1,300 results on '"matk"'
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2. Reinstatement of Acalypha fallax Mull. Arg. and description of A. brittoi sp. nov. based on micromorphological and molecular characters.
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Soosairaj, Sebastian, Soosai Mary Nithya, Maria, Raja, Prakasam, and John Peter Arulanandam, Lourdusamy
- Subjects
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SCANNING electron microscopy , *TRICHOMES , *MORPHOLOGY , *POLLEN , *SPECIES - Abstract
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]
- Published
- 2025
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3. Identification and Genetic Diversity Analysis of Cinnamomum parthenoxylon (Jack) Meisn Species in Song Hinh Protection Forest, Vietnam Based on Three Chloroplast Gene Regions
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Dinh Duy Vu, Mai Phuong Pham, Ngoc Huyen Dang, Xuan Dac Le, Hung Cuong Dang, Huu Thuc Nguyen, and Dang Hoi Nguyen
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cinnamomum parthenoxylon ,dna barcodes ,genetic diversity ,matk ,rbcl ,species identification ,trnh-psba ,Biotechnology ,TP248.13-248.65 - Abstract
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.
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- 2024
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4. Morpho-anatomical traits, DNA barcode and phytochemical screening of Aglaonema cochinchinense
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Hong Thien Van, Doan Trang Phan-thi, Ngoc Thuan Nguyen, Bach Bao Phuong Lam, Hong Truong Luu, Thu Trang Tran-thi, and Nga Nguyen-Phi
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aglaonema cochinchinense ,anatomy ,matk ,morphology ,phytochemistry ,Science - Abstract
Aglaonema cochinchinense is a rare species. It is found in some limited areas of southern Vietnam, Thailand and Cambodia. The present study provides its morphological, anatomical, phytochemical characteristics, and DNA barcode for the first time. The results from this study hold promise for using as a monographic literature in the identification of the medicinal plants as well as further application of this species in medicinal field and other related fields.
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- 2024
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5. DNA barcoding, pollen and seed characteristics for documentation of four monocot Mediterranean endemic plant species in Egypt.
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El-Khalafy, Mohamed M., El-Kholy, Aziza S., Ahmed, Dalia A., Al-Sodany, Yassin M., Haroun, Soliman A., Shaltout, Kamal H., and Salim, Mohamed A.
- Abstract
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]
- Published
- 2024
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6. Identification and Genetic Diversity Analysis of Cinnamomum parthenoxylon (Jack) Meisn Species in Song Hinh Protection Forest, Vietnam Based on Three Chloroplast Gene Regions.
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Vu, Dinh Duy, Pham, Mai Phuong, Dang, Ngoc Huyen, Le, Xuan Dac, Dang, Hung Cuong, Nguyen, Huu Thuc, and Nguyen, Dang Hoi
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GENETIC variation ,FOREST protection ,HABITAT destruction ,PLANT identification ,HAPLOTYPES ,CHLOROPLAST DNA - Abstract
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]
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- 2024
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7. Molecular characterization of some potential ethnomedicinal plants used for treatment of diabetes in Nagaland, India.
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Sharma, Takhelchangbam Ibeeka and Deb, Chitta Ranjan
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GENETIC barcoding , *GENETIC markers , *GENETIC distance , *PLANT identification , *MEDICINAL plants , *CHLOROPLAST DNA - Abstract
The use of medicinal plants for managing diabetes and related conditions has been an integral part of traditional healthcare systems throughout the world including Nagaland, India. Authentic identification of these medicinal plants is crucial for their safe and effective use. A study was aimed for authentic identification of some anti-diabetic potential ethnomedicinal plants from Nagaland, India using DNA sequence based molecular characterization by amplifying and sequencing of ITS, rbcL and matK barcode regions. DNA barcode loci from the nuclear and chloroplast genomes from 15 different ethnomedicinal anti-diabetic plants of Nagaland, India, were studied for molecular characterisation. Based on the ITS, rbcL and matK region sequences, three main discrimination methods, i.e., BLAST, Phylogenetic tree and genetic distance, were adopted to identify the species. Utilising DNA markers for identification is both highly advantageous and efficient due to its reliability and rapidity. Successful amplification across species and high blast hits (100 % identity) highlighted their potential for molecular characterisation. Phylogenetic trees constructed using various models showed distinct clades and subclades, with matK revealing hypervariability and rbcL demonstrating consistent matches. Genetic distances revealed varying levels of similarity, with certain species establishing close relationships based on pairwise comparisons. GC% variations were detected, potentially indicating nucleotide composition differences and functional constraints among species genomes. The findings of this study highlight that the ITS, rbcL , and matK regions serve as effective markers for verifying the authenticity of anti-diabetic medicinal plants indigenous to Nagaland, India. [Display omitted] • DNA markers based species identification of 15 antidiabetic plants from Nagaland. • ITS, matK and rbcL based identification complemented with phonological identification. • Consistency in rbcL and matK regions showing reliability as DNA barcode markers. • Sequence length variations attributed to genomic differences among plants. [ABSTRACT FROM AUTHOR]
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- 2024
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8. An overview of floral and vegetative evolution in the Asian clade of Bulbophyllum (Orchidaceae).
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Nicha Thawara, Panida Kongsawadworakul, Piyakaset Suksathan, Santi Watthana, Thitiporn Pingyot, Merckx, Vincent S. F. T., and Saroj Ruchisansakun
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MAXIMUM likelihood statistics ,NUCLEOTIDE sequence ,BAYESIAN field theory ,DNA sequencing ,PHYLOGENY - Abstract
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]
- Published
- 2024
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9. Chlorophytum kolliense (Asparagaceae), a new species from the Eastern Ghats of Tamil Nadu, India.
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Soosairaj, Sebastian, Raja, Prakasam, Balaguru, Balakrishnan, and Dhatchanamoorthy, Narayanasamy
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POLLEN , *ANTHER , *ASPARAGACEAE , *ELLIPSOIDS , *NERVES - Abstract
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]
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- 2024
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10. Genetic diversity of closely related Calligounum species collected from Saudi habitats by analyzing the matK and rpoC1 genes, and SCoT and IRAP markers
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AlGarawi, Amal Mohamed and Abd-Elgawad, Magda Elsayed
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- 2025
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11. Molecular identification of eight ethnomedicinal plants used by the indigenous communities of Bangladesh through the partial genome sequencing of three plastid markers.
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Mushwan, Khalid, Uddin, Shaikh Bokhtear, Siddiki, AMAM Zonaed, and Faruque, Mohammad Omar
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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]
- Published
- 2024
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12. Evaluating DNA barcoding using cpDNA matK and rbcL for species identification and phylogenetic analysis of Prunus armeniaca L. (Rosaceae) genotypes.
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Sevindik, Emre, Korkom, Yunus, and Murathan, Zehra Tuğba
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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]
- Published
- 2024
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13. Morphological and molecular characterization of two species of genus Ageratum.
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Kumari, Anita and Sidhu, Malkiat Chand
- Abstract
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]
- Published
- 2024
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14. Genome constitution and evolution of Elymus atratus (Poaceae: Triticeae) inferred from cytogenetic and phylogenetic analysis.
- Author
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Tan, Lu, Wu, Dan-Dan, Zhang, Chang-Bing, Cheng, Yi-Ran, Sha, Li-Na, Fan, Xing, Kang, Hou-Yang, Wang, Yi, Zhang, Hai-Qin, Escudero, Marcial, and Zhou, Yong-Hong
- Abstract
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]
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- 2024
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15. The Maturase K Region of Kebak, A Javanese Cultural Flora
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Primandiri, Poppy Rahmatika, Hariri, Muhammad Rifqi, Sulistiyowati, Tutut Indah, Santoso, Agus Muji, Striełkowski, Wadim, Editor-in-Chief, Black, Jessica M., Series Editor, Butterfield, Stephen A., Series Editor, Chang, Chi-Cheng, Series Editor, Cheng, Jiuqing, Series Editor, Dumanig, Francisco Perlas, Series Editor, Al-Mabuk, Radhi, Series Editor, Scheper-Hughes, Nancy, Series Editor, Urban, Mathias, Series Editor, Webb, Stephen, Series Editor, Khoerunnisa, Fitri, editor, Yuliani, Galuh, editor, and Zakwandi, Rizki, editor
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- 2024
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16. Analysis of trnL- trnL- trnF Intergenic Spacer and matK Sequences Combined with Morphological Observations Showed Pucuk Seminyak from Riau is Champereia manillana var. manillana Merr.
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Dewi Indriyani Roslim, Herman, Deanne Yoshe Fidela Budiono, Isa Endar Cahyati, Wahyu Lestari, Linda Novita, and Arief Priyadi
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champereia manillana var. manillana ,dna barcode ,matk ,morphology ,pucuk seminyak ,riau ,trnl-trnl-trnf intergenic spacer ,Biology (General) ,QH301-705.5 - Abstract
A taxonomic status of Pucuk Seminyak plant is still unclear. This plant has a fruit like Melinjo (Gnetum gnemon) fruit and is often classified as a member of Gnetaceae family. This study aims to determine the taxonomic status of Pucuk Seminyak from Riau using trnL-trnL-trnF intergenic spacer (IGS) and matK sequences. Methods included leaf samples from three individuals collected from the Kampar Regency, Riau Province, total DNA extraction, electrophoresis, polymerase chain reaction (PCR), and data analysis. The results showed that the trnL-trnL-trnF IGS DNA sequences from the three samples of Pucuk Seminyak were obtained 937 bp length, while the matK had a size of 775 bp. These sequences have been registered in GenBank with registration numbers OQ174512, OQ174513, and OQ174514 for trnL-trnL-trnF IGS, and OQ174525, OQ174526, and OQ174527 for matK. The highest similarity was found between Pucuk Seminyak and Champereia manillana with an identity value of 99.67% based on trnL-trnL-trnF IGS and 99.74% based on matK. BLASTn analysis by default settings and organism Champereia (taxid: 50116) resulted in hits on the Champereia genus of the Opiliaceae. Further phylogenetic analysis placed the study objects in the Champereia clade (bootstrap support 49 for trnL-trnL-trnF, 68 for matK, and 71 for concatenated sequences). Lastly, identification by morphological characters also confirmed that the specimen agreed with the description and identification key for C. manillana. The species is classified into two varieties: var. longistaminea and var. manillana. The former was distributed in Southwest China, and the latter was distributed in Malesia to India. Furthermore, the phylogenetic analysis separated the two varieties into different clades. Therefore, it can be concluded that our specimen of Pucuk Seminyak is identified as C. manillana var. manillana Merr. (Opiliaceae).
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- 2024
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17. Development of a standardized methodology for selecting candidate DNA barcodes of Trillium govanianum to combat biodiversity crime and environmental exploitation
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Tina Sharma and Mukesh Kumar Thakar
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Forensic Science ,Wildlife forensics ,Trillium govanianum ,MatK ,RbcL ,ITS ,Ecology ,QH540-549.5 ,Veterinary medicine ,SF600-1100 - Abstract
This study introduces an innovative method using DNA barcodes to accurately identify species, addressing the critical issue of trafficking invaluable medicinal plants like Trillium govanianum. The success rate in amplification and sequencing of barcoding regions was an impressive 100%. The Internal Transcribed Spacer (ITS) region proved most effective in distinguishing closely related Trillium species. By testing herbal products from markets, the study revealed extensive illegal trade, with 50% confirmed as Trillium govanianum and 30% adulterated with Dioscorea villosa. This research contributes new DNA sequences to identification databases, enhancing protocols. Genetic variations within Trillium govanianum were narrower than to the nearest non-conspecific neighbor in barcoding regions (matK: 0.006, rbcL: 0.003, ITS: 0.043). Combining coding and non-coding regions (matK + ITS) achieved 100% species discrimination. Market samples showed 30% product substitution, with varying success rates for amplification (rbcL: 70%, matK: 60%, ITS: 40%, improved with ITS2 primers). Half the sequences were Trillium govanianum, 30% were Dioscorea villosa, revealing covert substitution. ITS and matK sequences were effective, with a genetic distance gap, while rbcL had limited divergence (0.003), making it less suitable for accurate identification compared to matK and ITS.
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- 2024
- Full Text
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18. DNA barcoding using chloroplast matK and rbcL regions for the identification of bamboo species in Sabah
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Wilson Thau Lym Yong, Anis Adilah Mustafa, Mohammad Rahmat Derise, and Kenneth Francis Rodrigues
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Bamboo species ,DNA barcoding ,matK ,rbcL ,Species identification ,Forestry ,SD1-669.5 - Abstract
Bamboo species play pivotal roles in maintaining ecological diversity and driving socio-economic development in Sabah, Malaysia. However, due to overlapping traits among distinct bamboo species, identifying them based solely on morphological characteristics poses challenges. DNA barcoding emerges as a highly effective method, demonstrating potential accuracy in identifying diverse plant species across various taxa and ecosystems. In this study, we used the chloroplast matK and rbcL regions as barcode markers to identify 15 bamboo plants in Sabah. Both matK and rbcL exhibited a notable 100% accuracy at the genus level, indicating their reliability in capturing broader taxonomic categories during BLAST searches and genetic distance analysis. However, at the species level, the success rate was limited to 60%, revealing challenges in differentiating closely related bamboo species using the existing DNA barcodes. Our findings underscore the need for an advanced DNA barcode reference library with extensive species coverage for accurate species identification. This study not only unveiled crucial insights into bamboo diversity and taxonomy in Sabah but also contributes to ongoing bamboo resource conservation and supports sustainable resource management in the region.
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- 2024
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19. Генетический полиморфизм популяций и филогения среднесибирских спорышей секции Pоlygonum (Polygonaceae) с использованием ISSR и хлоропластных маркеров
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Ирина Евгеньевна Ямских, Наталья Николаевна Тупицына, Ксения Константиновна Рябова, and Максим Геннадьевич Куцев
- Subjects
генетическая структура ,популяция ,секция polygonum ,филогения ,issr-pcr анализ ,matk ,trnl-trnf ,Botany ,QK1-989 - Abstract
Статья посвящена исследованию генетического полиморфизма популяций и филогении видов секции Pоlygonum с использованием ISSR и хлоропластных маркеров. Спорыши представляют собой таксономически сложную группу. Идентификация особей осложняется мелкими размерами растений, процессами межвидовой гибридизации, гетерокарпией, фенологической и экологической пластичностью. В данной работе изучена генетическая изменчивость 6 популяций 5 видов спорышей, произрастающих в г. Красноярске. ISSR-анализом установлено, что уровень генетического разнообразия в популяциях варьирует от 4,17 % до 35,83 % и имеет максимальные показатели для генетически близких видов P. sabulosum (P = 35,83 %) и P. arenastrum (P = 22,5–30 %). Минимальные значения генетического разнообразия зафиксированы для популяций P. aviculare (P = 4,17 %) и P. calcatum (P = 5 %). Изученные популяции характеризуются очень высоким уровнем генетической дифференциации (Gst = 0,78) и достоверно относятся к разным видам. На UPGMA-дендрограмме сходства особи данных видов формируют четко обособленные клады. Анализ генотипов особей в программе STRUCTURE также показывает достоверное разделение на 5 кластеров, соответствующих исследуемым видам. Филогенетический анализ с использованием trnL-trnF участка хлоропластной ДНК показывает наличие 5-нуклеотидной делеции и двух трансверсий, позволяющих разделить изучаемую группу спорышей на два кластера, морфологически отличающихся друг от друга. Первую группу формируют виды P. arenastrum, P. calcatum, P. caspicum, P. sabulosum, характеризующиеся отсутствием выраженного главного побега, постепенным уменьшением листьев к верхушкам побегов и расчленением околоцветника на 1/2 своей длины. Во вторую группу входят P. aviculare, P. boreale, P. neglectum, P rectum с выраженным главным побегом, гетерофиллией, расчленением околоцветника на 2/3–3/4 своей длины. В последовательностях гена matKвыявлено 2 замены, он является менее информативным для решения вопросов таксономии изучаемой группы.
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- 2023
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20. Generating Long-Read Sequences of Balsa (Ochroma pyramidale (Cav. ex Lam.) Urb.) Using Minion Oxford Nanopore Technology and Utilization for Phylogenetic Study
- Author
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Siska Nurfajri, Fifi Gus Dwiyanti, Rahadian Pratama, Muhammad Majiidu, and Iskandar Z. Siregar
- Subjects
matk ,minion ,ochroma pyramidale ,phylogeny ,rbcl ,Agriculture ,Plant culture ,SB1-1110 - Abstract
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).
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- 2023
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21. Morpho-anatomical characterization and DNA barcoding of Artemesia vulgaris L.
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D. K. Wahyuni, D. T. Indriati, M. Ilham, A. A. A. Murtadlo, H. Purnobasuki, Junairiah, P. R. Purnama, N. K. K. Ikram, M. Z. Samian, and S. Subramaniam
- Subjects
Artemisia vulgaris ,DNA barcode ,morpho-anatomy ,matK ,phylogenetic tree ,rbcL ,Science ,Biology (General) ,QH301-705.5 ,Zoology ,QL1-991 ,Botany ,QK1-989 - Abstract
Abstract Artemisia vulgaris L. belongs to Asteraceae, is a herbal plant that has various benefits in the medical field, so that its use in the medical field can be explored optimally, the plant must be thoroughly identified. This study aims to identify A. vulgaris both in terms of descriptive morpho-anatomy and DNA barcoding using BLAST and phylogenetic tree reconstruction. The morpho-anatomical character was observed on root, stem, and leaf. DNA barcoding analysis was carried out through amplification and alignment of the rbcL and matK genes. All studies were conducted on three samples from Taman Husada (Medicinal Plant Garden) Graha Famili Surabaya, Indonesia. The anatomical slide was prepared by the paraffin method. Morphological studies revealed that the leaves of A. vulgaris both on the lower-middle part and on the upper part of the stem have differences, especially in the character of the stipules, petioles, and incisions they have. Meanwhile, from the study of anatomy, A. vulgaris has an anomocytic type of stomata and its distribution is mostly on the ventral part of the leaves. Through the BLAST process and phylogenetic tree reconstruction, the plant sequences being studied are closely related to several species of the genus Artemisia as indicated by a percentage identity above 98% and branch proximity between taxa in the reconstructed phylogenetic tree.
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- 2024
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22. Morpho-anatomical characterization and DNA barcoding of Artemesia vulgaris L.
- Author
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Wahyuni, D. K., Indriati, D. T., Ilham, M., Murtadlo, A. A. A., Junairiah, Purnama, P. R., Ikram, N. K. K., Samian, M. Z., and Subramaniam, S.
- Subjects
GENETIC barcoding ,ORNAMENTAL plants ,DNA analysis ,MEDICINAL plants ,ARTEMISIA - Abstract
Copyright of Brazilian Journal of Biology is the property of Instituto Internacional de Ecologia 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.)
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- 2024
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23. Verification of Maman (Cleome gynandra (L.) Briq.) from Riau Based on matK and trnL-trnL-trnF Intergenic Spacer.
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Roslim, Dewi Indriyani, Herman, Herman, Putri, Shalsadila Rahmadani, Furqoni, Aries Tri, Fidela Budiono, Deanne Yoshe, Fadhl Altuhaish, Adeel Abdulkarim, and Lestari, Wahyu
- Subjects
- *
GENETIC barcoding , *MALAYS (Asian people) , *DNA sequencing , *NUCLEOTIDES , *DATA analysis - Abstract
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]
- Published
- 2023
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24. DNA Barcoding of Orchids in India: A Systematic Survey.
- Author
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JYOTHSNA, B. S., SHARMA, KAVITA, and SRIVASTAVA, DEEPTI
- Subjects
ORCHIDS ,DNA ,PHYTOCHEMICALS ,METABOLITES ,COELOGYNE - Abstract
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]
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- 2023
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25. Distribution Mapping and Diversity Assessment of Ilex venulosa from Meghalaya Using Internal Transcribed Spacer Regions, matK and rbcL
- Author
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Nongbet, Amilia, Chrungoo, N. K., Uppaluri, Ramagopal V. S., editor, and Rangan, Latha, editor
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- 2023
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26. Phylogenetic Analysis of Rare and Endangered Tulipa Species (Liliaceae) of Kazakhstan Based on Universal Barcoding Markers
- Author
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Maxim Sutula, Ayan Kakanay, Dilnur Tussipkan, Samatulla Dzhumanov, and Shuga Manabayeva
- Subjects
Tulipa ,DNA barcoding ,hybridization ,ITS ,matK ,phylogenetics and systematics ,Biology (General) ,QH301-705.5 - Abstract
In Kazakhstan, the genus Tulipa is represented by 35 species, 18 of which are listed in the Red Data Book of Kazakhstan and protected by the state. Recent studies of tulip specimens from regions bordering Kazakhstan emphasize the significance of species inventory and report the discovery of several hybrids. In this study, eight tulip species were identified based on morphological characteristics and using DNA barcoding methods. Molecular genetic markers, including nrDNA (ITS) and cpDNA markers (rbcL, matK), of the studied species were sequenced and analyzed using the Bayesian inference and maximum likelihood phylogenetic analysis methods. Our work demonstrates that DNA barcodes based on the ITS, rbcL, and matK marker regions have successful practical applicability, with ITS being the most informative at the intragenic level. However, for distinguishing closely related taxa, the most effective approach would be to use a combined dataset of sequences from multiple DNA markers. The results showed discrepancies in the placement of several taxa (T. kaufmanniana, T. patens), likely due to introgression and natural spontaneous hybridization. The molecular phylogenetic analysis suggests the existence of a previously undescribed hybrid between T. patens and T. alberti. Further detailed population studies are needed to validate this hypothesis.
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- 2024
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27. Unraveling the secrets of Eclipta alba (L.) Hassk.: a comprehensive study of morpho-anatomy and DNA barcoding
- Author
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D. K. Wahyuni, B. F. Yoku, S. R. Mukarromah, P. R. Purnama, M. Ilham, G. A. Rakashiwi, D. T. Indriati, Junairiah, S. Wacharasindhu, S. Prasongsuk, S. Subramaniam, and H. Purnobasuki
- Subjects
Eclipta alba ,DNA barcode ,morpho-anatomy ,matK ,rbcL ,Science ,Biology (General) ,QH301-705.5 ,Zoology ,QL1-991 ,Botany ,QK1-989 - Abstract
Abstract Safety regarding herbal products is very necessary; therefore, routine identification of raw materials should be performed to ensure that the raw materials used in pharmaceutical products are suitable for their intended use. In order for the identification-related data obtained to be accurate, the identification of various kinds of markers is also very necessary. The purpose of this study was to describe the characteristics of Eclipta alba (L.) Hassk. based on qualitative morpho-anatomical markers and quantitative DNA coding. The morphology of this plant has herbaceous habit with a taproot and a stem with branches that appear from the middle. Leaves are single type imperfectly arranged oppositely, lanceolatus, finely serrated on the edges, tapered at the base, pointed at the end, and have a pinnate and hairy leaf surface. The flowers consist of ray flowers and tube flowers with a cup shape. Meanwhile, in terms of anatomy, E. alba has aerenchyma, which are scattered in the cortex of the root and stem. In addition, there are anisocytic stomata, glandular trichomes, and non-glandural trichomes with an elongated shape accompanied by ornamentation found on the leaf epidermis. The results of sequence alignment and phylogenetic tree reconstruction show that the sample plants are closely related to species in the genus Eclipta.
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- 2023
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28. Molecular classification of Barbeyaceae (Barbeya oleoides Schweinf.) using four different DNA barcodes
- Author
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Fatima Omari Alzahrani and Sami Al-Robai
- Subjects
DNA barcoding ,phylogenetic analysis ,ITS2 ,rbcL ,matK ,trnH-psbA ,Biology (General) ,QH301-705.5 ,Cytology ,QH573-671 - Abstract
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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- 2023
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29. Intraspecific identification of some pomegranate (Punica granatum L.) genotypes based on DNA barcoding and morpho-biochemical characteristics.
- Author
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Moradi Ashour, Behrouz, Rabiei, Mohammad, and Shiran, Behrouz
- Abstract
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]
- Published
- 2023
- Full Text
- View/download PDF
30. Generating Long-Read Sequences of Balsa (Ochroma pyramidale (Cav. ex Lam.) Urb.) Using Minion Oxford Nanopore Technology and Utilization for Phylogenetic Study.
- Author
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Nurfajri, Siska, Dwiyanti, Fifi Gus, Pratama, Rahadian, Majiidu, Muhammad, and Siregar, Iskandar Z.
- Subjects
CHLOROPLAST DNA ,PLANT species ,FOREST plants ,PHYLOGENY - Abstract
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]
- Published
- 2023
- Full Text
- View/download PDF
31. Typhonium rhizomatosum (Araceae), A NEW RECORD FOR THE FLORA OF VIETNAM.
- Author
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Nga Nguyen-Phi, Hong Thien Van, and Hong Truong Luu
- Subjects
- *
ARACEAE , *BOTANY , *PHOTOGRAPHS - Abstract
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]
- Published
- 2023
- Full Text
- View/download PDF
32. DNA barcodes in Egyptian olive cultivars (Olea europaea L.) using the rbcL and matK coding sequences.
- Author
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Said, Eglal M. and Hassan, M. E.
- Abstract
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]
- Published
- 2023
- Full Text
- View/download PDF
33. Genomic and Transcriptional Profiling Analysis and Insights into Rhodomyrtone Yield in Rhodomyrtus tomentosa (Aiton) Hassk.
- Author
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Nakkaew, Alisa, Masjon, Thipphanet, and Voravuthikunchai, Supayang Piyawan
- Subjects
RIBOSOMAL DNA ,ZINC transporters ,GENE expression ,CARRIER proteins ,ZINC proteins ,SUSTAINABILITY - Abstract
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 ZnSO
4 stress. The findings provide useful information for selection of cultivation sites to achieve high rhodomyrtone yields in R. tomentosa. [ABSTRACT FROM AUTHOR]- Published
- 2023
- Full Text
- View/download PDF
34. DNA Barcoding of Invasive Terrestrial Plant Species in India
- Author
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Lonare, Nayan, Patil, Gayatri, Waghmare, Suprriya, Bhor, Reshma, Hardikar, Hrishikesh, and Tembe, Sanket
- Published
- 2024
- Full Text
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35. MOLECULAR PHYLOGENETICS AND DATING OF ARECACEAE IN BANGLADESH INFERRED FROM MATK AND RBCL GENES.
- Author
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AHMED, SHEIKH SUNZID, RAHMAN, M. OLIUR, ALI, M. AJMAL, AL-HEMAID, FAHAD, and LEE, JOONGKU
- Subjects
- *
MOLECULAR phylogeny , *MESOZOIC Era , *CRETACEOUS Period , *MOLECULAR clock , *CENOZOIC Era , *PALMS , *CIRCADIAN rhythms - Abstract
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]
- Published
- 2023
- Full Text
- View/download PDF
36. ANÁLISIS MOLECULARES Y OBSERVACIONES MORFO-ANATÓMICAS DE CHEILANTHES VOLCANENSIS (PTERIDACEAE) DEFINEN SUS RELACIONES DENTRO DE LA SUBFAMILIA CHEILANTHOIDEAE EN SUDAMÉRICA.
- Author
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Mónica Ponce, M., Amalia Scataglini, M., Hernández, Marcela A., and Martínez, Olga. G.
- Subjects
- *
PETIOLES , *SPECIES , *A priori , *PHYLOGENY , *COLLECTIONS - Abstract
The circumscription of the genus Cheilanthes Sw. is supported by molecular and morphological characters; nevertheless, the taxonomic status of some species remains uncertain because they have not been molecularly tested yet. This study analyzes the belonging of Cheilanthes volcanensis de la Sota to this genus, since this species was treated with doubts about its generic identity. From a morphological approach, C. volcanensis is close to Cheilanthes species with pentagonal and highly divided leaf blades; petioles and rachises castaneous to black, glabrous, usually grooved adaxially; features that are also largely representative of the morphological circumscription of the genus Gaga Pryer, F.W. Li & Windham. The molecular analysis of a recent collection, identified a priori as C. volcanensis, demonstrated with high support that the species belongs to the genus Cheilanthes s. str., as was described originally. Finally, morpho-anatomical observations of this species and related species are also provided, which support its phylogenetic position and contribute to the correct generic delimitation of Cheilanthes s. str. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
37. Morphological and DNA Barcoding Based Identification of Calotropis procera (Aiton) Dryand. and Calotropis gigantea (L.) Dryand.
- Author
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Sidhu, M. C., Kumari, A., Jain, B., Kaur, S., Kamra, A., and Rai, J.
- Subjects
- *
GENETIC barcoding , *CALOTROPIS procera , *CALOTROPIS , *DNA analysis , *PLANT species , *PLANT DNA - Abstract
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]
- Published
- 2023
- Full Text
- View/download PDF
38. Phylogenetic analysis based on the ITS, matK and rbcL DNA barcodes and comparison of chemical contents of twelve Paeonia taxa in Türkiye.
- Author
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Cetiz, Mehmet Veysi, Turumtay, Emine Akyuz, Burnaz, Nesibe Arslan, Özhatay, Fatma Neriman, Kaya, Erdal, Memon, Abdulrezzak, and Turumtay, Halbay
- Abstract
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). SC
50 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]- Published
- 2023
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- View/download PDF
39. An Early Reference to DNA Barcode for the Anacardiaceae Family.
- Author
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Ryadi, Alberto, Siregar, Iskandar, de Melo Moura, Carina, Gailing, Oliver, and Amandita, Fitri Yola
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- *
GENETIC barcoding , *ANACARDIACEAE , *ENDANGERED species , *GENETIC markers , *PLANT DNA , *PLANT species , *MANGIFERA - Abstract
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]
- Published
- 2023
- Full Text
- View/download PDF
40. Molecular phylogenetics shed light on polyploid speciation in gorses (Ulex, Fabaceae: Genisteae) and on the origin of the invasive Ulex europaeus.
- Author
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Bellot, Sidonie, Dias, Paula M B, Affagard, Marc, Aïnouche, Malika-Lily, Misset, Marie-Thérèse, and Aïnouche, Abdelkader
- Subjects
- *
MOLECULAR phylogeny , *GENETIC speciation , *PLANT hybridization , *NUMBERS of species , *NUCLEOTIDE sequence , *TOXAPHENE - Abstract
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]
- Published
- 2023
- Full Text
- View/download PDF
41. Morphology, cross ability, and barcode analysis suggest the monotypic status of Benincasa and distinct genus status for Praecitrullus.
- Author
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Sonkamble, Priya, Narayanankutty, C., Mathew, Deepu, and John, K. Joseph
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- *
BAR codes , *MORPHOLOGY , *PLANT species , *CLUSTER analysis (Statistics) , *GOURDS , *WAREHOUSES - Abstract
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]
- Published
- 2023
- Full Text
- View/download PDF
42. CAMELLIA SINENSIS VAR. MADOENSIS (SECT. THEA, THEACEAE), A NEW TAXON FROM VIETNAM
- Author
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Tran Vu Nguyen, Thi Phuong Nhu Van, Xuan Son Le, Van Ngoc Nguyen, Van Dung Luong, Thi Huy Tra Trinh, Ba Nam Nguyen, and Ngoc Trieu Le
- Subjects
Camellia sinensis ,ITS ,Ma Do ,matK ,Section Thea ,Theaceae ,Science ,Social Sciences - Abstract
Camellia sinensis var. madoensis is described and illustrated as a new variety of Camellia sinensis (section Thea, Theaceae) from Xuan Loc Commune, Song Cau District, Phu Yen Province. The new variety is easily distinguishable from C. sinensis var. sinensis by style free ½ to the base. The ITS sequence of this variety is also different from that of Camellia sinensis and its other varieties, while the matK gene sequences are nearly identical among Camellia taxa.
- Published
- 2023
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43. Botanical Biometrics: Exploring Morphological, Palynological, and DNA Barcoding Variations in White Kwao Krua (Pueraria candollei Grah. ex Benth. and P. mirifica Airy Shaw & Suvat.)
- Author
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Wannaree Charoensup, Aekkhaluck Intharuksa, Suthira Yanaso, Suthiwat Khamnuan, Sunee Chansakaow, Panee Sirisa-ard, Pensak Jantrawut, Charan Ditchaiwong, and Kesorn Chaemcheun
- Subjects
DNA barcoding ,herbal medicine ,matK ,morphological characteristics ,palynological characters ,phylogentic analysis ,Plant culture ,SB1-1110 - Abstract
White Kwao Krua, a crucial Thai medicinal plant, contains various phytoestrogen substances used to alleviate menopausal symptoms in estrogen-deficient women. It originates from two species, namely Pueraria candollei Wall. ex Benth. and P. mirifica Airy Shaw & Suvat. However, there exists morphological variation, and the taxonomic status between both species is ambiguous, making discrimination challenging. In this study, we aim to clarify and differentiate the morphological characteristics, palynology, and DNA barcoding of both species. The morphological results showed the stipule size is a phenotypic marker for the differentiation of both species during the vegetative stage. The palynological results, however, exhibited similarity. Through an examination of nucleotide sequences and neighbor-joining tree analysis, it was determined that the DNA barcoding of the matK region has the capability to distinguish between P. candollei and P. mirifica at nucleotide position 702. Specifically, P. candollei manifested a G base, contrasting with the C base observed in P. mirifica. This study concludes that stipule size and the matK gene in DNA barcoding serve as a distinctive characteristic for distinguishing between P. candollei and P. mirifica. These methodologies prove valuable for ensuring the accurate identification of white Kwao Krua for horticulturists.
- Published
- 2024
- Full Text
- View/download PDF
44. Use of DNA Barcoding for Plant Species Identification
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Jossan, Jaskirandeep Kaur, Singh, Rajinder, Dash, Hirak Ranjan, editor, Shrivastava, Pankaj, editor, and Lorente, J. A., editor
- Published
- 2022
- Full Text
- View/download PDF
45. DNA Barcoding in Plants: Past, Present, and Future
- Author
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Mahadani, Pradosh, Dasgupta, Majusha, Vijayan, Joshitha, Kar, Chandan Sourav, Ray, Soham, Singh, Ram Lakhan, editor, Mondal, Sukanta, editor, Parihar, Akarsh, editor, and Singh, Pradeep Kumar, editor
- Published
- 2022
- Full Text
- View/download PDF
46. On species status of Carex sordida (Cyperaceae)
- Author
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Ирина Николаевна Шеховцова and Сергей Викторович Шеховцов
- Subjects
asian russia ,carex ,ets ,its2 ,matk ,new locations ,phylogeny ,Botany ,QK1-989 - Abstract
This article deals with the problem of species independence of Carex sordida. Closely related species of the sect. Carex, C. sordida, C. atherodes, and C. drymophila, were analyzed based on material from Asian Russia. Based on morphological characteristics, it was suggested that C. sordida is more closely related to C. atherodes than to C. drymophila. Molecular analysis using the matK plastid gene and the ITS2 and ETS nuclear ribosomal spacers confirmed that C. sordida is a distinct species closely related to C. atherodes. Several specimens of hybrid origin among the studied species were found. During the revision of herbarium samples, several new localities of C. sordida were identified, which significantly expanded its range to the west. In this study, for the first time, distribution maps of C. sordida, C. drymophila, and C. atherodes in the Asian part of Russia were published.
- Published
- 2022
- Full Text
- View/download PDF
47. Establishment of a dna barcoding database for legume and grass species identification
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Li, Yongqing, La Bu, Zunongjiang A., Cao, Lijun, and Zhao, Shengguo
- Published
- 2022
- Full Text
- View/download PDF
48. Authentication of Averrhoa carambola L. Using DNA Barcoding: Detection of SNPs and Evaluation of Phylogenetic Relationship.
- Author
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Giri, Alok Kumar, Biswal, Bhagyashree, Jena, Biswajit, and Acharya, Laxmikanta
- Subjects
GENETIC barcoding ,SINGLE nucleotide polymorphisms ,GENETIC distance ,NUTRITIONAL value ,LOCUS (Genetics) - Abstract
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]
- Published
- 2023
- Full Text
- View/download PDF
49. Integrative taxonomy using the plant core DNA barcodes in Sumatra's Burseraceae.
- Author
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Teklemariam, Daniel M., Gailing, Oliver, Siregar, Iskandar Z., Amandita, Fitri Yola, and Moura, Carina C. M.
- Subjects
- *
BIOLOGICAL classification , *PLANT classification , *BAR codes , *TROPICAL forests , *GENETIC markers - Abstract
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]
- Published
- 2023
- Full Text
- View/download PDF
50. Taxonomic Confirmation of Rare Fruits in West Kalimantan Using rbcL and matK Sequences.
- Author
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Candramila, Wolly, Fajri, Hayatul, Mardiyyaningsih, Asriah Nurdini, Firmansyah, Roby, and Akbar, Didi
- Subjects
- *
FRUIT , *GENETIC markers , *GEL electrophoresis , *ARTOCARPUS , *ALPINIA - Abstract
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]
- Published
- 2023
- Full Text
- View/download PDF
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