scholarly journals Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae

2018 ◽  
Author(s):  
Aisha Tahir ◽  
Fatma Hussain ◽  
Nisar Ahmed ◽  
Abdolbaset Ghorbani ◽  
Amer Jamil
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
Species Level ◽  
Practical Implementation ◽  
Medicinal Species ◽  
Level Identification ◽  
Geographically Isolated

In pursuit of developing fast and accurate species level molecular identification methods, we tested six DNA barcodes viz. ITS2, matK, rbcLa, ITS2+matK, ITS2+rbcLa, matK+rbcLa, ITS2+matK+rbcLa for their capacity to identify frequently consumed but geographically isolated medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan. Data were analysed by BLASTn sequence similarity, pairwise sequence divergence in TAXONDNA, and phylogenetic (neighbour-joining and maximum-likelihood trees) methods. Comparison of six barcode regions showed that ITS2 has the highest number of variable sites (209/360) for tested Fabaceae and (106/365) Poaceae species, the highest species level identification (40%) in BLASTn procedure, distinct DNA barcoding gap, 100% correct species identification in BM and BCM functions of TAXONDNA, and clear cladding pattern with high nodal support in phylogenetic trees in both families. ITS2+matK+rbcLa followed ITS2 in its species level identification capacity. The study was concluded with advocating the DNA barcoding as an effective tool for species identification and ITS2 as the best barcode region in identifying medicinal species of Fabaceae and Poaceae. Current research has practical implementation potential in the fields of pharmaco-vigilance, trade of medicinal plants and biodiversity conservation.

scholarly journals Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4499 ◽  
Author(s):  
Aisha Tahir ◽  
Fatma Hussain ◽  
Nisar Ahmed ◽  
Abdolbaset Ghorbani ◽  
Amer Jamil
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
Species Level ◽  
Practical Implementation ◽  
Medicinal Species ◽  
Level Identification ◽  
Geographically Isolated

In pursuit of developing fast and accurate species-level molecular identification methods, we tested six DNA barcodes, namely ITS2, matK, rbcLa, ITS2+matK, ITS2+rbcLa, matK+rbcLa and ITS2+matK+rbcLa, for their capacity to identify frequently consumed but geographically isolated medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan. Data were analysed by BLASTn sequence similarity, pairwise sequence divergence in TAXONDNA, and phylogenetic (neighbour-joining and maximum-likelihood trees) methods. Comparison of six barcode regions showed that ITS2 has the highest number of variable sites (209/360) for tested Fabaceae and (106/365) Poaceae species, the highest species-level identification (40%) in BLASTn procedure, distinct DNA barcoding gap, 100% correct species identification in BM and BCM functions of TAXONDNA, and clear cladding pattern with high nodal support in phylogenetic trees in both families. ITS2+matK+rbcLa followed ITS2 in its species-level identification capacity. The study was concluded with advocating the DNA barcoding as an effective tool for species identification and ITS2 as the best barcode region in identifying medicinal species of Fabaceae and Poaceae. Current research has practical implementation potential in the fields of pharmaco-vigilance, trade of medicinal plants and biodiversity conservation.

scholarly journals Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae

2018 ◽  
Author(s):  
Aisha Tahir ◽  
Fatma Hussain ◽  
Nisar Ahmed ◽  
Abdolbaset Ghorbani ◽  
Amer Jamil
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
Species Level ◽  
Practical Implementation ◽  
Medicinal Species ◽  
Level Identification ◽  
Geographically Isolated

In pursuit of developing fast and accurate species level molecular identification methods, we tested six DNA barcodes viz. ITS2, matK, rbcLa, ITS2+matK, ITS2+rbcLa, matK+rbcLa, ITS2+matK+rbcLa for their capacity to identify frequently consumed but geographically isolated medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan. Data were analysed by BLASTn sequence similarity, pairwise sequence divergence in TAXONDNA, and phylogenetic (neighbour-joining and maximum-likelihood trees) methods. Comparison of six barcode regions showed that ITS2 has the highest number of variable sites (209/360) for tested Fabaceae and (106/365) Poaceae species, the highest species level identification (40%) in BLASTn procedure, distinct DNA barcoding gap, 100% correct species identification in BM and BCM functions of TAXONDNA, and clear cladding pattern with high nodal support in phylogenetic trees in both families. ITS2+matK+rbcLa followed ITS2 in its species level identification capacity. The study was concluded with advocating the DNA barcoding as an effective tool for species identification and ITS2 as the best barcode region in identifying medicinal species of Fabaceae and Poaceae. Current research has practical implementation potential in the fields of pharmaco-vigilance, trade of medicinal plants and biodiversity conservation.

scholarly journals DEVELOPMENT OF SPECIFIC PRIMERS FOR INTER SPECIES PHYLOGENY RELATIONSHIP ON Crocodilian sp

2015 ◽  
Vol 2 (1) ◽  
pp. 301
Author(s):  
Herdhanu Jayanto ◽  
Budi Setiadi Daryono
Keyword(s):  
Phylogenetic Tree ◽  
Species Identification ◽  
Cytochrome B ◽  
Phylogenetic Trees ◽  
Species Level ◽  
False Identification ◽  
Specific Primer ◽  
Specific Primers ◽  
Species Phylogeny ◽  
Bioinformatics Tools

<p>Poaching, trafficking, and illegal product trading are classic activities which frequently faced by Crocodilian group. To overcome, laws need supporting methods for a decision of these all activities which threaten crocodile species. This will require species identification that associated to taxonomy classification. Crocodilian species are very similar in morphology. This may result to a false identification especially when working on incomplete specimen. Currently, twenty-four existing Crocodilian species are continuously revised to improve the precise placement and/or acceptance of certain species on Crocodilian classification. Herein we address this issue using Cytochrome-b. The idea was to obtain genus specific primer from Cytochrome-b and then tested the precision of the designed primers using bioinformatics tools’ Primer-BLAST and CLC sequence Viewer 6. The designed primers showed a highly specificity on species level. The phylogenetic tree constructed by is relatively precise compared to reported phylogenetic trees. These specific primers together with the genus specific primers may give valuable and important support for the effective and efficient identification of Crocodilian group.</p><p><br /><strong>Keywords</strong>: Crocodilian, illegal trading, Cytochrome-b , specific primer, bioinformatic</p>

scholarly journals MinION-Based DNA Barcoding of Preserved and Non-Invasively Collected Wildlife Samples

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 445 ◽  
Author(s):  
Adeline Seah ◽  
Marisa C.W. Lim ◽  
Denise McAloose ◽  
Stefan Prost ◽  
Tracie A. Seimon
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Wildlife Conservation ◽  
Sequence Similarity ◽  
Dna Barcode ◽  
Bioinformatics Pipeline ◽  
Tissue Samples ◽  
Consensus Sequences ◽  
Sequencing Errors ◽  
Fresh Frozen

The ability to sequence a variety of wildlife samples with portable, field-friendly equipment will have significant impacts on wildlife conservation and health applications. However, the only currently available field-friendly DNA sequencer, the MinION by Oxford Nanopore Technologies, has a high error rate compared to standard laboratory-based sequencing platforms and has not been systematically validated for DNA barcoding accuracy for preserved and non-invasively collected tissue samples. We tested whether various wildlife sample types, field-friendly methods, and our clustering-based bioinformatics pipeline, SAIGA, can be used to generate consistent and accurate consensus sequences for species identification. Here, we systematically evaluate variation in cytochrome b sequences amplified from scat, hair, feather, fresh frozen liver, and formalin-fixed paraffin-embedded (FFPE) liver. Each sample was processed by three DNA extraction protocols. For all sample types tested, the MinION consensus sequences matched the Sanger references with 99.29%–100% sequence similarity, even for samples that were difficult to amplify, such as scat and FFPE tissue extracted with Chelex resin. Sequencing errors occurred primarily in homopolymer regions, as identified in previous MinION studies. We demonstrate that it is possible to generate accurate DNA barcode sequences from preserved and non-invasively collected wildlife samples using portable MinION sequencing, creating more opportunities to apply portable sequencing technology for species identification.

On the use of ultrasonic detectors for bat species identification and the calibration of QMC Mini Bat Detectors

1984 ◽  
Vol 62 (12) ◽  
pp. 2677-2679 ◽  
Author(s):  
Donald W. Thomas ◽  
Stephen D. West
Keyword(s):  
Species Identification ◽  
Species Level ◽  
Ultrasonic Detection ◽  
Echolocation Call ◽  
Echolocation Calls ◽  
Reliable Identification ◽  
Level Identification

Several ultrasonic detection and analysis systems are currently used to provide information on the echolocation calls of bats, in many cases permitting species-level identification. This note briefly describes these systems and alerts potential users of the inaccuracies of the simplest device, the superheterodyne QMC Mini Bat Detector. Without adequate calibration, the error in this latter detector is such that reliable identification of bats by echolocation call characteristics cannot be achieved.

scholarly journals Assessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hoi-Yan Wu ◽  
Kwun-Tin Chan ◽  
Grace Wing-Chiu But ◽  
Pang-Chui Shaw
Keyword(s):  
Species Identification ◽  
Dna Sequences ◽  
Species Level ◽  
Research Groups ◽  
Voucher Specimen ◽  
Botanical Species ◽  
Promising Tool ◽  
Chloroplast Genomes ◽  
Level Identification ◽  
Annotation Quality

AbstractDNA-based method is a promising tool in species identification and is widely used in various fields. DNA barcoding method has already been included in different pharmacopoeias for identification of medicinal materials or botanicals. Accuracy and validity of DNA-based methods rely on the accuracy and taxonomic reliability of the DNA sequences in the database to be compared against. Here we evaluated the annotation quality and taxonomic reliability of selected barcode loci (rbcL, matK, psbA-trnH, trnL-trnF and ITS) of 41 medicinal Dendrobium species downloaded from GenBank. Annotations of most accessions are incomplete. Only 53.06% of the 2041 accessions downloaded contain a reference to a voucher specimen. Only 31.60% and 4.8% of the entries are annotated with country of origin and collector or assessor, respectively. Taxonomic reliability of the sequences was evaluated by a Megablast search based on similarity to sequences submitted by other research groups. A small number of sequences (211, 7.14%) was regarded as highly doubted. Moreover, 10 out of 60 complete chloroplast genomes contain highly doubted sequences. Our findings suggest that sequences of GenBank should be used with caution for species-level identification. The scientific community should provide more important information regarding identity and traceability of the sample when they deposit sequences to public databases.

scholarly journals DNA barcoding British Euphrasia reveals deeply divergent polyploids but lack of species-level resolution

2017 ◽  
Author(s):  
Xumei Wang ◽  
Galina Gussarova ◽  
Markus Ruhsam ◽  
Natasha de Vere ◽  
Chris Metherell ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Dna Barcoding ◽  
Species Identification ◽  
Dna Barcode ◽  
Species Level ◽  
Ecological Processes ◽  
Evolutionary Patterns ◽  
Ploidy Levels ◽  
Self Fertilization ◽  
Phylogenetic Framework

ABSTRACTBackground and aimsDNA barcoding is emerging as a useful tool not only for species identification but for studying evolutionary and ecological processes. Although plant DNA barcodes do not always provide species-level resolution, the generation of large DNA barcode datasets can provide insights into the mechanisms underlying the generation of species diversity. Here, we use DNA barcoding to study evolutionary processes in taxonomically complex British Euphrasia, a group with multiple ploidy levels, frequent self- fertilization, young species divergence and widespread hybridisation.MethodsWe sequenced the core plant barcoding loci, supplemented with additional nuclear and plastid loci, in representatives of all 19 British Euphrasia species. We analyse these data in a population genetic and phylogenetic framework. We then date the divergence of haplotypes in a global Euphrasia dataset using a time-calibrated Bayesian approach implemented in BEAST.Key resultsNo Euphrasia species has a consistent diagnostic haplotype. Instead, haplotypes are either widespread across species, or are population specific. Nuclear genetic variation is strongly partitioned by ploidy levels, with diploid and tetraploid British Euphrasia possessing deeply divergent ITS haplotypes (DXY = 5.1%), with haplotype divergence corresponding to the late Miocene. In contrast, plastid data show no clear division by ploidy, and instead reveal weakly supported geographic patterns.ConclusionsUsing standard DNA barcoding loci for species identification in Euphrasia will be unsuccessful. However, these loci provide key insights into the maintenance of genetic variation, with divergence of diploids and tetraploids suggesting that ploidy differences act as a barrier to gene exchange in British Euphrasia, with rampant hybridisation within ploidy levels. The scarcity of shared diploid-tetraploid ITS haplotypes supports the polyploids being allotetraploid in origin. Overall, these results show that even when lacking species-level resolution, DNA barcoding can reveal insightful evolutionary patterns in taxonomically complex genera.

DNA barcoding for identification of the endangered species Aquilaria sinensis: comparison of data from heated or aged wood samples

Holzforschung ◽  
2014 ◽  
Vol 68 (4) ◽  
pp. 487-494 ◽  
Author(s):  
Lichao Jiao ◽  
Yafang Yin ◽  
Yeming Cheng ◽  
Xiaomei Jiang
Keyword(s):  
Dna Barcoding ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Species Level ◽  
Related Genus ◽  
Illegal Logging ◽  
Aquilaria Sinensis ◽  
Long Period ◽  
High Temperature Drying ◽  
Barcoding Technology

Abstract Aquilaria sinensis (Lour.) Gilg is an evergreen tree and produces agarwood used for incense and as a uniquely precious medicine. It is in danger of disappearing due to illegal logging and its identification and protection is crucial. However, it is difficult or impossible to distinguish A. sinensis from other species of the genus Aquilaria Lam. and its closely related genus Gyrinops Gaertn. based on wood anatomical characteristics. Probably, DNA barcoding technology might provide an improvement in species identification. In this study, wood samples were tested, which were submitted to high-temperature drying and were stored for a long period in a xylarium. The factors should be identified that hinder the efficiency of wood DNA extraction from this species. The results indicate that the DNA from the wood tissues could be successfully amplified, apart from some DNA regions from the heartwood of the dried samples and the xylarium samples. The DNA sequences from the wood tissues mostly matched with the sequences of A. sinensis deposited in the GenBank. Moreover, analyses of phylogenetic trees based on trnL-trnF and ITS1 regions indicated that the wood tissues in the tests clustered together with the A. sinensis species from the GenBank, with bootstrap values of 74% and 94%, respectively. Consequently, it is feasible to identify A. sinensis wood on a species level based on the DNA barcoding technology.

scholarly journals Evaluating multi-locus phylogenies for species boundaries determination in the genusDiaporthe

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3120 ◽  
Author(s):  
Liliana Santos ◽  
Artur Alves ◽  
Rui Alves
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Open Problem ◽  
Phylogenetic Trees ◽  
Species Boundaries ◽  
Species Separation ◽  
Phytosanitary Measures ◽  
Optimal Set ◽  
Disease Understanding

BackgroundSpecies identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genusDiaporthe. AccurateDiaporthespecies separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species identification is still an open problem.MethodsHere we addressed that problem by identifying five loci that have been sequenced in 142Diaportheisolates representing 96 species:TEF1,TUB,CAL,HISand ITS. We then used every possible combination of those loci to build, analyse, and compare phylogenetic trees.ResultsAs expected, species separation is better when all five loci are simultaneously used to build the phylogeny of the isolates. However, removing the ITS locus has little effect on reconstructed phylogenies, identifying theTEF1-TUB-CAL-HIS4-loci tree as almost equivalent to the 5-loci tree. We further identify the best 3-loci, 2-loci, and 1-locus trees that should be used for species separation in the genus.DiscussionOur results question the current use of the ITS locus for DNA barcoding in the genusDiaportheand suggest thatTEF1might be a better choice if one locus barcoding needs to be done.

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