scholarly journals Molecular identification of species of Physalis (Solanaceae) using a candidate DNA barcode: the chloroplast psbA–trnH intergenic region

Genome ◽  
2018 ◽  
Vol 61 (1) ◽  
pp. 15-20 ◽  
Author(s):  
Shangguo Feng ◽  
Kaili Jiao ◽  
Yujia Zhu ◽  
Hongfen Wang ◽  
Mengying Jiang ◽  
...  
Keyword(s):  
Intergenic Region ◽  
Morphological Traits ◽  
Dna Barcode ◽  
Pcr Amplification ◽  
Genetic Distances ◽  
Success Rates ◽  
Medicinal Species ◽  
Distance Methods ◽  
Identification Of Species ◽  
Related Plant

Physalis L., an important genus of the family Solanaceae, includes many commercially important edible and medicinal species. Traditionally, species identification is based on morphological traits; however, the highly similar morphological traits among species of Physalis make this approach difficult. In this study, we evaluated the feasibility of using a popular DNA barcode, the chloroplast psbA–trnH intergenic region, in the identification of species of Physalis. Thirty-six psbA–trnH regions of species of Physalis and of the closely related plant Nicandra physalodes were analyzed. The success rates of PCR amplification and sequencing of the psbA–trnH region were 100%. MEGA V6.0 was utilized to align the psbA–trnH sequences and to compute genetic distances. The results show an apparent barcoding gap between intra- and interspecific variations. Results of both BLAST1 and nearest-distance methods prove that the psbA–trnH regions can be used to identify all species examined in the present study. In addition, phylogenetic analysis using psbA–trnH data revealed a distinct boundary between species. It also confirmed the relationship between species of Physalis and closely related species, as established by previous studies. In conclusion, the psbA–trnH intergenic region can be used as an efficient DNA barcode for the identification of species of Physalis.

scholarly journals Toward a comprehensive COI DNA barcode library for Swiss Stoneflies (Insecta: Plecoptera) with special emphasis on the genus Leuctra

Zoosymposia ◽  
2016 ◽  
Vol 11 ◽  
pp. 135-155 ◽  
Author(s):  
JEAN-LUC GATTOLLIAT ◽  
GILLES VINÇON ◽  
SOFIA WYLER ◽  
JAN PAWLOWSKI ◽  
MICHEL SARTORI
Keyword(s):  
Mitochondrial Gene ◽  
Dna Barcode ◽  
Pcr Amplification ◽  
Species Group ◽  
Genetic Distances ◽  
Gene Trees ◽  
Closely Related Species ◽  
Additional Tool ◽  
Non Destructive ◽  
Level Identification

The Swiss Barcode of Life initiative (SwissBOL) aims to inventory the genetic biodiversity in Switzerland using a short DNA sequence. DNA barcoding provides an additional tool for species identification that complements traditional morphological approaches. We report on the establishment of a DNA barcode library for Plecoptera, taxa that are of great importance as bioindicators of water quality and that often present difficulties in species-level identification for larvae and female specimens. Non-destructive DNA extraction, PCR amplification and sequencing of part of the mitochondrial gene Cytochrome Oxidase I (COI) was conducted for 440 individuals (one to eight per species) belonging to 90 species (of the 112 reported from Switzerland). Intra and interspecific distances were calculated and gene trees reconstructed. In most cases, COI was efficient in delimiting stonefly species. Some doubtful specimens were subsequently re-examined and a few misidentifications were found, especially in some problematic groups in the genus Leuctra Stephens, 1836. Larger genetic distances in some species (e.g. Leuctra nigra (Olivier 1811)) indicate the possible presence of sibling species, while in a few cases closely related species are genetically difficult to separate (within the Leuctra fusca species group).

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 Typing with COI - DNA Barcode of mosquitoes with medical importance from rural area of La Pintada, Antioquia, Colombia

2018 ◽  
Author(s):  
Richard Hoyos-López
Keyword(s):  
Aedes Aegypti ◽  
Rural Area ◽  
Molecular Typing ◽  
Mosquito Species ◽  
Dna Barcode ◽  
Genetic Distances ◽  
Neighbor Joining ◽  
Identification Of Species ◽  
Medical Importance

SummaryDNA barcode is a methodology that allows the identification of species using a short fragment of cytochrome oxidase I and library sequences stored in the barcode of life database (bold>), make up an alternative tool for mosquito identification in areas epidemiologically active for arboviruses, protozoa and bacteria. In our study, we collected 114 adult mosquitoes in a rural area in the municipality of La Pintada (Antioquia, Colombia), and were separate for genus and species using morphological keys. Two Legs were taken of specimens mounted, and these were used for DNA extraction, amplification of COI-Barcode through PCR and sequencing. 38 sequences were characterized of seven mosquito species and used in bold> for molecular identification, subsequent characterization of genetic distances intra/interspecies, and MOTUs grouping by neighbor-joining analyses. Seven MOTUs were separate corresponding to seven species identify by morphological keys. bold> was able to identify five species, and two were identified to the genre. The following medically important mosquitoes were recorded in the rural area from La Pintada(Antioquia): Aedes aegypti, Anopheles triannulatus, Coquillettidia nigricans, Mansonia titillans, Ochlerotatus angustivitatus, Psorophora ferox and Psorophora (Grabhamia)sp.

Testing three proposed DNA barcodes for the wood identification of Dalbergia odorifera T. Chen and Dalbergia tonkinensis Prain

Holzforschung ◽  
2016 ◽  
Vol 70 (2) ◽  
pp. 127-136 ◽  
Author(s):  
Min Yu ◽  
Kai Liu ◽  
Liang Zhou ◽  
Lei Zhao ◽  
Shengquan Liu
Keyword(s):  
Economic Value ◽  
Dna Barcode ◽  
Pcr Amplification ◽  
First Grade ◽  
Wood Identification ◽  
Dna Barcodes ◽  
Success Rates ◽  
Interspecific Differences ◽  
Dalbergia Odorifera ◽  
Dalbergia Tonkinensis

Abstract Dalbergia odorifera T. Chen is a first-grade state protected plant in China. However, it is difficult to distinguish it from the closely related species Dalbergia tonkinensis Prain, which is less important in economic value, by wood anatomical features. In this study, three potential DNA barcode sequences, namely rpoC1, trnH-psbA and internal transcribed spacer (ITS), were used to differentiate wood of D. odorifera from D. tonkinensis. The average quantities of DNA extracts from twigs, sapwood and heartwood were 16.3, 11.5 and 6.0 ng mg-1, respectively. The success rates for polymerase chain reaction (PCR) amplification for three loci, namely ITS, trnH-psbA and rpoC1, were 62.5, 100 and 81.25%, respectively. The success rate for bidirectional sequencing of amplified products was 100% for all the three loci. The identification power of the three proposed DNA barcodes has been calculated by the BLAST, tree-based method and the TAXONDNA method. The interspecific differences of the trnH-psbA region were greater than intraspecific variations. Moreover, the identification power of trnH-psbA was higher than that of ITS and rpoC1 regions at the species level. Finally, the trnH-psbA region is proposed as a DNA barcode for wood identification between D. odorifera and D. tonkinensis.

scholarly journals Molecular identification and evolutionary relationships between the subspecies of Musa by DNA barcodes

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
S. Dhivya ◽  
S. Ashutosh ◽  
I. Gowtham ◽  
V. Baskar ◽  
A. Baala Harini ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Evolutionary Relationship ◽  
Genetic Distances ◽  
Its2 Region ◽  
Potential Candidate ◽  
Dna Barcodes ◽  
Somaclonal Variations ◽  
Distance Methods ◽  
Significant Divergence ◽  
Comprehensive Study

Abstract Background The banana (Musa sp., AAA) genome is constantly increasing due to high-frequency of somaclonal variations. Due to its large diversity, a conventional numerical and morphological based taxonomic identification of banana cultivars is laborious, difficult and often leads to subject of disagreements. Results Hence, in the present study, we used universal DNA barcode ITS2 region to identify and to find the genetic relationship between the cultivars and varieties of banana. Herein, a total of 16 banana cultivars were PCR amplified using ITS2 primer pair. In addition, 321 sequences which were retrieved from GenBank, USA, were used in this study. The sequences were then aligned using Clustal W and genetic distances were computed using MEGA V5.1. The study showed significant divergence between the intra- and inter-specific genetic distances in ITS2 region. BLAST1 and Distance methods proved that ITS2 DNA barcode region successfully identified and distinguished the cultivar and varieties of banana. Conclusion Thus, from the results of the present study, it is clear that ITS2 is not only an efficient DNA barcode to identify the banana species but also a potential candidate for enumerating the phylogenetic relationships between the subspecies and cultivars. This is the first comprehensive study to categorically distinguish the economically important banana subspecies and varieties using DNA barcodes and to understand its evolutionary relationship.

scholarly journals DNA Barcoding Mushroom Spawn Using EF-1α Barcodes: A Case Study in Oyster Mushrooms (Pleurotus)

2021 ◽  
Vol 12 ◽  
Author(s):  
Peng Zhao ◽  
Sen-Peng Ji ◽  
Xian-Hao Cheng ◽  
Tolgor Bau ◽  
Hong-Xin Dong ◽  
...  
Keyword(s):  
Species Identification ◽  
Dna Barcode ◽  
Elongation Factor ◽  
Pcr Amplification ◽  
Interspecific Variation ◽  
28S Rdna ◽  
Oyster Mushroom ◽  
Success Rates ◽  
Mushroom Species ◽  
Oyster Mushrooms

Oyster mushrooms (genus Pleurotus) are widespread and comprise the most commonly cultivated edible mushrooms in the world. Species identification of oyster mushroom spawn based on cultural, morphological, and cultivated characteristics is time consuming and can be extraordinarily difficult, which has impeded mushroom breeding and caused economic loss for mushroom growers. To explore a precise and concise approach for species identification, the nuclear ribosomal internal transcribed spacer (ITS), 28S rDNA, and the widely used protein-coding marker translation elongation factor 1α (EF-1α) gene were evaluated as candidate DNA barcode markers to investigate their feasibility in identifying 13 oyster mushroom species. A total of 160 sequences of the candidate loci were analyzed. Intra- and interspecific divergences and the ease of nucleotide sequence acquisition were the criteria used to evaluate the candidate genes. EF-1α showed the best intra- and interspecific variation among the candidate markers and discriminated 84.6% of the species tested, only being unable to distinguish two closely related species Pleurotus citrinopileatus and Pleurotus cornucopiae. Furthermore, EF-1α was more likely to be acquired than ITS or 28S rDNA, with an 84% success rate of PCR amplification and sequencing. For ITS and 28S rDNA, the intraspecific differences of several species were distinctly larger than the interspecific differences, and the species identification efficiency of the two candidate markers was worse (61.5 and 46.2%, respectively). In addition, these markers had some sequencing problems, with 55 and 76% success rates of sequencing, respectively. Hence, we propose EF-1α as a possible DNA barcode marker for oyster mushroom spawn.

scholarly journals Identification of Tinomiscium petiolare from Vietnam using the DNA barcode

2021 ◽  
Vol 182 (2) ◽  
pp. 114-122
Author(s):  
B. B. Thinh ◽  
R. V. Doudkin ◽  
L. D. Chac ◽  
H. V. Chinh ◽  
Q. V. Hoi ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Pcr Amplification ◽  
Rapid Identification ◽  
Medicinal Species ◽  
Cycle Sequencing ◽  
Stage Of Development ◽  
Pcr Products ◽  
Genetic Sequences ◽  
Total Dna

Background. Tinomiscium petiolare Hook.f. & Thomson is a medicinal species of the family Menispermaceae. This species is currently being intensively exploited for therapeutic purposes. Precise and rapid identification of T. petiolare is critical and essential for the classification, propagation, use and conservation of its genetic resources. In recent years, DNA barcoding has been known to be a fast and sensitive method for identifying species at any stage of development, using short DNA sequences. In this study we have performed the identification of T. petiolare specimens in Vietnam based on the sequence analysis of 4 DNA barcode loci: ITS, matK, rbcL and rpoC.Materials and methods. Total DNA was extracted from leaf samples using DNeasy Plant Mini Kit. PCR amplification of the ITS, matK, rbcL and rpoC regions was carried out on the GeneAmp PCR System 9700 with specific primers. The purified PCR products were sequenced on the ABI 3500 Genetic Analyzer system, using BigDye®Terminator v3.1 Cycle Sequencing Kit. These genetic sequences were analyzed and compared, and a phylogenetic tree was constructed using BioEdit, BLAST, and MEGA 6 programs.Results and conclusion. The success rate of amplification and sequencing was 100% for all 4 DNA barcode loci (ITS, matK, rbcL and rpoC) in the studied specimens. The produced sequence sizes of ITS, matK, rbcL and rpoC in the specimens were 574 bp, 810 bp, 527 bp and 488 bp, respectively. Further, we identified that all studied specimens were genetically related to each other and associated with the same species T. petiolare. Overall, the results of the study generated the most complete DNA barcode database of T. petiolare collected in Vietnam, contributing to the taxonomy and identification of this species. 

Corrigendum: Molecular identification of species of Physalis (Solanaceae) using a candidate DNA barcode: the chloroplast psbA–trnH intergenic region

Genome ◽  
2018 ◽  
Vol 61 (6) ◽  
pp. 467-467
Author(s):  
Shangguo Feng ◽  
Kaili Jiao ◽  
Yujia Zhu ◽  
Hongfen Wang ◽  
Mengying Jiang ◽  
...  
Keyword(s):  
Molecular Identification ◽  
Intergenic Region ◽  
Dna Barcode ◽  
Identification Of Species

scholarly journals Molecular identification and evolutionary relationships between the subspecies of Musa by DNA barcodes

2020 ◽  
Author(s):  
Dhivya Selvaraj ◽  
Ashutosh I ◽  
Gowtham I ◽  
Baskar V ◽  
Baala harini A ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Evolutionary Relationship ◽  
Genetic Distances ◽  
Its2 Region ◽  
Potential Candidate ◽  
Dna Barcodes ◽  
Musa Sp ◽  
Somaclonal Variations ◽  
Distance Methods ◽  
Significant Divergence

Abstract Background: The banana ( Musa sp., AAA ) genome is constantly increasing due to high frequency somaclonal variations. Due to its large diversity, a conventional numerical and morphological based taxonomic identification of banana cultivars is laborious, difficult, and often is a subject of disagreements. Results: In study, we used ITS2 region to identify and determine the genetic relationship between the cultivars and varieties of banana. Herein, a total of 16 banana cultivars were PCR amplified using ITS2 region. In addition, 321 sequences were retrieved from GenBank, USA, and used for the study. The sequences were aligned using Clustal W and genetic distances computed using MEGA V5.1. The significant divergence between the intra- and -specific genetic distances of ITS2 region was observed and the presence of a DNA barcoding gap was obvious. Based on BLAST1 and Distance methods, the results proved that ITS2 region can be successfully identified and distinguished for the cultivar and varieties of banana. Secondly, in this study, ITS2 revealed the relations between the cultivar and varieties of banana. Conclusion: Thus, from this study, it is clear that ITS2 is not only an efficient DNA barcode to identify the banana species but also a potential candidate to study phylogenetic relationships between subspecies and cultivars. This is the first comprehensive study to categorically distinguish the economically important banana sub-species and varieties using DNA barcodes and to understand its evolutionary relationship

scholarly journals Evaluation of five regions as DNA barcodes for identification of Lepista species (Tricholomataceae, Basidiomycota) from China

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7307
Author(s):  
Siyu Wang ◽  
Hongbo Guo ◽  
JiaJia Li ◽  
Wei Li ◽  
Qin Wang ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Internal Transcribed Spacer ◽  
Dna Barcode ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
Its Region ◽  
Small Subunit ◽  
Dna Barcodes ◽  
Success Rates ◽  
Small Subunit Rdna

Background Distinguishing among species in the genus Lepista is difficult because of their similar morphologies. Methods To identify a suitable DNA barcode for identification of Lepista species, we assessed the following five regions: internal transcribed spacer (ITS), the intergenic spacer (IGS), nuclear ribosomal RNA subunit, mitochondrial small subunit rDNA, and tef1. A total of 134 sequences from 34 samples belong to eight Lepista species were analyzed. The utility of each region as a DNA barcode was assessed based on the success rates of its PCR amplification and sequencing, and on its intra- and inter-specific variations. Results The results indicated that the ITS region could distinguish all species tested. We therefore propose that the ITS region can be used as a DNA barcode for the genus Lepista. In addition, a phylogenetic tree based on the ITS region showed that the tested eight Lepista species, including two unrecognized species, formed eight separate and well-supported clades.

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