scholarly journals DNA Barcoding Dalugha (Cyrtosperma Merkusii) di Kepulauan Talaud dan Minahasa Selatan Berdasarkan Gen rbcL

2021 ◽  
Vol 11 (2) ◽  
pp. 134
Author(s):  
Marlin Bernadet Taariwuan ◽  
Jantje Ngangi ◽  
Yermia Mokosuli ◽  
Sukmarayu Gedoan
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Local Alignment ◽  
Rbcl Gene ◽  
Endemic Plant ◽  
Bisphosphate Carboxylase ◽  
Large Gene ◽  
North Sulawesi ◽  
Barcode Dna ◽  
Search Tool

(Article History: Received June 28, 2021; Revised August 30, 2021; Accepted Sept 3, 2021) ABSTRAKDalugha (Cyrtospera merkusii (Hassk.)Schott) merupakan tanaman endemik Sulawesi Utara yang digunakan sebagai pangan alternatif (penganti beras). Penelitian ini bertujuan untuk membandingkan spesies daluga di Kepulauan Talaud dan Minahasa Selatan menggunakan DNA barcode gen rbcL (ribulose 1,5 bisphosphate carboxylase large). Perbandingan barcode DNA yang dilakukan pada empat sampel yang berbeda lokasi tersebut keduanya menghasilkan tingkat kesamaan 100% (identik). Dengan demikian, tidak ada variasi intra spesies yang ditemukan dari semua sampel yang ada. Selanjutnya, kemiripan sampel-sampel ini telusuri kemiripannya dengan kerabat terdekat yang tercatat di GenBank menggunakan BLAST (Basic Local Alignment Search Tool).  Tanaman dalugha dalam penelitian ini memiliki kemiripan 99,82% dengan tumbuhan Anaphyllopsis americana (AM905753.1), dan kemiripannya 99,63% dengan Cyrtosperma macrotum (AM905750.1), Lasimorpha senegalensis (AM905755.1), Pycnospatha arietina (AM905751.1), dan Podolasia stipitata (AM905752.1). Belum ada rekor sekuens DNA gen rbcL dari spesies ini yang dibisa dibandingkan di GenBank.Kata Kunci: Dalugha; DNA barcoding; gen rbcL ABSTRACTDalugha (Cyrtospera merkusii (Hassk.) Schott) is an endemic plant in North Sulawesi that is used as alternative food (substitute for rice). This research aimed to compare the DNA barcode of dalugha in Talaud Islands and in South Minahasa using rbcL (ribulose 1,5 bisphosphate carboxylase large) gene. The DNA barcoding comparison of all four samples in both area resulted in 100% similarity (identical). Therefore, there is no intraspecific variation found in all samples. Furthermore, the similarity of these samples were conducted with BLAST (Basic Local Alignment Search Tool) to compare with its closest relatives in GenBank. The closest relatives of this plant, based on similarity information, are 99.82% with Anaphyllopsis americana (AM905753.1) and all 99.63% with Cyrtosperma macrotum (AM905750.1), Lasimorpha senegalensis (AM905755.1), Pycnospatha arietina (AM905751.1), and Podolasia stipitata (AM905752.1).  There is no record yet of rbcL gene sequence of C. merkusii in GenBank for comparison.Keywords: Dalugha; DNA barcoding; rbcL gene

scholarly journals The perspectives for DNA barcoding of Rhaponticum carthamoides (Willd.) Iljin using rbcL gene sequence

2021 ◽  
Vol 908 (1) ◽  
pp. 012030
Author(s):  
M V Protopopova ◽  
N A Shvetsova ◽  
V V Pavlichenko
Keyword(s):  
Dna Barcoding ◽  
Large Subunit ◽  
Dna Barcode ◽  
Natural Populations ◽  
Rbcl Gene ◽  
Ribulose Bisphosphate Carboxylase ◽  
Bisphosphate Carboxylase ◽  
Rhaponticum Carthamoides ◽  
South Siberia ◽  
Illegal Harvesting

Abstract The methods of biological species identification using nucleotide sequences of short genome regions (DNA barcoding) are actively developed. The universal DNA barcode for plants remains to be discovered, and one of the leading candidates is the plastid gene of the large subunit of ribulose-bisphosphate carboxylase gene (rbcL). In our study, we estimated the part of rbcL gene as a possible marker for molecular identification of Rhaponticum carthamoides (Willd.) Iljin. Due to its officinal properties, the species is susceptible to uncontrolled and illegal harvesting from natural populations. Today, the species needs to be protected and therefore is included into the Red Data Books of the Russian Federation and certain regions. The study was carried out using plants from the natural populations sampled from the Khamar-Daban Ridge (South Siberia) and considering now as Rh. carthamoides var. chamarense (Peschkova) O S Zhirova. It was shown that rbcL gene can be used to identify Rh. carthamoides at least from the populations of the Khamar-Daban Ridge using a fragment of the maximum length or its 3’ region. Apparently, the 5’ region of the gene (rbcLa) most often used as DNA barcode for plants may be of lesser importance for Rh. carthamoides. The rbcL gene sequences can be also used for the development of approaches for Rh. carthamoides identification in the medicinal preparations and products containing dried tissues to prevent their falsification and illegal harvesting of this species. The combination of rbcL gene with additional markers seems to be highly desirable to create effective DNA barcodes for Rhaponticum species.

scholarly journals An Integrated Approach for Efficient and Accurate Medicinal Cuscutae Semen Identification

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1410
Author(s):  
Inkyu Park ◽  
Sungyu Yang ◽  
Goya Choi ◽  
Byeong Cheol Moon ◽  
Jun-Ho Song
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Northeast Asia ◽  
Herbal Medicines ◽  
Integrated Approach ◽  
Rbcl Gene ◽  
Accurate Identification ◽  
Diagnostic Characteristics ◽  
Microscopic Techniques ◽  
Cuscuta Species

To guarantee the safety and efficacy of herbal medicines, accurate identification and quality evaluation are crucial. The ripe dried seeds of Cuscuta australis R.Br. and C. chinensis Lam. are known as Cuscutae Semen (CS) and are widely consumed in Northeast Asia; however, the seeds of other species can be misidentified as CS owing to morphological similarities, leading to misuse. In this report, we propose a multilateral strategy combining microscopic techniques with statistical analysis and DNA barcoding using a genus-specific primer to facilitate the identification and authentication of CS. Morphology-based identification using microscopy revealed that the useful diagnostic characteristics included general shape, embryo exudation, hairiness, and testa ornamentation, which were used to develop an effective identification key. In addition, we conducted DNA barcoding-based identification to ensure accurate authentication. A novel DNA barcode primer was produced from the chloroplast rbcL gene by comparative analysis using Cuscuta chloroplast genome sequences, which allowed four Cuscuta species and adulterants to be discriminated completely. Therefore, this investigation overcame the limitations of universal DNA barcodes for Cuscuta species with high variability. We believe that this integrated approach will enable CS to be differentiated from other species, thereby improving its quality control and product safety in medicinal markets.

scholarly journals Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward

2022 ◽  
Vol 2022 ◽  
pp. 1-19
Author(s):  
Sarfraz Ahmed ◽  
Muhammad Ibrahim ◽  
Chanin Nantasenamat ◽  
Muhammad Farrukh Nisar ◽  
Aijaz Ahmad Malik ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Elongation Factor ◽  
Species Level ◽  
Ribulose Bisphosphate Carboxylase ◽  
Bacterial Strains ◽  
Accurate Identification ◽  
Bisphosphate Carboxylase ◽  
Parallel Acquisition ◽  
Invertebrate Animal

DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.

scholarly journals Isolation of high lipids content microalgae from Wonorejo rivers, Surabaya, Indonesia and its identification using rbcL marker gene

2019 ◽  
Vol 20 (5) ◽  
Author(s):  
TRIONO BAGUS SAPUTRO ◽  
KRISTANTI INDAH PURWANI ◽  
DINI ERMAVITALINI ◽  
ARIF FUAD SAIFULLAH
Keyword(s):  
Marker Gene ◽  
River Estuary ◽  
Biologically Active ◽  
Local Alignment ◽  
Rbcl Gene ◽  
Freshwater Algae ◽  
Active Metabolites ◽  
Bisphosphate Carboxylase ◽  
Chlorella Sp ◽  
Identification Technique

Abstract. Saputro TB, Purwani KI, Ermavitalini D, Saifullah AF. 2019. Isolation of high lipids content microalgae from Wonorejo river, Surabaya, Indonesia and its identification using rbcL marker gene. Biodiversitas 20: 1380-1388. Microalgae are unicellular organism which possesses various biologically active metabolites that used in food, cosmetic, pharmaceutical, nutraceutical, and bioenergy industries. One of the most important active metabolites found in microalgae is lipid which can be converted into biodiesel. The higher amount of lipid produced will increases the amount of biodiesel that can be obtained. Although, the production of active metabolites in microalgae has rather fluctuated as it is difficult to obtain the pure cultures of microalgae since it has a cryptic phenomenon. This problem can be solved through identification technique using molecular markers or DNA Barcoding. This research used rbcL gene as the molecular marker in species identification. rbcL gene encode ribulose-1,5-bisphosphate carboxylase (RubisCo) in chloroplast genome. Furthermore, microalgae were isolated from 3 different stations of Wonorejo river estuary, Surabaya, East Java, Indonesia. The isolated microalgae were then identified based on Freshwater algae: identification and use as bioindicators book. Eight isolates were successfully identified as Mycrocystis sp., Nostoc sp., Chlorella sp., Tabellaria, Synedra, Nitzschia, Navicula, and Closteriopsis. Out of eight, only 3 species that has a good potential to be developed as biodiesel sources i.e Chlorella sp., Synedra sp., and Navicula sp. that produce 21,20%, 20,30%, 27,20% of total lipids over their biomass. The genomic DNA from those three candidates were then isolated and used as a template to amplify rbcL gene. The obtained fragment of rbcL gene was sequenced and then submitted to the Basic Local Alignment Search Tool (BLAST). The result of BLAST used for alignment and phylogenetic tree construction. The result from BLAST shows the same results as the genus observed by microscopy observation. Overall, this research provides information about the genetic variety of microalgae in Wonorejo which has high potential to be further developed as biodiesel.

scholarly journals Identifikasi Barcode Tumbuhan Gedi Merah (Abelmoschus manihot L. medik) dan Gedi Hijau (Abelmoschus moschatus) Berdasarkan Gen matK

Jurnal MIPA ◽  
2014 ◽  
Vol 3 (2) ◽  
pp. 120
Author(s):  
Yusuf R. Fattah ◽  
Vanda S. Kamu ◽  
Max R. J. Runtuwene ◽  
Lidya I. Momuat
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Barcoding ◽  
In Silico ◽  
Dna Barcode ◽  
In Silico Analysis ◽  
Chain Reaction ◽  
Barcode Dna ◽  
Matk Gene ◽  
Polymerase Chain ◽  
Silico Analysis

Gedi (Abelmoschus L.) merupakan tumbuhan tropis. Tumbuhan ini memilki efek farmakologis. Masyarakat Minahasa mengkonsumsi daun gedi yang direbus tanpa diberi bumbu sebagai obat tradisional untuk menurunkan kadar kolesterol, antihipertensi dan antidiabetes. Suatu metode baru untuk mengidentifikasi dan menganalisis keanekaragaman genetika spesies telah dikembangkan dengan menggunakan potongan gen standar yang dikenal dengan teknik DNA barcoding. Salah satu gen yang terdapat pada tumbuhan yaitu gen matK telah digunakan sebagai gen standar untuk barcoding. Pada penelitian ini telah dilakukan isolasi DNA total dan gen matK penanda barcode DNA dari gedi merah dan gedi hijau, serta analisis in-silico terhadap produk gen matK gedi merah, gedi hijau, dan kerabat terdekatnya. Gen matK diisolasi dan diamplifikasi menggunakan metode Polymerase Chain Reaction (PCR) menggunakan primer forward (5’-CGTACAGTACTTTTGTGTTT ACGAG-3’) dan primer reverse (5’-ACCCAGTCCATCTGGAAATCTTGGTTC-3’). Hasil pengurutan nukleotida DNA barcode matK menunjukkan bahwa sebanyak 828 pb matK berhasil diisolasi untuk tumbuhan gedi merah dan tumbuhan gedi hijau. Urutan nukleotida matK gedi merah dan gedi hijau menunjukkan tingkat kemiripan yang tinggi, yaitu > 95%. Selain itu, hasil analisis in-silico menunjukkan bahwa protein MatK gedi dan kerabat terdekatnya bersifat hidrofobik.Gedi (Abelmoschus L.) is a tropical plant. This plant has the pharmacological effects. Minahasan people consumed boiled gedi without any spices addition to lower cholesterol level, blood pressure, and glucose level. A new method for identifying and analyzing the genetic diversity of species has been developed using standard gene known as DNA barcoding technique. One of the genes found in plants called matK gene was used as standard for DNA barcoding. In this research, identification of DNA barcode of red gedi and green gedi based on matK gene, and in-silico analysis on the matK gene products of red gedi, green gedi, and its closest relatives gedi have been done. matK gene was isolated with Polymerase Chain Reaction (PCR) using forward primer (5'-CGTACAGTACTTTTGTGTTTACGAG-3') and reverse primer (5'-ACCCAGTCCATCTGGAAATCTTGGTTC-3'). Barcode DNA of red and green gedi showed 828 bp nucleotide sequence based on matK gene. In addition, matK of both gedi showed high similarity, i.e. >95%. Furthermore, in-silico analysis of MatK gedi and its closest relative showed that this protein is hidrophobic.

scholarly journals Barcode DNA Anthurium Gelombang Cinta (Anthurium plowmanii) berdasarkan gen rbcL dan matK (The DNA Barcode of Anthurium Wave of Love (Anthurium plowmanii) based on rbcL and matK Genes)

2013 ◽  
Vol 3 (1) ◽  
Author(s):  
Beivy J Kolondam ◽  
Edy Lengkong ◽  
J Polii-Mandang ◽  
Runtunuwu Semuel ◽  
Arthur Pinaria
Keyword(s):  
Polymerase Chain Reaction ◽  
Species Identification ◽  
Leaf Shape ◽  
Dna Barcode ◽  
Universal Primers ◽  
Rbcl Gene ◽  
Chain Reaction ◽  
Barcode Dna ◽  
Polymerase Chain ◽  
Close Relatives

AbstrakMetode standar untuk identifikasi spesies tumbuhan melalui barcode DNA telah direkomendasikan untuk menggunakan dua gen plastida yaitu rbcL dan matK. Tujuan penelitian ini yaitu untuk menentukan tingkat kemiripan sekuens barcode DNA tanaman Anthurium Gelombang Cinta (Anthurium plowmanii) dibandingkan spesies kerabatnya yang sudah terdata dalam BOLD Systems dan untuk merekomendasi penggunaan barcode DNA yang bisa diandalkan dalam mengidentifikasi spesies ini. Teknik Polymerase Chain Reaction (PCR) digunakan dalam perbanyakan sekuens fragmen gen rbcL dan gen matK oleh primer universal yang tersedia. Hasil penelitian menyimpulkan bahwa sampel tanaman A. plowmanii menghasilkan sekuens barcode rbcL yang mirip 100% (identik) dengan spesies A. cubense. Ini berarti barcode DNA rbcL tidak dapat digunakan untuk identifikasi tingkat spesies. Sekuens barcode matK sampel menunjukkan kemiripan 99,1% dengan A. ravenii yang berbeda dalam morfologi daun. Sekuens matK sampel bersifat unik diantara anggota-anggota genus Anthurium sehingga direkomendasikam penggunaannya untuk identifikasi sampai tingkat spesies.Kata Kunci: barcode, rbcL, matK, Anthurium plowmaniiAbstractStandard method for plant species identification through DNA barcode has been recommended to use two plastids genes; the rbcL and matK. The aims of this research were to determine similarities in DNA barcode sequences of Anthurium Wave of Love (Anthurium plowmanii) with its close relatives that listed in BOLD Systems and to recommend the reliable DNA barcode for identification of this species. Polymerase Chain Reaction was employed to amplify rbcL and matK genes fragments using available universal primers. The result showed that A. plowmanii sample was 100% similar to A. cubense. For that reason, the rbcL gene is not a reliable for species identification. Sequence of matK barcode showed 99.1% in similarity with A. ravenii which has different leaf shape. The matK sequence of sample was unique among all listed Anthurium members, therefore, this barcode are recommended for plant identification to the species level.Keywords: barcode, rbcL, matK, Anthurium plowmanii

scholarly journals Deteksi dan Identifikasi Nematoda Puru Akar (Meloidogyne spp.) pada Tanaman Bit Menggunakan Metode DNA Barcoding

2020 ◽  
Vol 16 (1) ◽  
pp. 1-8
Author(s):  
Ni Wayan Kartika Pratiwi ◽  
Rosyid Amrulloh ◽  
Fawwaz El Auly ◽  
Fitrianingrum Kurniawati
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Purposive Sampling ◽  
Barcode Dna ◽  
Meloidogyne Spp

Identifikasi nematoda berdasarkan karakter morfologi memerluan ketelitian tinggi dan perlu didukung hasil identifikasi secara molekuler. Salah satu metode identifikasi molekuler ialah dengan DNA barcode. DNA barcode merupakan identifikasi molekuler dengan menggunakan gen cytochrome oksidase sub unit 1 (CO1). Penelitian ini bertujuan untuk mengidentifikasi NPA yang berasosiasi pada tanaman bit berdasarkan PCR dan perunutan nukleotida gen CO1 Meloidogyne. Sampel umbi bit diperoleh dari lahan pertanian yang terletak di Kecamatan Cipanas, Kabupaten Cianjur, Jawa Barat. Pengambilan sampel dilakukan dengan metode purposive sampling. Identifikasi morfologi dengan mengamati pola perineal NPA betina.  Identifikasi molekuler meliputi ekstraksi, amplifikasi, visualisasi DNA, analisis peruntutan nukleotida dan filogenetika. Hasil pengamatan pola perineal secara morfologi didapatkan spesies M. incognita dan M. arenaria. Amplifikasi DNA yang dilakukan menggunakan primer spesifik CO1SIF (5’-GCCTGCATTTGGTTAG-‘3) dan CO1SIR (5’-TCAAACCAGTCCT-‘3), CO1SAF (5’-GGGTACTGGATGAACATTA-‘3) dan CO1SAR (5’-ACTTCAGGATGACCAAA-‘3)berhasil mendapatkan pita DNA berukuran ± 360 untuk M. arenaria dan ± 326 untuk M. incognita. Hasil sekuensing menunjukkan bahwa isolat M. incognita asal Indonesia berkerabat dekat dengan isolat M. incognita asal Cina, Amerika Serikat, Vietnam, dan Inggris dengan tingkat homologi 100%. Hasil analisis filogenetika menunjukkan bahwa M. incognita Indonesia masih satu kelompok dengan M. incognita asal Cina, Amerika Serikat, Vietnam dan Inggris. Adapun isolat M. arenaria berkerabat dekat dengan isolat M. arenaria asal Argentina dan Amerika Serikat dengan tingkat homologi 100%.  Hasil analisis filogenetika menunjukkan bahwa M. arenaria asal Indonesia masih satu kelompok dengan M. arenaria asal Argentina dan Amerika Serikat.

scholarly journals Micropropagtion and DNA-barcoding of the endangered endemic Phlomis aurea plant of Saint Katherine

Plant Omics ◽  
2020 ◽  
pp. 65-77
Author(s):  
Heba El-Sayed Ghareb ◽  
Shafik Darwish Ibrahim ◽  
Ghada Abd El-Moneim Hegazi
Keyword(s):  
Dna Barcoding ◽  
Large Subunit ◽  
Ex Situ ◽  
Nodal Segments ◽  
Naphthalene Acetic Acid ◽  
Endemic Plant ◽  
Indolebutyric Acid ◽  
Accurate Identification ◽  
Bisphosphate Carboxylase

Saint Katherine is considered a “biodiversity hotspot” because of the high level of endemism of reported plant species. In this study, conservation of the endangered endemic plant; Phlomis aurea of Saint Katherine, Southern Sinai, Egypt, was carried out through micropropagation and DNA barcoding. The first efficient micropropagation protocol for Phlomis aurea was established as a mean of ex situ conservation of the plant. Shoot tips and nodal segments of in vitro germinated seedlings were established on Murashige and Skoog medium supplemented with 0.54 µM β-naphthalene acetic acid (NAA) and 2.46 µM N6-(2-isopentenyl) adenine (2iP) in combination with 6-benzylaminopurine (BA) or kinetin (Kin). The medium supplemented with 3.48 µM Kin considered optimum for both explants. For multiplication, BA was the most efficient cytokinin. The percentage of rooted explants reached 100% at the concentration of 14.7 µM indolebutyric acid (IBA), whereas the highest number of roots was recorded for 4.90 µM, which considered the optimum concentration with a percentage of 80% of rooting. Rooted plantlets were transplanted in the greenhouse with 75% survival rate. The present study also aimed to carry out DNA barcoding of Phlomis aurea for accurate identification to provide a database for establishing an efficient conservation program for the plant. Three chloroplast DNA markers were used [ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL), maturase K (matK) and RNA polymerase C1 (rpoC1)] and all were successful in amplifying target regions, however the performance of both rbcL and matK markers seemed to be species‐specific. The similarity percentage was maximum for rbcL (99.81%) and matK (100%) compared to the database of the same species.

The Influence of Memory-Aware Computation on Distributed BLAST

2019 ◽  
Vol 14 (2) ◽  
pp. 157-163
Author(s):  
Majid Hajibaba ◽  
Mohsen Sharifi ◽  
Saeid Gorgin
Keyword(s):  
Search Time ◽  
Genomic Research ◽  
Local Alignment ◽  
Negative Effects ◽  
Sequencing Technologies ◽  
Percent Improvement ◽  
Fast Processing ◽  
Search Tool ◽  
Memory Awareness ◽  
Generation Sequencing

Background: One of the pivotal challenges in nowadays genomic research domain is the fast processing of voluminous data such as the ones engendered by high-throughput Next-Generation Sequencing technologies. On the other hand, BLAST (Basic Local Alignment Search Tool), a longestablished and renowned tool in Bioinformatics, has shown to be incredibly slow in this regard. Objective: To improve the performance of BLAST in the processing of voluminous data, we have applied a novel memory-aware technique to BLAST for faster parallel processing of voluminous data. Method: We have used a master-worker model for the processing of voluminous data alongside a memory-aware technique in which the master partitions the whole data in equal chunks, one chunk for each worker, and consequently each worker further splits and formats its allocated data chunk according to the size of its memory. Each worker searches every split data one-by-one through a list of queries. Results: We have chosen a list of queries with different lengths to run insensitive searches in a huge database called UniProtKB/TrEMBL. Our experiments show 20 percent improvement in performance when workers used our proposed memory-aware technique compared to when they were not memory aware. Comparatively, experiments show even higher performance improvement, approximately 50 percent, when we applied our memory-aware technique to mpiBLAST. Conclusion: We have shown that memory-awareness in formatting bulky database, when running BLAST, can improve performance significantly, while preventing unexpected crashes in low-memory environments. Even though distributed computing attempts to mitigate search time by partitioning and distributing database portions, our memory-aware technique alleviates negative effects of page-faults on performance.

scholarly journals Differentiation of Mitragyna speciosa, a narcotic plant, from allied Mitragyna species using DNA barcoding-high-resolution melting (Bar-HRM) analysis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chayapol Tungphatthong ◽  
Santhosh Kumar J. Urumarudappa ◽  
Supita Awachai ◽  
Thongchai Sooksawate ◽  
Suchada Sukrong
Keyword(s):  
High Resolution ◽  
Dna Barcoding ◽  
High Resolution Melting ◽  
Dna Barcode ◽  
Herbal Medicines ◽  
Efficient Tool ◽  
Hrm Analysis ◽  
Mitragyna Speciosa ◽  
Leaf Powder

AbstractMitragyna speciosa (Korth.) Havil. [MS], or “kratom” in Thai, is the only narcotic species among the four species of Mitragyna in Thailand, which also include Mitragyna diversifolia (Wall. ex G. Don) Havil. [MD], Mitragyna hirsuta Havil. [MH], and Mitragyna rotundifolia (Roxb.) O. Kuntze [MR]. M. speciosa is a tropical tree belonging to the Rubiaceae family and has been prohibited by law in Thailand. However, it has been extensively covered in national and international news, as its abuse has become more popular. M. speciosa is a narcotic plant and has been used as an opium substitute and traditionally used for the treatment of chronic pain and various illnesses. Due to morphological disparities in the genus, the identification of plants in various forms, including fresh leaves, dried leaf powder, and finished products, is difficult. In this study, DNA barcoding combined with high-resolution melting (Bar-HRM) analysis was performed to differentiate M. speciosa from allied Mitragyna and to assess the capability of Bar-HRM assays to identify M. speciosa in suspected kratom or M. speciosa-containing samples. Bar-HRM analysis of PCR amplicons was based on the ITS2, rbcL, trnH-psbA, and matK DNA barcode regions. The melting profiles of ITS2 amplicons were clearly distinct, which enabled the authentication and differentiation of Mitragyna species from allied species. This study reveals that DNA barcoding coupled with HRM is an efficient tool with which to identify M. speciosa and M. speciosa-containing samples and ensure the safety and quality of traditional Thai herbal medicines.

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