that 161 Camellia species form paraphyletic groups, rather than a monophyletic group. And they demonstrated that the taxonomic position of related species could be resolved to some extent via sequencing markers in organelle genome, thus providing valuable cytoplasmic genetic information or maternal genetic information for accurately identifying species, clarifying taxonomy and reconstructing the phylogeny of various Camellia species. [ABSTRACT FROM AUTHOR]

There is currently international interest in applying DNA barcoding as a tool for plant species discrimination and identification. In this study, we evaluated the utility of four candidate plant DNA barcoding regions [rbcL, matK, trnL-F, and internal transcribed spacer (ITS)] in seven genera of Gramineae including Agropyron, Bromus, Elymus, Elytrigia, Festuca, Leymus, and Lolium. Fourteen accessions were analyzed, and matK and ITS showed the highest species, subspecies, and variety discriminatory power, each resolving 11 accessions. Species discrimination using rbcL and trnL-F was lower, resolving 7 and 8 accessions, respectively. Subspecies and variety discrimination using rbcL and trnL-F could not identify 4 accessions of Agropyron. A technical system can be established using the proposed DNA barcode to rapidly and reliably identify the seven genera of Gramineae. This study serves as a "useful reference" for identifying the genetic diversity of grass germplasm resources. DNA barcoding can be utilized to uncover the relatives of different species within the same family or between different families. It can also be used to determine the related groups of important herbage, turfgrass, and crops and provide crucial background information for discovering excellent genes and improving existing crop varieties. [ABSTRACT FROM AUTHOR]

ABSTRACT Background: DNA barcoding, an emerging approach, is being widely used to accurately and quickly identify species using conserved DNA sequences. Methods: Herein we designed seven universal primers for matK (matK1, matK2, matK3 and matK4), rbcL, psbA-trnH and ITS based on their nucleotide sequences in GenBank to amplify 40 species of leguminosae and grass forages. Sequence alignment was performed using MEGA 5.0 and haplotype and mutation sites were analyzed with DnaSP 5.10. PCR amplification efficiency on using the primers designed for psbA-trnH and ITS was relatively low, making these sequences unsuitable for DNA barcoding. Further, we optimized target fragment amplification conditions for all 40 species analyzed in this study. On purifying, sequencing and analysing amplification products, we selected 5 - and 3 -end conserved fragments in four marked fragments. Result: Sequences of each maker loci showed that there were 12, 17 and 6 haplotypes of matK1, matK2 and matK3, respectively and 13 of rbcL. Based on these haplotypes of matK1, matK2, matK3 and rbcL, we established a DNA barcoding database for 20 forage species. [ABSTRACT FROM AUTHOR]

The genus Paracladopus was established based on the type species P. chiangmaiensis in 2006. The two Paracladopus species are distributed in Thailand and Laos; however, neither of them has been documented in China to date. During our field work in 2020, we collected a river-weed in Wuzhi Mountain, Hainan Province of China. After checking the morphological characters, it was identified as P. chiangmaiensis. Then, we assembled and annotated its chloroplast genome based on the genome skimming data. The results showed that the complete chloroplast genome was 133,748 bp with 35% GC content, consisting of 76 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. A maximum-likelihood tree constructed based on the matk genes showed that WuMS109 was clustered with P. chiangmaiensis (AB537420, AB698348) without base difference and together with the remains of Paracladopus formed a sister clade to Cladopus. This is the first report of P. chiangmaiensis that represents a new generic record for China. The discovery of this river-weed could lay the foundation for investigating their biogeographical patterns and species evolution in further studies. [ABSTRACT FROM AUTHOR]

The Global Genome Initiative for Gardens (GGI-Gardens) is an international partnership of botanic gardens and arboreta that aims to preserve and understand the genomic diversity of plants on Earth. GGI-Gardens has organized a collection program focused on the living collections that partner institutions and supports the preservation of herbarium and genomic vouchers. Collections made through GGI-Gardens are deposited in recognized herbaria and Global Genome Biodiversity Network-partnered biorepositories worldwide, meaning that they are made available to the public. With support from its parent organization, the Global Genome Initiative (GGI), plant DNA barcode sequencing is performed using tissues collected through this partnership that represent taxa without barcode sequences in GenBank. This is the second data release published by GGI-Gardens and constitutes 2722 barcode sequences from 174 families and 702 genera of land plants. All DNA barcodes generated in this study are now available through the Barcode of Life Data Systems (BOLD) and GenBank. [ABSTRACT FROM AUTHOR]

The Dasylirion genus is highly represented in the arid and semi-arid regions of Mexico and USA, playing important ecological and economical roles. Inferring the evolutionary patterns of this group will eventually facilitate understanding biological phenomena and outlining conservation and usage strategies. We performed a molecular phylogenetic analysis based on two chloroplast DNA regions: maturase-K gene (matK) and the large subunit of ribulose-1,5-bisphosphate carboxylase gene (rbcL). We constructed a phylogenetic tree by maximum likelihood with GTR as the sequence substitution model and a relaxed clock, inferred diversification patterns by lineage through time and explored the diversification rates of Dasylirion by the Yule model. The study included 11 species of the genus, which represent 50% of all its known species. We used two calibration points to date the tree, one based on fossil records of Acorus gramineus , and the other on the estimated stem age of the Yucca genus. The combined sequences of the two partial genes comprised 1455 bp and 18 polymorphic sites. We estimated an average substitution rate of 0.0005 nucleotide per million years for the concatenated DNA sequences. The molecular dating analysis estimated that the Dasylirion genus appeared more than 5.46 million years ago, with a rate of diversification of 0.0466 net speciation events per million years. The estimated age represents a lower bound, since not all Dasylirion species are included. These findings are consistent with other origin and diversification hypotheses for arid-land Asparagaceae in the Mexican highlands as a result of geomorphological events in North America. [ABSTRACT FROM AUTHOR]

Background: Comparative genomic analysis exhibits dynamic evolution of plastid genome (plastome) in the clusioid clade of Malpighiales, which comprise five families, including multiple inversions and gene losses. Little is known about the plastome evolution in Hypericaceae, a large family in the clade. Only the plastome of one species, Cratoxylum cochinchinense, has been published. Results: We generated a complete plastome sequence for Hypericum ascyron, providing the first complete plastome from the tribe Hypericeae (Hypericaceae). The H. ascyron plastome exhibits dynamic changes in gene and intron content, structure, and sequence divergence compared to the C. cochinchinense plastome from the tribe Cratoxyleae (Hypericaceae). Transcriptome data determined the evolutionary fate of the missing plastid genes infA, rps7, rps16, rpl23, and rpl32 in H. ascyron. Putative functional transfers of infA, rps7, and rpl32 were detected to the nucleus, whereas rps16 and rpl23 were substituted by nuclear-encoded homologs. The plastid rpl32 was integrated into the nuclear-encoded SODcp gene. Our findings suggested that the transferred rpl32 had undergone subfunctionalization by duplication rather than alternative splicing. The H. ascyron plastome rearrangements involved seven inversions, at least three inverted repeat (IR) boundary shifts, which generated gene relocations and duplications. Accelerated substitution rates of plastid genes were observed in the H. ascyron plastome compared with that of C. cochinchinense plastid genes. The higher substitution rates in the accD and clpP were correlated with structural change, including a large insertion of amino acids and losses of two introns, respectively. In addition, we found evidence of positive selection of the clpP, matK, and rps3 genes in the three branches related to H. ascyron. In particular, the matK gene was repeatedly under selection within the family Hypericaceae. Selective pressure in the H. ascyron matK gene was associated with the loss of trnK-UUU and relocation into the IR region. Conclusions: The Hypericum ascyron plastome sequence provides valuable information for improving the understanding of plastome evolution among the clusioid of the Malpighiales. Evidence for intracellular gene transfer from the plastid to the nucleus was detected in the nuclear transcriptome, providing insight into the evolutionary fate of plastid genes in Hypericaceae. [ABSTRACT FROM AUTHOR]

Malaxidinae are a cosmopolitan higher Epidendroid subtribe of > 1250 species that exhibit wide morphological and ecological diversity. Despite almost two centuries of taxonomic deliberation, controversy persists regarding the delimitation of practically all Malaxidinae genera, the most important of which are Crepidium , Dienia , Liparis and Malaxis. Previous attempts to classify these genera using a molecular phylogenetic approach showed Liparis and Malaxis to be polyphyletic and the floral characters traditionally used to define them as homoplastic. Emphasis has instead shifted to vegetative and ecological traits. Here, we conduct an expanded analysis of nuclear (ITS) and plastid (matK) sequences focused on terrestrial taxa, with the resulting phylogram largely corroborating the emerging picture, and we test the efficacy of four previously highlighted traits to recover the same relationships. Although growth habit is underscored as important for resolving a natural distinction between epiphytic Liparis and terrestrial ' Crepidium clade' plus ' Malaxis clade' taxa, leaf shape and venation and habitat preference are shown to be poor predictors of phylogenetic affiliation. Instead, perennating organ structure (heteroblastic or homoblastic) and placement (predominantly above- or below-ground) – are incisive, with leaf number and texture apparently correlated. These findings are discussed in the context of an inferred evolutionary history of the subtribe. Although homoplastic at the subtribe level, some floral characters are shown to be useful for resolving identities at the species level. Accordingly, the status of four long-confused species (Crepidium acuminatum , C. allanii , C. purpureum and Microstylis biloba) is resolved. [ABSTRACT FROM AUTHOR]

Rheum Species (Rhubarb) was widely known as a purgative and antiinflammatory agent. In the Chinese Pharmacopoeia, rhubarb was prescribed for three Rheum species, Rheum palmatum, R. tanguticum and R. officinale. Due to huge market demand, its fake or adulteration is frequently found in the market. To explore the cultivated germplasm resource of medicinal rhubarb and develop an ultimate identification method for plants and drugs, molecular identification of the chloroplast matK gene and rpl32 gene were performed on 41 samples from main planting area in northwest China. The results showed that the matK and rpl32 regions showed high success rate of PCR amplification and DNA sequencing, as well as superior discriminatory ability, and we found that there were mixed planting of different medicinal rhubarb in the Minle, Huzhu, Datong county and adulteration in the Longde county. The analysis of NJ trees indicated that the same species clustered together, the three medicinal Rheum species and adulteration can be distinguished by nucleotide differences. In future, we suggest that conservation and efficient management should be strengthened for cultivated germplasm resource of medicinal rhubarb, we should also pay more attention to super-barcoding or specific barcode that enhance ability to discriminate the closely related medicinal plants. [ABSTRACT FROM AUTHOR]

Wild coffee species are the reservoirs of genetic diversity and could play a critical role in the genetic improvement of coffee. However, the conservation and genetic assessment of wild coffee species has been largely neglected. In the present study, DNA barcoding approaches were employed to assess the phylogenetic relationships between five indigenous wild coffee species from India and compared with two cultivated, and four wild coffee species of African origin. The efficacy of three barcoding loci namely matK, rbcL, and trnL-trnF was investigated using PCR amplification and sequence characterization. The intergenic spacer trnL-trnF is the highly polymorphic loci followed by matK and rbcL chloroplast gene. Among the three barcoding loci, the matK locus has the maximum number of parsimony informative sites, whereas the trnL-trnF locus contains maximum singleton variable sites. Although all the three loci contain a few unique fixed nucleotides (UFNs), no individual barcode locus has the critical nucleotide sequence tags for all the five Indian wild coffee species that help in species discrimination. However, the multilocus combinations are efficient in discriminating the species due to the presence of SNPs and specific sequence tags. The phylogenetic tree constructed using the maximum likelihood analysis of the combined barcoding loci separated all the Indian wild coffee species from African wild coffee species compared to phylogeny inferred using individual barcoding loci. Our study supports the utility of DNA barcoding as a useful tool for coffee species identification, which can be used for conservation purposes. [ABSTRACT FROM AUTHOR]

DNA barcodes are standardized sequences that range between 400 and 800 bp, vary at different taxonomic levels, and make it possible to assign sequences to species that have been previously taxonomically characterized. Several DNA barcodes have been postulated for plants, nonetheless, their classification potential has not been evaluated for metabarcoding, and as a result, it would appear as none of them excels above the others in this area. One tool that has been widely used and served as a baseline when evaluating new approaches is Naïve Bayesian Classifiers (NBC). The present study aims at evaluating the classification power of several plant chloroplast genetic markers that have been proposed as barcodes (trnL , rpoB , rbcL , matK , psbA-trnH , and psbK) using an NBC. We performed the classification at different taxonomic levels, and identified problematic genera when resolution was desired. We propose matK and trnL as potential candidate markers with resolution up to genus level. Some problematic genera within certain families could lead to the misclassification no matter which marker is used (i.e., Aegilops , Gueldenstaedtia , Helianthus , Oryza , Shorea , Thysananthus , and Triticum). Finally, we suggest recommendations for the taxonomic identification of plants in samples with potential mixtures. [ABSTRACT FROM AUTHOR]

Jasminanthes tuyetanhiae is one of the precious herbs and good for human health, discovered in the Da-Bia Mountain (Phu Yen province, Vietnam). The identification of the CTW species (species believed to be J. tuyetanhiae collected in 2019) by molecular indicators showed that this species belongs to the Apocynaceae family. High similarity (98.2%) in the ITS1-5.8SrRNA-ITS2 gene sequence of CTW when compared on Genbank with J. tuyetanhiae and genetic distance difference (1.3%) - in the limit of difference of the same taxon considered on matK sequence shows that CTW is likely to belong to this species. Surface sterilization of ex vitro explants with HgCl2 (0.1%) for 3 min gave the highest sterilization efficiency compared to the remaining treatments with the induction explant rate of 93.33%. BA (0.5 mg l−1) is the most optimal for effective in vitro shoot multiplication in this species. Adding IBA to culture media at the appropriate concentration (0.5 mg l−1) increased rooting ability, shortened rooting time (13 days) and increased root length (6.53 mm). The ventilation culture system improves rooting efficiency, stimulates growth and induces secondary root formation—which is a suitable system for in vitro propagation of the Jasminanthes tuyetanhiae in this study. Key message: Jasminanthes tuyetanhiae is one of the precious herbs and good for human health, discovered in the Da Bia mountain of Phu Yen province. High similarity (98.2%) in the ITS1-5.8SrRNA-ITS2 gene sequence of CTW when compared on Genbank with Jaminanthes tuyetanhiae. In vitro propagation is an effective method for the conservation and development of the Jaminanthes tuyetanhiae plantlets on a commercial scale. [ABSTRACT FROM AUTHOR]

The jewel orchids (Goodyerinae), named after their often colourful leaves, have a pantropical distribution with a clear Asian centre of diversity. However, the Nearctic and Neotropical America together form a second centre of diversity, with one-third of known species of Goodyerinae. Previously, only a few American samples have been included in phylogenetic studies, and their putatively Asian origins and American divergence times were poorly known. To elucidate these topics, we inferred phylogenetic trees, performed molecular dating and reconstructed biogeographic history using nuclear ribosomal ITS and plastid matK sequences for 34 species of Goodyerinae from the New World and 76 previously published accessions of Cranichideae. Our well-supported phylogenetic topology suggests two independent dispersal events to the New World from the Indomalesian region during the Miocene. The first inferred dispersal of a Neotropical clade diverged c. 11 Mya from their most recent common ancestor (MRCA), comprising three highly supported subclades that do not match the limits of Aspidogyne , Kreodanthus and Microchilus as previously circumscribed. The second dispersal involved a largely Nearctic clade of Goodyera s.l. diverging c. 8.4 Mya from the MRCA and exhibiting a complex biogeographic history with subsequent dispersals between the Nearctic and Indomalesia. The occurrence of these species in gallery forests putatively prevented vicariance events imposed by the expansion of the Chacoan region as previously detected for epiphytic Orchidaceae. Eighty-nine nomenclatural combinations and three new names in Microchilus are proposed. [ABSTRACT FROM AUTHOR]

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]