DNA Barcoding of Cyprinid Fish Chagunius chagunio Hamilton,1822 from Phewa Lake, Nepal

The present study is the first of its type that uses a technique of DNA barcoding to determine identification and relationship of a species of fish from Phewa lake, Nepal. The mitochondrial DNA from two ethanol-preserved samples of fish, randomly collected from Phewa lake, was extracted using Gene AllExgene TMtissue extraction kit. 650 base pair of mitochondrial cytochrome c oxidase subunit 1 (CO1) was amplified using a cocktail of four primers and was sequenced bidirectionaly using Sanger sequence method. The DNA sequences were edited using AliView software. The sequences confirmed Chagunius chagunio as their alignment with 16 reference sequences belonging to Chagunius chagunio in the NCBI GenBank, scored highest percentage of Query Cover (75% to 100%) and Percentage Identity (97.29% to 100%). The MEGA software analysed the DNA sequences to obtain their corresponding protein sequences. The DNA sequences were submitted to the GenBank and accession numbers (MN087472 and MN087473) were obtained. Clustal Omega software analysed multiple sequence alignment among 19 homologous DNA sequences of Chagunius chagunio from India, Bangladesh and Phewa lake, Nepal. The percentage of similarity among the aligned sequences was calculated as 39.3%. Based on the neighbour joining tree, the Chagunius chagunio of Phewa lake is found closely related with Chagunius chagunio of Bangladesh.

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DNA Barcoding of Fungi in the Forest Ecosystem of the Psunj and Papuk Mountains in Croatia

South-east European forestry ◽

10.15177/seefor.20-17 ◽

2020 ◽

Vol 11 (2) ◽

pp. 145-152

Author(s):

Nevenka Ćelepirović ◽

Sanja Novak Agbaba ◽

Monika Karija Vlahović

Keyword(s):

Dna Barcoding ◽

Dna Sequences ◽

Cryphonectria Parasitica ◽

Species Level ◽

Diagnostic Purpose ◽

Fungal Culture ◽

Fruiting Bodies ◽

Automated Identification ◽

Parasitic Fungi ◽

Reference Sequences

The saprotrophic, endophytic, and parasitic fungi were detected from the samples collected in the forest of the management unit East Psunj and Papuk Nature Park in Croatia. The disease symptoms, the morphology of fruiting bodies and fungal culture, and DNA barcoding were combined for determining the fungi at the genus or species level. DNA barcoding is a standardized and automated identification of species based on recognition of highly variable DNA sequences. DNA barcoding has a wide application in the diagnostic purpose of fungi in biological specimens. DNA samples for DNA barcoding were isolated from infected tree tissues, fungal fruiting bodies or fungal cultures. The ITS or ITS2 sequences of the fungal DNA were sequenced and aligned with the reference sequences in GenBank (NCBI) using BLAST. The size of ITS and ITS2 sequences were 512-584 bp and 248-326 bp, respectively. The sequences showed a high identity of 97.21%-100% at 98%-100% coverage with reference sequences in GenBank (NCBI). The exception was the species Amphilogia gyrosa that showed 95.65% identity at 100% coverage. Two fungi were determined at genus level: Cladosporium sp., and Cytospora sp., while 11 fungi were determined at species level: Alternaria alternata, Aureobasidium pullulans, Amphilogia gyrosa, Capronia pilosella, Cryphonectria parasitica, Exidia glandulosa, Epicoccum nigrum, Penicillium glabrum, Pezicula carpinea, Rosellinia corticium, and Stereum hirsutum.

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Phylogenetic Relationship of Ramie and Its Wild Relatives Based on Cytoge-netics and DNA Sequences

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2009.01778 ◽

2009 ◽

Vol 35 (10) ◽

pp. 1778-1790

Author(s):

Liang LIAO ◽

Tong-Jian LI ◽

Zhong-Lai LIU ◽

Hui-Sheng DENG ◽

Ling-Ling XU ◽

...

Keyword(s):

Phylogenetic Relationship ◽

Dna Sequences ◽

Wild Relatives ◽

Relationship Of

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Deoxyribonucleic Acid as a Tool for Digital Information Storage: An Overview

THE INDIAN JOURNAL OF VETERINARY SCIENCES AND BIOTECHNOLOGY ◽

10.21887/ijvsbt.15.1.1 ◽

2019 ◽

Vol 15 (01) ◽

pp. 1-8

Author(s):

Ashish C Patel ◽

C G Joshi

Keyword(s):

Data Storage ◽

Dna Sequences ◽

Consensus Sequence ◽

Random Access ◽

Information Storage ◽

Digital Data ◽

Digital Information ◽

Multiple Sequence ◽

Digital World ◽

Digital File

Current data storage technologies cannot keep pace longer with exponentially growing amounts of data through the extensive use of social networking photos and media, etc. The "digital world” with 4.4 zettabytes in 2013 has predicted it to reach 44 zettabytes by 2020. From the past 30 years, scientists and researchers have been trying to develop a robust way of storing data on a medium which is dense and ever-lasting and found DNA as the most promising storage medium. Unlike existing storage devices, DNA requires no maintenance, except the need to store at a cool and dark place. DNA has a small size with high density; just 1 gram of dry DNA can store about 455 exabytes of data. DNA stores the informations using four bases, viz., A, T, G, and C, while CDs, hard disks and other devices stores the information using 0’s and 1’s on the spiral tracks. In the DNA based storage, after binarization of digital file into the binary codes, encoding and decoding are important steps in DNA based storage system. Once the digital file is encoded, the next step is to synthesize arbitrary single-strand DNA sequences and that can be stored in the deep freeze until use.When there is a need for information to be recovered, it can be done using DNA sequencing. New generation sequencing (NGS) capable of producing sequences with very high throughput at a much lower cost about less than 0.1 USD for one MB of data than the first sequencing technologies. Post-sequencing processing includes alignment of all reads using multiple sequence alignment (MSA) algorithms to obtain different consensus sequences. The consensus sequence is decoded as the reversal of the encoding process. Most prior DNA data storage efforts sequenced and decoded the entire amount of stored digital information with no random access, but nowadays it has become possible to extract selective files (e.g., retrieving only required image from a collection) from a DNA pool using PCR-based random access. Various scientists successfully stored up to 110 zettabytes data in one gram of DNA. In the future, with an efficient encoding, error corrections, cheaper DNA synthesis,and sequencing, DNA based storage will become a practical solution for storage of exponentially growing digital data.

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DNA barcoding of bats (Chiroptera) from the Colombian northern region

Mammalia ◽

10.1515/mammalia-2020-0138 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Álvaro J. Benítez ◽

Dina Ricardo-Caldera ◽

María Atencia-Pineda ◽

Jesús Ballesteros-Correa ◽

Julio Chacón-Pacheco ◽

...

Keyword(s):

Dna Barcoding ◽

Species Identification ◽

Dna Sequences ◽

Genetic Distances ◽

Northern Region ◽

Coi Gene ◽

Individual Species ◽

Species Variation ◽

Molossus Molossus ◽

Artibeus Lituratus

Abstract Bats are mammals of great ecological and medical importance, which have associations with different pathogenic microorganisms. DNA barcoding is a tool that can expedite species identification using short DNA sequences. In this study, we assess the DNA barcoding methodology in bats from the Colombian Northern region, specifically in the Córdoba department. Cytochrome oxidase subunit I (COI) gene sequences of nine bat species were typified, and their comparison with other Neotropic samples revealed that this marker is suitable for individual species identification, with ranges of intra-species variation from 0.1 to 0.9%. Bat species clusters are well supported and differentiated, showing average genetic distances ranging from 3% between Artibeus lituratus and Artibeus planirostris, up to 27% between Carollia castanea and Molossus molossus. C. castanea and Glossophaga soricina show geographical structuring in the Neotropic. The findings reported in this study confirm DNA barcoding usefulness for fast species identification of bats in the region.

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Nothing in (sponge) biology makes sense – except when based on holotypes

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315415000521 ◽

2015 ◽

Vol 96 (2) ◽

pp. 305-311 ◽

Cited By ~ 10

Author(s):

Dirk Erpenbeck ◽

Merrick Ekins ◽

Nicole Enghuber ◽

John N.A. Hooper ◽

Helmut Lehnert ◽

...

Keyword(s):

New Species ◽

Reference Material ◽

Species Identification ◽

Dna Sequences ◽

Morphological Plasticity ◽

Morphological Characters ◽

Molecular Techniques ◽

Reference Sequences ◽

Species Descriptions ◽

Preservation History

Sponge species are infamously difficult to identify for non-experts due to their high morphological plasticity and the paucity of informative morphological characters. The use of molecular techniques certainly helps with species identification, but unfortunately it requires prior reference sequences. Holotypes constitute the best reference material for species identification, however their usage in molecular systematics and taxonomy is scarce and frequently not even attempted, mostly due to their antiquity and preservation history. Here we provide case studies in which we demonstrate the importance of using holotype material to answer phylogenetic and taxonomic questions. We also demonstrate the possibility of sequencing DNA fragments out of century-old holotypes. Furthermore we propose the deposition of DNA sequences in conjunction with new species descriptions.

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Benchmarking DNA barcodes: an assessment using available primate sequences

Genome ◽

10.1139/g06-025 ◽

2006 ◽

Vol 49 (7) ◽

pp. 851-854 ◽

Cited By ~ 48

Author(s):

Mehrdad Hajibabaei ◽

Gregory AC Singer ◽

Donal A Hickey

Keyword(s):

New Species ◽

Cryptic Species ◽

Dna Barcoding ◽

Species Identification ◽

Dna Sequences ◽

Phylogenetic Relationships ◽

Primate Species ◽

Dna Barcodes ◽

Global Biodiversity ◽

Efficient Sequence

DNA barcoding has been recently promoted as a method for both assigning specimens to known species and for discovering new and cryptic species. Here we test both the potential and the limitations of DNA barcodes by analysing a group of well-studied organisms—the primates. Our results show that DNA barcodes provide enough information to efficiently identify and delineate primate species, but that they cannot reliably uncover many of the deeper phylogenetic relationships. Our conclusion is that these short DNA sequences do not contain enough information to build reliable molecular phylogenies or define new species, but that they can provide efficient sequence tags for assigning unknown specimens to known species. As such, DNA barcoding provides enormous potential for use in global biodiversity studies.Key words: DNA barcoding, species identification, primate, biodiversity.

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DNA barcoding and phylogenetic relationship of shrimps (Crustacea: Decapoda) of Bangladesh

Bioresearch Communications ◽

10.3329/brc.v7i1.54248 ◽

2021 ◽

Vol 7 (1) ◽

pp. 941-946

Author(s):

Md Sagir Ahmed ◽

Sumaiya Salam ◽

Sayeda Sabrina Sarwar Rumana ◽

Anindita Barua

Keyword(s):

Dna Barcoding ◽

Genetic Divergence ◽

New Records ◽

Coi Gene ◽

Identification System ◽

Taxonomic Rank ◽

Macrobrachium Nipponense ◽

Shrimp Species ◽

The Mean ◽

Relationship Of

We adopted DNA barcoding technique using a 658-bp fragment of the mitochondrial cytochrome c oxidase I (COI) gene to identify shrimp species collected from the different areas of Bangladesh. A total of 24 sequences were generated belonging to 14 species including four new records- Macrobrachium nipponense, Macrobrachium kistnense, Exopalaemon carinicauda and Alpheus malleator. Genetic distance measured with Kimura 2 parameter showed that genetic divergence increased with higher taxonomic rank. The mean genetic divergence was evaluated and found to be 0.935%, 22.67% and 30.92% within species, genus and family, respectively. In addition to the barcode-based species identification system, phylogenetic relationships were established where individuals belonging to the same species were grouped under the same clade. Maximum likelihood (ML) was preferred as the statistical method and as expected, the phylogenetic tree complemented and ensured the conventional taxonomy. The present study evidently showed that DNA barcoding can be served as an effective tool to discriminate the shrimp species and this will enhance the understanding on evolution and conservation biology. Bioresearch Commu. 7(1): 941-946, 2021 (January)

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Thermodynamic Model for B-Z Transition of DNA Induced by Z-DNA Binding Proteins

Molecules ◽

10.3390/molecules23112748 ◽

2018 ◽

Vol 23 (11) ◽

pp. 2748 ◽

Cited By ~ 5

Author(s):

Ae-Ree Lee ◽

Na-Hyun Kim ◽

Yeo-Jin Seo ◽

Seo-Ree Choi ◽

Joon-Hwa Lee

Keyword(s):

Dna Binding ◽

Dna Sequences ◽

Genomic Dna ◽

Binding Proteins ◽

Dna Binding Proteins ◽

Multiple Sequence ◽

Left Handed ◽

Transition Mechanism ◽

Dna Strands ◽

Z Dna

Z-DNA is stabilized by various Z-DNA binding proteins (ZBPs) that play important roles in RNA editing, innate immune response, and viral infection. In this review, the structural and dynamics of various ZBPs complexed with Z-DNA are summarized to better understand the mechanisms by which ZBPs selectively recognize d(CG)-repeat DNA sequences in genomic DNA and efficiently convert them to left-handed Z-DNA to achieve their biological function. The intermolecular interaction of ZBPs with Z-DNA strands is mediated through a single continuous recognition surface which consists of an α3 helix and a β-hairpin. In the ZBP-Z-DNA complexes, three identical, conserved residues (N173, Y177, and W195 in the Zα domain of human ADAR1) play central roles in the interaction with Z-DNA. ZBPs convert a 6-base DNA pair to a Z-form helix via the B-Z transition mechanism in which the ZBP first binds to B-DNA and then shifts the equilibrium from B-DNA to Z-DNA, a conformation that is then selectively stabilized by the additional binding of a second ZBP molecule. During B-Z transition, ZBPs selectively recognize the alternating d(CG)n sequence and convert it to a Z-form helix in long genomic DNA through multiple sequence discrimination steps. In addition, the intermediate complex formed by ZBPs and B-DNA, which is modulated by varying conditions, determines the degree of B-Z transition.

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