Phylogenetic Analysis of Black Peper (Piper Spp.) Population Collected in Different Locations of Vietnam Based on the ITSU1-4 Gene Region

2021 ◽  
Author(s):  
Sonexay Rasphone ◽  
Long Thanh Dang ◽  
Hoan Nguyen ◽  
Ngoc Quang Nguyen ◽  
Oanh Thi Duong ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Ribosomal Dna ◽  
Maximum Likelihood Method ◽  
Dna Barcode ◽  
Population Expansion ◽  
Nuclear Ribosomal Dna ◽  
Likelihood Method ◽  
Gene Region ◽  
Universal Primers ◽  
Intraspecific Distance

Abstract Background: The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. To compare and find out the analysis genetic diversity difference some pepper individuals collected in different localities in Vietnam when using the ITS of nuclear ribosomal DNA. The ITS gene region from the nuclear genomes were tested for their suitability as DNA barcoding regions of thirty-nine pepper individuals. Universal primers were used, and sequenced products were analyzed using the Maximum Likelihood method and Tamura-Nei model in the MEGA X program.Results: We did not observe high variability in intraspecific distance within the ITSu1-4 gene region between individuals, ranged from 0.000 to 0.155 (mean = 0.033). The size of the gene region has fluctuated from 667 to 685 bp between different individuals with the percentage (G + C) contained in the ITSu1-4 gene region was ranged from 54.776% to 60.805%, mean = 60.174%. The values of Fu’s Fs, D, Fu and Li’s D* and F* were negative as well (Fs = -0.209, D = -1.824; P < 0.05, D* = -1.205; not significant, P > 0.10 and F* = -1.699; not significant, 0.10 > P > 0.05), indicating an excess of recently derived haplotypes and suggesting that either population expansion or background selection has occurred. The value Strobeck’s S the obtained between individuals in a population is high (S = 0.684). The results of evolutionary relationships of taxa obtained 3 groups with the highest value of Fst is shown in the pairs of groups II and III (Fst = 0.151), and the lowest is in groups II and I (Fst = 0.015). All of the new sequences have been deposited in GeneBank under the following accession numbers MZ636718 to MZ636756.Conclusions: This database is an important resource for researchers working on Species of pepper in Vietnam and also provides a tool to create ITSu1-4 databases for any given taxonomy.

scholarly journals DNA barcoding to resolve the confusion in identifying Tribolium confusum and Tribolium castaneum

2019 ◽  
Vol 47 (2) ◽  
pp. 333-342
Author(s):  
Abu Faiz Md Aslam ◽  
Sharmin Sultana ◽  
Sumita Rani Das ◽  
Abdul Jabber Howlader
Keyword(s):  
Dna Barcoding ◽  
Tribolium Castaneum ◽  
Life Stage ◽  
Dna Barcode ◽  
Tribolium Confusum ◽  
Likelihood Method ◽  
Coi Gene ◽  
Pest Species ◽  
Stored Grain ◽  
Accurate Identification

Tribolium confusum and Tribolium castaneum (Coleoptera: Tenebrionidae) are two very confusing pest species while identification is done on the basis of morphology only. Such pests are discovered in stored grain as immature stages, which further complicates the identification process. Accurate identification of these pests is urgently required for integrated pest management. In this research, DNA barcoding was used to identify these pests accurately at any life stage. A 658 bp fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene was analyzed. DNA barcode dataset of T. confusum (GeneBank Acc. no. MK120453.1) and T. castaneum (Acc. no. MK411585.1) were constructed. The nucleotide composition reveals that average AT contents (59.9%) were higher than the GC contents (38.6%). Phylogenetic analysis by maximum likelihood method showed that both the species were originated from a common major clade. About 17.13% nucleotide differences were noted between the CO1 sequences by multiple sequence alignment. The interspecies nucleotide genetic distance (0.200) was calculated using Kimura 2 parameter. Haplotype analysis showed high genetic diversity (112 mutaional steps) among them. Bangladesh J. Zool. 47(2): 333-342, 2019

scholarly journals Land plants and DNA barcodes: short-term and long-term goals

2005 ◽  
Vol 360 (1462) ◽  
pp. 1889-1895 ◽  
Author(s):  
Mark W Chase ◽  
Nicolas Salamin ◽  
Mike Wilkinson ◽  
James M Dunwell ◽  
Rao Prasad Kesanakurthi ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Plastid Dna ◽  
Land Plant ◽  
Land Plants ◽  
Nuclear Ribosomal Dna ◽  
Short Term ◽  
Species Limits ◽  
Variable Regions

Land plants have had the reputation of being problematic for DNA barcoding for two general reasons: (i) the standard DNA regions used in algae, animals and fungi have exceedingly low levels of variability and (ii) the typically used land plant plastid phylogenetic markers (e.g. rbcL , trnL-F , etc.) appear to have too little variation. However, no one has assessed how well current phylogenetic resources might work in the context of identification (versus phylogeny reconstruction). In this paper, we make such an assessment, particularly with two of the markers commonly sequenced in land plant phylogenetic studies, plastid rbcL and internal transcribed spacers of the large subunits of nuclear ribosomal DNA (ITS), and find that both of these DNA regions perform well even though the data currently available in GenBank/EBI were not produced to be used as barcodes and BLAST searches are not an ideal tool for this purpose. These results bode well for the use of even more variable regions of plastid DNA (such as, for example, psbA-trnH ) as barcodes, once they have been widely sequenced. In the short term, efforts to bring land plant barcoding up to the standards being used now in other organisms should make swift progress. There are two categories of DNA barcode users, scientists in fields other than taxonomy and taxonomists. For the former, the use of mitochondrial and plastid DNA, the two most easily assessed genomes, is at least in the short term a useful tool that permits them to get on with their studies, which depend on knowing roughly which species or species groups they are dealing with, but these same DNA regions have important drawbacks for use in taxonomic studies (i.e. studies designed to elucidate species limits). For these purposes, DNA markers from uniparentally (usually maternally) inherited genomes can only provide half of the story required to improve taxonomic standards being used in DNA barcoding. In the long term, we will need to develop more sophisticated barcoding tools, which would be multiple, low-copy nuclear markers with sufficient genetic variability and PCR-reliability; these would permit the detection of hybrids and permit researchers to identify the ‘genetic gaps’ that are useful in assessing species limits.

scholarly journals DNA Barcoding Analysis and Phylogenetic Relation of Mangroves in Guangdong Province, China

Forests ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 56 ◽  
Author(s):  
Feng Wu ◽  
Mei Li ◽  
Baowen Liao ◽  
Xin Shi ◽  
Yong Xu
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Barcode ◽  
Phylogenetic Reconstruction ◽  
Pcr Amplification ◽  
Guangdong Province ◽  
Nuclear Ribosomal Dna ◽  
Success Rates ◽  
Mangrove Species ◽  
Identification Rate

Mangroves are distributed in the transition zone between sea and land, mostly in tropical and subtropical areas. They provide important ecosystem services and are therefore economically valuable. DNA barcoding is a useful tool for species identification and phylogenetic reconstruction. To evaluate the effectiveness of DNA barcoding in identifying mangrove species, we sampled 135 individuals representing 23 species, 22 genera, and 17 families from Zhanjiang, Shenzhen, Huizhou, and Shantou in the Guangdong province, China. We tested the universality of four DNA barcodes, namely rbcL, matK, trnH-psbA, and the internal transcribed spacer of nuclear ribosomal DNA (ITS), and examined their efficacy for species identification and the phylogenetic reconstruction of mangroves. The success rates for PCR amplification of rbcL, matK, trnH-psbA, and ITS were 100%, 80.29% ± 8.48%, 99.38% ± 1.25%, and 97.18% ± 3.25%, respectively, and the rates of DNA sequencing were 100%, 75.04% ± 6.26%, 94.57% ± 5.06%, and 83.35% ± 4.05%, respectively. These results suggest that both rbcL and trnH–psbA are universal in mangrove species from the Guangdong province. The highest success rate for species identification was 84.48% ± 12.09% with trnH-psbA, followed by rbcL (82.16% ± 9.68%), ITS (66.48% ± 5.97%), and matK (65.09% ± 6.00%), which increased to 91.25% ± 9.78% with the addition of rbcL. Additionally, the identification rate of mangroves was not significantly different between rbcL + trnH-psbA and other random fragment combinations. In conclusion, rbcL and trnH-psbA were the most suitable DNA barcode fragments for species identification in mangrove plants. When the phylogenetic relationships were constructed with random fragment combinations, the optimal evolutionary tree with high supporting values (86.33% ± 4.16%) was established using the combination of matK + rbcL + trnH-psbA + ITS in mangroves. In total, the 476 newly acquired sequences in this study lay the foundation for a DNA barcode database of mangroves.

scholarly journals Molecular phylogeny based on its sequences of nrDNA of some species belonging to dodder (Cuscuta L.) genus from various ecological sites of Turkey

2020 ◽  
Vol 48 (3) ◽  
pp. 1332-1340
Author(s):  
Ilhan KAYA ◽  
Ibrahim DEMIR ◽  
Mustafa USTA ◽  
Hikmet M. SIPAHIOĞLU
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Its Sequences ◽  
Nuclear Ribosomal Dna ◽  
Universal Primers ◽  
Morphological Examination ◽  
Internal Transcribed Spacer Region ◽  
Tissue Samples ◽  
Geographical Regions

Nuclear ribosomal DNA (nrDNA) sequence data of the Cuscuta genus, which have been considered as one of the most popular sequences for phylogenetic inference in plants, have been studied from a phylogenetic perspective in agricultural and non-agricultural lands of Turkey. The samples of Cuscuta spp. were collected from different geographical regions of Turkey between the years of 2013-2015. Some other species, not available locally, were taken from the herbarium samples of some research units. In order to study the phylogenetic relations of collected species, DNA isolations were made from body tissue samples. Conserved regions on ribosomal DNA (rDNA) were amplified by universal primers via PCR method and cloned into a proper cloning vector. The cloned DNA fragments were sequenced and analysed by web-based and computer programs. DNA sequences of certain species were recorded to the National Center for Biotechnology Information (NCBI) database. Based on the morphological examination and molecular analyses of fresh and the herbarium specimen, 8 species were identified. The identified species were C. hyalina (Gene bank accession no. KY020420), C. monogyna (KY020421), C. europaea (KY020422), C. palaestina (KY020423), C. approximata (KY020424), C. kurdica (KY020427), C. kotschyana (KY020430) and C. babylonica (KY020431). The ITS (Internal Transcribed Spacer) region contains several indels in identified Cuscuta species with the length varying from 668 to 730 bp. Sequence divergence ranges from 1.00% to 8.00% within Cuscuta spp. Based on our findings, the ITS sequences provided phylogenetically informative results in combination with the secondary structures.

scholarly journals Identification of Vietnamese Native Rhododendron and Enkianthus Species of Ericaceae Family Based on Ribosomal DNA Internal Transcribed Spacer (ITS) Sequence

2018 ◽  
Vol 2 ◽  
pp. 33-42
Author(s):  
T.V. Tam ◽  
D.V. Dong ◽  
D.V. Lam ◽  
T.H. Anh ◽  
N.D. Van ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Dna Barcode ◽  
Nuclear Ribosomal Dna ◽  
Its Sequence ◽  
Subspecies Level ◽  
Plant Group ◽  
Family Based ◽  
Quang Ninh ◽  
Recognition Molecule

The genusRhododendronandEnkianthusare belonging theEricaceaefamily. In Vietnam there have diversified with 12 genera and about 90 species, of which morerhododendrons30 species with beautiful flowers and two ofEnkianthusspecies, widely distributed across the regions of the country. In this study, twelve Vietnamese nativeRhododendronandEnkianthusspecies collected from Quang Ninh province were identified based on sequences of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA. Comparison on sequencing among 12 Vietnamese nativeRhododendronandEnkianthuswith world'sRhododendronandEnkianthusspecies, we have determined the accurate same pattern the 5/10 species by recognition molecule forms such as DQ2, DQ5, DQ6, DQ7, DQ8 and five species as DQ1, DQ9, DQ10, DQ11 and DQ12 were determined in genusRhododendronspecies. Two varieties ofEnkianthusas DQ3 and DQ4 were identified asEnkianthus quinqueflorus. Although the species is still limited but the ITS sequences application revealed the strength of promotion of universal DNA barcode in the delimitation of species and subspecies level for plant group flowering.

scholarly journals Inclusion of Kickxia abhaica D.A. Sutton in the genus Nanorrhinum (Plantaginaceae): Evidence from its nuclear ribosomal DNA sequences

2018 ◽  
Vol 25 (2) ◽  
pp. 209-214
Author(s):  
M. Ajmal Ali
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Molecular Phylogenetics ◽  
Taxonomic Status ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Universal Primers ◽  
Discrimination Power ◽  
Molecular Phylogenetic ◽  
Endemic Taxon

The nuclear ribosomal DNA (nrDNA) internal transcribed spacers (ITS) sequences is extensively used in the plant molecular phylogenetics for plant taxonomic identification and DNA barcoding purposes because the nrDNA ITS gene is easy to amplify by using the universal primers, its length is shorter and thus easy to sequence, and has strong discrimination power to distinguish the taxon at the species level. The present molecular phylogenetic analysis of ITS nrDNA sequences focuses to determine the taxonomic status of an unresolved endemic taxon Kickxia abhaica D.A. Sutton (Family Plantaginaceae, tribe Antirrhineae) reported from Saudi Arabia. The analysis supports the transfer of K. abhaica under the genus Nanorrhinum.

scholarly journals Research on Phylogenetic Relationship of Lotus Populations Collected in Thua Thien Hue Province, Vietnam based on the Chloroplast Genome by DNA Barcode

2021 ◽  
Author(s):  
Dang Thanh Long ◽  
Hoang Thi Kim Hong ◽  
Le Ly Thuy Tram ◽  
Nguyen Thi Quynh Trang
Keyword(s):  
Chloroplast Genome ◽  
Dna Barcoding ◽  
Phylogenetic Analyses ◽  
Dna Barcode ◽  
Haplotype Diversity ◽  
Universal Primers ◽  
Nucleotide Position ◽  
Accurate Identification ◽  
Low Levels ◽  
Relationship Of

Background: The DNA barcoding is currently an effective and widely used tool that enables rapid and accurate identification of plant species. Methods: DNA barcoding of 9 chloroplast genes (rbcL, matK, trnH-psbA, accD-psaI, ndhA, psbE-petL, Rpl32-trnL, trnW-psaJ, trnSGCU-trnGGCC) were used to provide the theoretical basis for species identification, genetic diversity analysis of lotus population collected in Thua Thien Hue province, Vietnam. Universal primers were used and sequence products were analyzed using the MEGA X program. Result: The results showed that high levels of haplotype diversity (Hd), ranging from 0.618-0.869 and low levels of nucleotide diversity (Pi), ranging from 0.180 × 10-3-3.280 × 10-3 base on a total of nine gene regions of chloroplast genome. The neutrality tests show an excess of rare nucleotide position variations in individuals’ white lotus and derived haplotypes recent expansion. While the evolution of the individuals in the pink lotus may have to decrease. The phylogenetic analyses indicated that combined sequences were not insufficient to make a difference to the DNA barcoding in the individual’s lotus of the N. nucifera species this is in the study. The standardized and accurate barcode information of lotus is provided for researchers. It lays the foundation for the conservation, evaluation, innovative utilization and protection of Nelumbonaceae germplasm resources.

scholarly journals Molecular authentication of Euphorbia schimperiana Scheele using internal transcribed spacer sequences of nuclear ribosomal DNA

2021 ◽  
Vol 28 (1) ◽  
pp. 125-130
Author(s):  
Mesfer M Alqahtani ◽  
M Ajmal Ali ◽  
M Oliur Rahman ◽  
Fahad M Al Hemaid ◽  
Sidanand V Kambhar ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Molecular Phylogenetics ◽  
Taxonomic Status ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Universal Primers ◽  
Important Species ◽  
Discrimination Ability ◽  
Plant Taxon

The Internal Transcribed Spacers (ITS) sequences of nuclear ribosomal DNA (nrDNA) are commonly used in plant molecular phylogenetics for the molecular based taxonomic identification and DNA barcoding because of shorter length and easy to amplify by using the universal primers, and further has discrimination ability to distinguish the taxon at lower taxonomic level. The present molecular phylogenetic analysis of ITS nrDNA sequences focuses to determine the taxonomic status of an unresolved medicinally important species Euphorbia schimperiana Scheele of the family Euphorbiaceae reported from Saudi Arabia. The combined length of the entire ITS region in E. schimperiana is 644 nucleotides. The study reveals that E. schimperiana shows a close proximity with the members of the subgenus Esula. Bangladesh J. Plant Taxon. 28(1): 125-130, 2021 (June)

Difficulties barcoding in the dark: the case of crustacean stygofauna from eastern Australia

2012 ◽  
Vol 26 (6) ◽  
pp. 583 ◽  
Author(s):  
Maria G. Asmyhr ◽  
Steven J. B. Cooper
Keyword(s):  
Dna Barcoding ◽  
Assessment Tool ◽  
Dna Barcode ◽  
Pcr Amplification ◽  
Universal Primers ◽  
Sequence Comparisons ◽  
Technical Problems ◽  
Groundwater Fauna ◽  
Taxonomic Descriptions ◽  
Eastern Australia

The eastern Australian aquifers remain mostly unexplored; however, recent surveys suggest that there could be substantial levels of subterranean biodiversity hidden in these aquifers. Groundwater fauna (stygofauna) is often characterised by short-range endemism. Furthermore, high levels of cryptic species, and lack of formal taxonomic descriptions and taxonomic expertise for many of the groups demand innovative approaches for assessing subterranean biodiversity. Here we evaluate the potential of using DNA barcoding as a rapid biodiversity assessment tool for the subterranean groundwater fauna of New South Wales, Australia. We experienced low amplification success using universal and more taxon-specific primers for PCR amplification of the barcoding gene (COI) in a range of crustacean stygofauna. Sequence comparisons of the most commonly used COI universal primers in selected crustacean taxa revealed high levels of variability. Our results suggest that successful amplification of the COI region from crustacean stygofauna is not straightforward using the standard ‘universal’ primers. We propose that the development of a multiprimer (taxon specific) and multigene approach for DNA barcode analyses, using next-generation sequencing methodologies, will help to overcome many of the technical problems reported here and provide a basis for using DNA barcoding for rapid biodiversity assessments of subterranean aquatic ecosystems.

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