Systematic Approach to Establish DNA Barcode of Medicinally Important Plants in Nepal

DNA barcoding is an emerging tool for species identification that uses internationally agreed protocols and regions of DNA to create a global database of living organisms. Initiatives are taking place to generate DNA ba rcodes for all groups of living organisms make these genomic identity publically available to understand, conserve, and utilize the world 's biodiversity. Most of the terrestrial plants are characterized using two section of coding region within chloplast, part of chloroplast gene, a more conserved rbcl and more polymorphic MatK gene. In order to create high quality databases, each plants are characterized not only with the rbcl and MatK DNA sequences, an additional sequence information from internal transcribed spacer (ITS) region is more efficient. The quality of barcode depends on the various factors such as efficient primers, purity of DNA templates, as well as the quality of PCR amplicon from which the sequence data will derive. The protocol described here led to the generation of high efficient PCR amplicon which will aid in the minimization of erroneous DNA sequence infonnation from which bioinformatics procedure will generate efficient barcodes. The primers used to amplified MatK, rbcl and ITS sequence were MatK-4 13f-1 and MatK- 1227r-1, rbcl-1F and rbcl-724R, ITS1 and ITS4 showed a strong amplification successes of 80% of each in the tasted medicinal plants of Nepal. This study propose that the used sets of primers and amplification condition will help, in part, the development of DNA barcode for medicinally important plants of Nepal to conserve their identity with its nativeness.

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Scalable Classification of Organisms into a Taxonomy Using Hierarchical Supervised Learners

10.1101/2020.02.04.933374 ◽

2020 ◽

Author(s):

Gihad N. Sohsah ◽

Ali Reza Ibrahimzada ◽

Huzeyfe Ayaz ◽

Ali Cakmak

Keyword(s):

Dna Sequence ◽

Dna Sequences ◽

Kernel Method ◽

Sequence Data ◽

Dna Barcode ◽

Living Organism ◽

Large Datasets ◽

Living Organisms ◽

Hierarchical Classifier

Taxonomy of living organisms gains major importance in making the study of vastly heterogeneous living things easier. In addition, various fields of applied biology (e.g., agriculture) depend on classification of living creatures. Specific fragments of the DNA sequence of a living organism have been defined as DNA barcodes and can be used as markers to identify species efficiently and effectively. The existing DNA barcode-based classification approaches suffer from three major issues: (i) most of them assume that the classification is done within a given taxonomic class and/or input sequences are prealigned, (ii) highly performing classifiers, such as SVM, cannot scale to large taxonomies due to high memory requirements, (iii) mutations and noise in input DNA sequences greatly reduce the taxonomic classification accuracy. In order to address these issues, we propose a multi-level hierarchical classifier framework to automatically assign taxonomy labels to DNA sequences. We utilize an alignment-free approach called spectrum kernel method for feature extraction. We build a proof-of-concept hierarchical classifier with two levels, and evaluated it on real DNA sequence data from BOLD systems. We demonstrate that the proposed framework provides higher accuracy than regular classifiers. Besides, hierarchical framework scales better to large datasets enabling researchers to employ classifiers with high accuracy and high memory requirement on large datasets. Furthermore, we show that the proposed framework is more robust to mutations and noise in sequence data than the non-hierarchical classifiers.

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The dna barcoding data and genetic distance of leaf beetles (Coleoptera, Chrysomelidae) in Vietnam

ACADEMIA JOURNAL OF BIOLOGY ◽

10.15625/2615-9023/v42n4.15124 ◽

2020 ◽

Vol 42 (4) ◽

Author(s):

Nguyen Thi Dinh

Keyword(s):

Genetic Distance ◽

Dna Barcoding ◽

Dna Sequences ◽

Phylogenetic Relationships ◽

Dna Barcode ◽

Coi Gene ◽

Biodiversity Assessment ◽

Leaf Beetles ◽

The World ◽

Living Organisms

DNA barcoding is a useful tool in identifying species, biodiversity assessment, and revealing phylogenetic relationships of living organisms in the world. However, the DNA barcode data for leaf beetles in Vietnam is lacking. In this study, sixteen DNA sequences of 658 bp of COI gene from nine species (five genera; three subfamilies) of Chrysomelidae in Vietnam were (obtained). Intra- and inter-specific diversities, and phylogenetic relationships of these species were analyzed.

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Scalable classification of organisms into a taxonomy using hierarchical supervised learners

Journal of Bioinformatics and Computational Biology ◽

10.1142/s0219720020500262 ◽

2020 ◽

Vol 18 (05) ◽

pp. 2050026

Author(s):

Gihad N. Sohsah ◽

Ali Reza Ibrahimzada ◽

Huzeyfe Ayaz ◽

Ali Cakmak

Keyword(s):

Dna Sequence ◽

Dna Sequences ◽

Kernel Method ◽

Sequence Data ◽

Genetic Material ◽

Dna Barcode ◽

Living Organism ◽

Large Datasets ◽

Data Systems ◽

Hierarchical Classifier

Accurately identifying organisms based on their partially available genetic material is an important task to explore the phylogenetic diversity in an environment. Specific fragments in the DNA sequence of a living organism have been defined as DNA barcodes and can be used as markers to identify species efficiently and effectively. The existing DNA barcode-based classification approaches suffer from three major issues: (i) most of them assume that the classification is done within a given taxonomic class and/or input sequences are pre-aligned, (ii) highly performing classifiers, such as SVM, cannot scale to large taxonomies due to high memory requirements, (iii) mutations and noise in input DNA sequences greatly reduce the taxonomic classification score. In order to address these issues, we propose a multi-level hierarchical classifier framework to automatically assign taxonomy labels to DNA sequences. We utilize an alignment-free approach called spectrum kernel method for feature extraction. We build a proof-of-concept hierarchical classifier with two levels, and evaluated it on real DNA sequence data from barcode of life data systems. We demonstrate that the proposed framework provides higher f1-score than regular classifiers. Besides, hierarchical framework scales better to large datasets enabling researchers to employ classifiers with high classification performance and high memory requirement on large datasets. Furthermore, we show that the proposed framework is more robust to mutations and noise in sequence data than the non-hierarchical classifiers.

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Divergence, demography and gene loss along the human lineage

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2010.0004 ◽

2010 ◽

Vol 365 (1552) ◽

pp. 2451-2457 ◽

Cited By ~ 18

Author(s):

Hie Lim Kim ◽

Takeshi Igawa ◽

Ayaka Kawashima ◽

Yoko Satta ◽

Naoyuki Takahata

Keyword(s):

Dna Sequences ◽

Sequence Data ◽

Homo Sapiens ◽

Divergence Time ◽

Cell Receptor ◽

Middle Pleistocene ◽

Human Lineage ◽

Modern Humans ◽

Olfactory Receptor Genes ◽

Living Organisms

Genomic DNA sequences are an irreplaceable source for reconstructing the vanished past of living organisms. Based on updated sequence data, this paper summarizes our studies on species divergence time, ancient population size and functional loss of genes in the primate lineage leading to modern humans ( Homo sapiens sapiens ). The inter- and intraspecific comparisons of DNA sequences suggest that the human lineage experienced a rather severe bottleneck in the Middle Pleistocene, throughout which period the subdivided African population played a predominant role in shaping the genetic architecture of modern humans. Also, published and newly identified human-specific pseudogenes (HSPs) are enumerated in order to infer their significance for human evolution. Of the 121 candidate genes obtained, authentic HSPs turn out to comprise only 25 olfactory receptor genes, four T cell receptor genes and nine other genes. The fixation of HSPs has been too rare over the past 6–7 Myr to account for species differences between humans and chimpanzees.

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From Space to Sequence and Back Again: Iterative DNA Proximity Ligation and its Applications to DNA-Based Imaging

10.1101/470211 ◽

2018 ◽

Cited By ~ 1

Author(s):

Alexander A. Boulgakov ◽

Erhu Xiong ◽

Sanchita Bhadra ◽

Andrew D. Ellington ◽

Edward M. Marcotte

Keyword(s):

Dna Sequences ◽

Dna Barcode ◽

Positional Information ◽

Theoretical Work ◽

Sequence Information ◽

Sequencing Data ◽

Experimental Proof ◽

Proximity Ligation ◽

Geometric Patterns ◽

The Individual

AbstractWe extend the concept of DNA proximity ligation from a single readout per oligonucleotide pair to multiple reversible, iterative ligations re-using the same oligonucleotide molecules. Using iterative proximity ligation (IPL), we can in principle capture multiple ligation events between each oligonucleotide and its various neighbors and thus recover a far richer knowledge about their relative positions than single, irreversible ligation events. IPL would thus act to sample and record local molecular neighborhoods. By integrating a unique DNA barcode into each participating oligonucleotide, we can catalog the individual ligation events and thus capture the positional information contained therein in a high throughput manner using next-generation DNA sequencing. We propose that by interpreting IPL sequencing results in the context of graph theory and by applying spring layout algorithms, we can recover geometric patterns of objects labeled by DNA. Using simulations, we demonstrate that we can in principle recover letter patterns photolithographed onto slide surfaces using only IPL sequencing data, illustrating how our technique maps complex spatial configurations into DNA sequences and then – using only this sequence information – recovers them. We complement our theoretical work with an experimental proof-of-concept of iterative proximity ligation on an oligonucleotide population.

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DMSO Improves the Ski-Slope Effect in Direct PCR

Applied Sciences ◽

10.3390/app11041943 ◽

2021 ◽

Vol 11 (4) ◽

pp. 1943

Author(s):

Joo-Young Kim ◽

Ju Yeon Jung ◽

Da-Hye Kim ◽

Seohyun Moon ◽

Won-Hae Lee ◽

...

Keyword(s):

Dna Sequences ◽

Pcr Amplification ◽

Analytical Techniques ◽

Direct Pcr ◽

Dna Profile ◽

Novel Technologies ◽

Specific Amplification ◽

Polymerase Chain ◽

Dna Profiles

Analytical techniques such as DNA profiling are widely used in various fields, including forensic science, and novel technologies such as direct polymerase chain reaction (PCR) amplification are continuously being developed in order to acquire DNA profiles efficiently. However, non-specific amplification may occur depending on the quality of the crime scene evidence and amplification methods employed. In particular, the ski-slope effect observed in direct PCR amplification has led to inaccurate interpretations of the DNA profile results. In this study, we aimed to reduce the ski-slope effect by using dimethyl sulfoxide (DMSO) in direct PCR. We confirmed that DMSO (3.75%, v/v) increased the amplification yield of large-sized DNA sequences more than that of small-sized ones. Using 50 Korean buccal samples, we further demonstrated that DMSO reduced the ski-slope effect in direct PCR. These results suggest that the experimental method developed in this study is suitable for direct PCR and may help to successfully obtain DNA profiles from various types of evidence at crime scenes.

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Characterization of squalene synthase gene from Gymnema sylvestre R. Br.

Beni-Suef University Journal of Basic and Applied Sciences ◽

10.1186/s43088-020-00094-4 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Kuldeepsingh A. Kalariya ◽

Ram Prasnna Meena ◽

Lipi Poojara ◽

Deepa Shahi ◽

Sandip Patel

Keyword(s):

Dna Sequences ◽

Genomic Dna ◽

Competitive Inhibition ◽

Sequence Data ◽

Homology Model ◽

Squalene Synthase ◽

Gymnema Sylvestre ◽

Gardenia Jasminoides ◽

Ramachandran Plots ◽

Flanking Regions

Abstract Background Squalene synthase (SQS) is a rate-limiting enzyme necessary to produce pentacyclic triterpenes in plants. It is an important enzyme producing squalene molecules required to run steroidal and triterpenoid biosynthesis pathways working in competitive inhibition mode. Reports are available on information pertaining to SQS gene in several plants, but detailed information on SQS gene in Gymnema sylvestre R. Br. is not available. G. sylvestre is a priceless rare vine of central eco-region known for its medicinally important triterpenoids. Our work aims to characterize the GS-SQS gene in this high-value medicinal plant. Results Coding DNA sequences (CDS) with 1245 bp length representing GS-SQS gene predicted from transcriptome data in G. sylvestre was used for further characterization. The SWISS protein structure modeled for the GS-SQS amino acid sequence data had MolProbity Score of 1.44 and the Clash Score 3.86. The quality estimates and statistical score of Ramachandran plots analysis indicated that the homology model was reliable. For full-length amplification of the gene, primers designed from flanking regions of CDS encoding GS-SQS were used to get amplification against genomic DNA as template which resulted in approximately 6.2-kb sized single-band product. The sequencing of this product through NGS was carried out generating 2.32 Gb data and 3347 number of scaffolds with N50 value of 457 bp. These scaffolds were compared to identify similarity with other SQS genes as well as the GS-SQSs of the transcriptome. Scaffold_3347 representing the GS-SQS gene harbored two introns of 101 and 164 bp size. Both these intronic regions were validated by primers designed from adjoining outside regions of the introns on the scaffold representing GS-SQS gene. The amplification took place when the template was genomic DNA and failed when the template was cDNA confirmed the presence of two introns in GS-SQS gene in Gymnema sylvestre R. Br. Conclusion This study shows GS-SQS gene was very closely related to Coffea arabica and Gardenia jasminoides and this gene harbored two introns of 101 and 164 bp size.

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

Scientific Reports ◽

10.1038/s41598-021-86228-9 ◽

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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DNA sonification for public engagement in bioinformatics

BMC Research Notes ◽

10.1186/s13104-021-05685-7 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Heleen Plaisier ◽

Thomas R. Meagher ◽

Daniel Barker

Keyword(s):

Dna Sequence ◽

Public Engagement ◽

Sequence Data ◽

Sensory Perception ◽

Data Representation ◽

Sequence Information ◽

Dna Sequence Data ◽

Public Events ◽

Dna Base ◽

Alternative Means

Abstract Objective Visualisation methods, primarily color-coded representation of sequence data, have been a predominant means of representation of DNA data. Algorithmic conversion of DNA sequence data to sound—sonification—represents an alternative means of representation that uses a different range of human sensory perception. We propose that sonification has value for public engagement with DNA sequence information because it has potential to be entertaining as well as informative. We conduct preliminary work to explore the potential of DNA sequence sonification in public engagement with bioinformatics. We apply a simple sonification technique for DNA, in which each DNA base is represented by a specific note. Additionally, a beat may be added to indicate codon boundaries or for musical effect. We report a brief analysis from public engagement events we conducted that featured this method of sonification. Results We report on use of DNA sequence sonification at two public events. Sonification has potential in public engagement with bioinformatics, both as a means of data representation and as a means to attract audience to a drop-in stand. We also discuss further directions for research on integration of sonification into bioinformatics public engagement and education.

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