scholarly journals Endorsement and Phylogenetic Analysis of some Fabaceae Plants based on DNA Barcoding gene MatK

2021 ◽  
Author(s):  
Nader R. Abdelsalam ◽  
Mohamed E. Hasan ◽  
Samar M.A. Rabie ◽  
Houssam El-Din M.F. El-wakeel ◽  
Amera F. Zaitoun ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Dna Barcoding ◽  
Dna Sequences ◽  
Phylogenetic Reconstruction ◽  
Sequence Length ◽  
Morphological Identification ◽  
Phylogenetic Tree Analysis ◽  
Parkinsonia Aculeata ◽  
Link Type ◽  
Matk Gene

DNA barcodes have been considered as a tool to facilitate species identification based on their simplicity and high-level accuracy compression to the complexity and subjective biases linked to morphological identification of taxa. MaturaseK gene “ MatK” of the chloroplast is very crucial in the plant system which is involved in the group II intron splicing. The main objective of this current study is determining the relative utility of the “ MatK” chloroplast gene for barcoding in fifteen legume trees by both single region and multiregional approaches. The chloroplast “ MatK” gene sequences were submitted to GenBank and accession numbers (GenBank: LC602060, LC602154, LC602263, LC603347, LC603655, LC603845, LC603846, LC603847, LC604717, LC604718, LC605994, LC604799, LC605995, LC606468, LC606469) were obtained with sequence length ranging from 730 to 1545 nucleotides. These DNA sequences were aligned with database sequence using PROMALS server , Clustal Omega server and Bioedit program. Also,  the maximum likelihood and neighbor-joining algorithms for phylogenetic reconstruction using the MEGA-X program were employed. Overall, these results indicated that the phylogenetic tree analysis and the evolutionary distances of an individual dataset of each species were agreed with a phylogenetic tree of all each other consisting of two clades, the first clade comprising (Enterolobium contortisiliquum, Albizia lebbek), Acacia saligna , Leucaena leucocephala, Dichrostachys Cinerea, (Delonix regia, Parkinsonia aculeata), (Senna surattensis, Cassia fistula, Cassia javanica) and Schotia brachypetala were more closely to each other, respectively. The remaining four species of Erythrina humeana, (Sophora secundiflora, Dalbergia Sissoo, Tipuana Tipu) constituted the second clade. Therefore, MatK gene is considered promising a candidate for DNA barcoding in plant family Fabaceae and providing a clear relationship between the families. Moreover, their sequences could be successfully utilized in single nucleotide polymorphism (SNP) or part of the sequence as DNA fragment analysis utilizing polymerase chain reaction (PCR) in plant systematic.

DNA barcoding of five common stored-product pest species of genus Cryptolestes (Coleoptera: Laemophloeidae)

2014 ◽  
Vol 104 (4) ◽  
pp. 486-493 ◽  
Author(s):  
Y.J. Wang ◽  
Z.H. Li ◽  
S.F. Zhang ◽  
Z. Varadínová ◽  
F. Jiang ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Dna Sequences ◽  
Morphological Identification ◽  
Pest Species ◽  
Dna Barcodes ◽  
Molecular Approaches ◽  
Worldwide Distribution ◽  
Haplotype Networks ◽  
Stored Product Pest ◽  
The Usa

AbstractSeveral species of the genus Cryptolestes Ganglbauer, 1899 (Coleoptera: Laemophloeidae) are commonly found in stored products. In this study, five species of Cryptolestes, with almost worldwide distribution, were obtained from laboratories in China, Czech Republic and the USA: Cryptolestes ferrugineus (Stephens, 1831), Cryptolestes pusillus (Schönherr, 1817), Cryptolestes turcicus (Grouvelle, 1876), Cryptolestes pusilloides (Steel & Howe, 1952) and Cryptolestes capensis (Waltl, 1834). Molecular identification based on a 658 bp fragment from the mitochondrial DNA cytochrome c oxidase subunit I (COI) was adopted to overcome some problems of morphological identification of Cryptolestes species. The utility of COI sequences as DNA barcodes in discriminating the five Cryptolestes species was evaluated on adults and larvae by analysing Kimura 2-parameter distances, phylogenetic tree and haplotype networks. The results showed that molecular approaches based on DNA barcodes were able to accurately identify these species. This is the first study using DNA barcoding to identify Cryptolestes species and the gathered DNA sequences will complement the biological barcode database.

scholarly journals DNA Barcoding: A Study of Guppy Fish (Poecilia reticulata) in East Java, Indonesia

2019 ◽  
Vol 11 (2) ◽  
pp. 272-278
Author(s):  
Sucipto Hariyanto ◽  
Hasan Adro’i ◽  
Mahrus Ali ◽  
Bambang Irawan
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
Dna Sequences ◽  
Poecilia Reticulata ◽  
Phylogenetic Reconstruction ◽  
Coi Gene ◽  
West Java ◽  
Advance Research ◽  
Phylogeny And Evolution ◽  
Guppy Fish

Poecilia reticulata is a freshwater fish from the northeastern part of South America and spread widely to various countries in Asia and other continents. However, research about P. reticulate is limited even though it is a well-known fish species in Indonesia. The purpose of study was to identify the fish species of P. reticulata through DNA barcoding using the COI gene to determine the phylogenetic relationships among fish populations in East Java, Indonesia. In a present study, there were eight samples of P. reticulata from four different freshwater locations in East Java. Extraction, amplification, and sequencing of DNA samples were conducted to obtain the genetic data and construct a phylogenetic tree based on DNA sequences. The COI gene is the most popular markers to study genetic populations and phylogeography among the animal kingdom. Our phylogenetic reconstruction showed a clear that there were two groups of P. reticulata. The first group was obtain through species from East Java, Sukabumi, West Java (KU692776.1), Dominican Republic, Pandeglang, Banten and Myanmar. The second group was P. reticulata from southern Africa, Brazil, and Sukabumi, West Java (KU692775.1). The result of this study indicate that the guppy fish in East Java identic with P. reticulata from West Java (KU692776.1), which a widely used in classification based on evolutionary relationships. The findings of this study have important implication for the development of advance research about adaptation, phylogeny, and evolution of fish, especially of guppy fish.

scholarly journals Molecular Phylogenetic of Cerithidea anticipata (Iredale, 1929) (Mollusk: Gastropod)

2021 ◽  
Vol 9 (1) ◽  
pp. 9
Author(s):  
Dandi Saleky ◽  
Sendy Lely Merly
Keyword(s):  
Dna Barcoding ◽  
Phylogenetic Reconstruction ◽  
Dna Amplification ◽  
Mangrove Ecosystem ◽  
Coi Gene ◽  
Sequence Length ◽  
Local Alignment ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Degree Of Similarity

Species identification is very important and an important part of bioecological studies, so phylogenetic studies of Cerithidea anticipata (Iredale, 1929) was conducted in September 2020 to identify C. anticipata (Iredale, 1929) based on DNA barcoding techniques. Samples of C. anticipata (Iredale, 1929) were collected from the mangrove ecosystem of Payum Merauke Beach Papua (Indonesia), where the genes used were primary COI Gene forward LCO1490 and reverse HCO2198. The result of DNA amplification obtained DNA sequence length of 660 bp, then based on the identification of Basic Local Alignment Search Tools (BLAST) obtained a similarity level of 98.42% and phylogenetic reconstruction showed the existence of grouping based on the degree of similarity and genetic distance between populations.Keywords: Cerithidea anticipata; COI genes; DNA barcoding; phylogeneticsAbstrakIdentifikasi spesies sangat penting dilakukan dan menjadi bagian penting dalam studi bioekologi, sehingga kajian filogenetik Cerithidea anticipata (Iredale, 1929) telah dilakukan pada bulan September 2020 dengan tujuan untuk mengidentifikasi C. anticipata (Iredale, 1929) berdasarkan teknik DNA barcoding. Sampel C. anticipata (Iredale, 1929) dikoleksi dari ekosistem mangrove Pantai Payum Merauke Papua (Indonesia), dimana gen yang digunakan adalah Gen COI primer forward LCO1490 dan reverse HCO2198. Hasil dari amplifikasi DNA diperoleh panjang sekuen DNA 660 bp, kemudian berdasarkan identifikasi Basic Local Alignment Search Tools (BLAST) diperoleh tingkat kemiripannya 98.42% dan rekonstruksi filogenetiknya memperlihatkan adanya pengelompokan berdasarkan tingkat kemiripan maupun jarak genetik antar populasi.Kata kunci: Cerithidea anticipata; Gen COI; DNA barcoding; filogenetik

scholarly journals SANS serif: alignment-free, whole-genome based phylogenetic reconstruction

2021 ◽  
Author(s):  
Andreas Rempel ◽  
Roland Wittler
Keyword(s):  
Phylogenetic Tree ◽  
Source Code ◽  
Phylogenetic Reconstruction ◽  
Whole Genome ◽  
Link Type ◽  
Alignment Free ◽  
Phylogeny Estimation

AbstractSummarySANS serif is a novel software for alignment-free, whole-genome based phylogeny estimation that follows a pangenomic approach to efficiently calculate a set of splits in a phylogenetic tree or network.Availability and ImplementationImplemented in C++ and supported on Linux, MacOS, and Windows. The source code is freely available for download at https://gitlab.ub.uni-bielefeld.de/gi/[email protected]

scholarly journals DNA barcoding approach to identification of Cassidula angulifera (Petit, 1841) (Mollusca: Gastropoda)

2021 ◽  
Vol 5 (1) ◽  
pp. 55
Author(s):  
Dandi Saleky ◽  
Sendy L Merly
Keyword(s):  
Genetic Distance ◽  
Dna Barcoding ◽  
Dna Sequence ◽  
Phylogenetic Reconstruction ◽  
Coi Gene ◽  
Sequence Length ◽  
Gastropod Species ◽  
Gene Markers ◽  
Entire Sequence ◽  
High Bootstrap

A large number of gastropod species have similarities in morphology (cryptic) makes misidentification probably happen/occurred. Accurate species identification is needed in studying bioecology of species. This research aims to identify the species of Cassidulla sp. Which was collected from Peyum Beach Merauke with DNA barcoding techniques using COI gene markers. The primers used in this study are forward primers (LCO1490) and reverse primers (HCO2198). The result of identification with DNA barcoding showed that the species analyzed was Cassidula angulifera with a 99.53% similarity level with a DNA sequence length of 650 bp. Phylogenetic reconstruction showing the entire sequence of Cassidula sp. which were analyzed separately based on the type and genetic distance with high bootstrap value. Phylogenetic reconstruction of Cassidula sp. form a monophyletic group, which means that the species come from the same ancestors. DNA barcoding is very good and accurate in identifying species.

scholarly journals Taxonomical Study of Spiders (Order, Araneae) from Different Localities of Iraq

2020 ◽  
Vol - (38) ◽  
pp. 1-51
Author(s):  
Ishraq Mohammed Baker ◽  
◽  
Hayder Badri Ali ◽  
Keyword(s):  
Cytochrome C ◽  
Phylogenetic Tree ◽  
Cytochrome C Oxidase ◽  
Dna Sequences ◽  
Coi Gene ◽  
Morphological Identification ◽  
Neighbor Joining ◽  
Climate Conditions ◽  
Molecular Barcoding ◽  
Taxonomical Study

This study represents the first molecular and morphological work on spiders of Iraq. Specimens were collected from different localities in seven provinces during June 2018-July 2019 in different climate conditions. Using both molecular and morphological approaches, eight families representing 17 genera and nine species were identified. Eight genera: Cryptachaea Archer, 1946; Micaria Western, 1851; Ozyptila Simon, 1864; Paramicromerys Millot, 1946; Tegenaria Latreille, 1804; Trachyzelotes Lohmander, 1944; Uroctea Dufour, 1820 and Zelotes Gistel, 1848; and five species: Cryptachaea riparia (Blackwall, 1834); Tegenaria pagana C. L. Koch, 1840; Trachyzelotes jaxartensis (Kroneberg, 1875); Pardosa amentata (Clerck, 1757) and Oecobius putus O. Pickard-Cambridge, 1876 were first recorded for the Iraqi spider fauna. Identification keys for distinguishing families and genera based on the main characteristics were constructed. Molecular-identification was performed for specimens that were difficult to identify by morphological methods, and to confirm the results of the morphological identification. DNA was extracted from 28 spiders’ specimens; PCR-amplified the mtDNA fragment of 710bp of the Cytochrome C Oxidase Subunit I (COI) gene using the primers LCO 1490 Forward / HCO-700ME Reverse. The results of DNA sequences showed 16 samples successful in sequencing. Sixteen local sequenced specimens were submitted to GenBank and edited and combined with COI gene sequences that are associated in GenBank using the neighbor-joining method and the phylogenetic tree was drawn. Eight species of 16 genera belonging to eight families were confirmed by molecular barcoding. The DNA sequences and associated information about the specimens (collection and locality date) deposited in GenBank.

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

Mammalia ◽  
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.

scholarly journals Benchmarking DNA barcodes: an assessment using available primate sequences

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 851-854 ◽  
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.

scholarly journals Phylogenetic Analysis of Kobuvirus and Astrovirus From Korean Wild Boars: 2016-2018

2021 ◽  
Author(s):  
Jihye Shin ◽  
SeEun Choe ◽  
Bang-Hun Hyun ◽  
Dong-Jun An
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Porcine Kobuvirus ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Wild Boars ◽  
Porcine Astrovirus ◽  
The One

Abstract The prevalence of porcine kobuvirus (PKoV) and porcine astrovirus (PAstV) in 845 Korean wild boars (KWB) during 2016-2018 were 28.0% and 10.6%, respectively, and co-infection of two viruses showed 5.1%. Phylogenetic tree analysis also revealed that 236 PKoVs from KWB were divided to diverse lineages within Aichivirus C group but the one strain (WKoV16CN-8627) was included the same cluster with bovine kobuvirus (Achivirus B). Eighty-nine PAstVs from KWB was belonged predominantly to lineage PAstV4 and only one strain (WAst17JN-10931) included novel to lineage PAstV2. Two viruses are epidemic more in young (≤ 12 months) than in old pigs (> 12 months).

scholarly journals First Complete Genome Sequence of Brucella abortus 2308 isolated from an abortion storm in a dairy farm in India

2021 ◽  
Author(s):  
Amit Kumar ◽  
Malyaj R Prajapati ◽  
Surendra Upadhyay ◽  
Anamika Bhordia ◽  
Vinod Kumar Singh ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Dna Sequences ◽  
Brucella Abortus ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Messenger Rna ◽  
Gc Content ◽  
Dairy Farm ◽  
Rrna Genes ◽  
Sequence Length

Abstract The present report communicates the first complete genome sequence of Brucella abortus 2308 strain isolated from a an abortion storm in a dairy farm located at Kanpur, Uttar Pradesh in India. It caused the last trimester abortions of 32 animals out of 100 cows in a dairy over a period of 60 days. The bacteria were isolated in pure culture from the placenta of aborted cows. The genome sequence length of isolated bacteria is 3,285,606 bp with a 57.25 % GC content, an N50 value of 296,426, L50 value of 4 containing 3,119 coding DNA sequences (CDSs), 49 tRNAs, 1 transfer messenger RNA (mRNA), and 3 rRNA genes. It is the first report of Brucella abortus 2308 isolation and complete genome sequence from Indian subcontinent.

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