scholarly journals DNA barcode data accurately assign higher spider taxa

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2201 ◽  
Author(s):  
Jonathan A. Coddington ◽  
Ingi Agnarsson ◽  
Ren-Chung Cheng ◽  
Klemen Čandek ◽  
Amy Driskell ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Accurate Method ◽  
Reference Database ◽  
Sequencing Errors ◽  
Sequence Identity ◽  
Percent Sequence Identity ◽  
Near Term ◽  
Accuracy Of Results ◽  
Global Inventory

The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75–100%). Accurate assignment of higher taxa (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values >95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of the underlying database impacts accuracy of results; many outliers in our dataset could be attributed to taxonomic and/or sequencing errors in BOLD and GenBank. It seems that an accurate and complete reference library of families and genera of lifecouldprovide accurate higher level taxonomic identifications cheaply and accessibly, within years rather than decades.

scholarly journals DNA barcode data accurately identify higher taxa

2016 ◽  
Author(s):  
Jonathan A Coddington ◽  
Ingi Agnarsson ◽  
Ren-Chung Cheng ◽  
Klemen Čandek ◽  
Amy Driskell ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Accurate Method ◽  
Reference Database ◽  
Accurate Identification ◽  
Sequencing Errors ◽  
Sequence Identity ◽  
Percent Sequence Identity ◽  
Near Term ◽  
Accuracy Of Results

The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level identifications. We used BLAST queries of each sequence against the entire library and got the top ten hits resulting in 8160 hits. The percent sequence identity was reported from these hits (PIdent, range 75-100%). Accurate identification (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values > 95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all identifications were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of the underlying database impacts accuracy of results; many outliers in our dataset could be attributed to taxonomic and/or sequencing errors in BOLD and GenBank. It seems that an accurate and complete reference library of families and genera of life could provide accurate higher level taxonomic identifications cheaply and accessibly, within years rather than decades.

scholarly journals DNA barcode data accurately identify higher taxa

2016 ◽  
Author(s):  
Jonathan A Coddington ◽  
Ingi Agnarsson ◽  
Ren-Chung Cheng ◽  
Klemen Čandek ◽  
Amy Driskell ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Accurate Method ◽  
Reference Database ◽  
Accurate Identification ◽  
Sequencing Errors ◽  
Sequence Identity ◽  
Percent Sequence Identity ◽  
Near Term ◽  
Accuracy Of Results

The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level identifications. We used BLAST queries of each sequence against the entire library and got the top ten hits resulting in 8160 hits. The percent sequence identity was reported from these hits (PIdent, range 75-100%). Accurate identification (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values > 95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all identifications were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of the underlying database impacts accuracy of results; many outliers in our dataset could be attributed to taxonomic and/or sequencing errors in BOLD and GenBank. It seems that an accurate and complete reference library of families and genera of life could provide accurate higher level taxonomic identifications cheaply and accessibly, within years rather than decades.

scholarly journals Overcoming limitations to environmental DNA studies: A coastal temperate reference sequence database for multiple chloroplast gene regions generated in a single assay.

2021 ◽  
Author(s):  
Nicole Foster ◽  
Kor-jent Dijk ◽  
Ed Biffin ◽  
Jennifer Young ◽  
Vicki Thomson ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Reference Sequence ◽  
Reference Database ◽  
Chloroplast Gene ◽  
Coastal Plants ◽  
Reference Databases ◽  
Targeted Capture ◽  
Comprehensive Reference

A proliferation in environmental DNA (eDNA) research has increased the reliance on reference sequence databases to assign unknown DNA sequences to known taxa. Without comprehensive reference databases, DNA extracted from environmental samples cannot be correctly assigned to taxa, limiting the use of this genetic information to identify organisms in unknown sample mixtures. For animals, standard metabarcoding practices involve amplification of the mitochondrial Cytochrome-c oxidase subunit 1 (CO1) region, which is a universally amplifyable region across majority of animal taxa. This region, however, does not work well as a DNA barcode for plants and fungi, and there is no similar universal single barcode locus that has the same species resolution. Therefore, generating reference sequences has been more difficult and several loci have been suggested to be used in parallel to get to species identification. For this reason, we developed a multi-gene targeted capture approach to generate reference DNA sequences for plant taxa across 20 target chloroplast gene regions in a single assay. We successfully compiled a reference database for 93 temperate coastal plants including seagrasses, mangroves, and saltmarshes/samphire’s. We demonstrate the importance of a comprehensive reference database to prevent species going undetected in eDNA studies. We also investigate how using multiple chloroplast gene regions impacts the ability to discriminate between taxa.

scholarly journals Database establishment for the secondary fungal DNA barcodetranslational elongation factor 1α(TEF1α)

Genome ◽  
2019 ◽  
Vol 62 (3) ◽  
pp. 160-169 ◽  
Author(s):  
Wieland Meyer ◽  
Laszlo Irinyi ◽  
Minh Thuy Vi Hoang ◽  
Vincent Robert ◽  
Dea Garcia-Hermoso ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Fungal Infections ◽  
Dna Barcode ◽  
Elongation Factor ◽  
Its Region ◽  
Reference Sequence ◽  
Diagnostic Tools ◽  
Reference Database ◽  
Elongation Factor 1Α ◽  
Fungal Dna

With new or emerging fungal infections, human and animal fungal pathogens are a growing threat worldwide. Current diagnostic tools are slow, non-specific at the species and subspecies levels, and require specific morphological expertise to accurately identify pathogens from pure cultures. DNA barcodes are easily amplified, universal, short species-specific DNA sequences, which enable rapid identification by comparison with a well-curated reference sequence collection. The primary fungal DNA barcode, ITS region, was introduced in 2012 and is now routinely used in diagnostic laboratories. However, the ITS region only accurately identifies around 75% of all medically relevant fungal species, which has prompted the development of a secondary barcode to increase the resolution power and suitability of DNA barcoding for fungal disease diagnostics. The translational elongation factor 1α (TEF1α) was selected in 2015 as a secondary fungal DNA barcode, but it has not been implemented into practice, due to the absence of a reference database. Here, we have established a quality-controlled reference database for the secondary barcode that together with the ISHAM-ITS database, forms the ISHAM barcode database, available online at http://its.mycologylab.org/ . We encourage the mycology community for active contributions.

scholarly journals Documenting decapod biodiversity in the Caribbean from DNA barcodes generated during field training in taxonomy

2020 ◽  
Vol 8 ◽  
Author(s):  
Dagoberto Venera-Pontón ◽  
Amy Driskell ◽  
Sammy De Grave ◽  
Darryl Felder ◽  
Justin Scioli ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Dna Sequences ◽  
Marine Invertebrates ◽  
Graduate Training ◽  
Dna Barcode ◽  
Reference Database ◽  
Diagnostic Features ◽  
Operational Taxonomic Units ◽  
As Species ◽  
Coi Sequences

DNA barcoding is a useful tool to identify the components of mixed or bulk samples, as well as to determine individuals that lack morphologically diagnostic features. However, the reference database of DNA barcode sequences is particularly sparsely populated for marine invertebrates and for tropical taxa. We used samples collected as part of two field courses, focused on graduate training in taxonomy and systematics, to generate DNA sequences of the barcode fragments of cytochrome c oxidase subunit I (COI) and mitochondrial ribosomal 16S genes for 447 individuals, representing at least 129 morphospecies of decapod crustaceans. COI sequences for 36% (51/140) of the species and 16S sequences for 26% (37/140) of the species were new to GenBank. Automatic Barcode Gap Discovery identified 140 operational taxonomic units (OTUs) which largely coincided with the morphospecies delimitations. Barcode identifications (i.e. matches to identified sequences) were especially useful for OTUs within Synalpheus, a group that is notoriously difficult to identify and rife with cryptic species, a number of which we could not identify to species, based on morphology. Non-concordance between morphospecies and barcode OTUs also occurred in a few cases of suspected cryptic species. As mitochondrial pseudogenes are particularly common in decapods, we investigate the potential for this dataset to include pseudogenes and discuss the utility of these sequences as species identifiers (i.e. barcodes). These results demonstrate that material collected and identified during training activities can provide useful incidental barcode reference samples for under-studied taxa.

scholarly journals Toward a global reference database of COI barcodes for marine zooplankton

2021 ◽  
Vol 168 (6) ◽  
Author(s):  
Ann Bucklin ◽  
Katja T. C. A. Peijnenburg ◽  
Ksenia N. Kosobokova ◽  
Todd D. O’Brien ◽  
Leocadio Blanco-Bercial ◽  
...  
Keyword(s):  
Species Diversity ◽  
Dna Sequences ◽  
Reference Sequence ◽  
Global Ocean ◽  
Reference Database ◽  
Data Repositories ◽  
Marine Zooplankton ◽  
The North ◽  
Coi Sequences ◽  
Taxonomic Groups

AbstractCharacterization of species diversity of zooplankton is key to understanding, assessing, and predicting the function and future of pelagic ecosystems throughout the global ocean. The marine zooplankton assemblage, including only metazoans, is highly diverse and taxonomically complex, with an estimated ~28,000 species of 41 major taxonomic groups. This review provides a comprehensive summary of DNA sequences for the barcode region of mitochondrial cytochrome oxidase I (COI) for identified specimens. The foundation of this summary is the MetaZooGene Barcode Atlas and Database (MZGdb), a new open-access data and metadata portal that is linked to NCBI GenBank and BOLD data repositories. The MZGdb provides enhanced quality control and tools for assembling COI reference sequence databases that are specific to selected taxonomic groups and/or ocean regions, with associated metadata (e.g., collection georeferencing, verification of species identification, molecular protocols), and tools for statistical analysis, mapping, and visualization. To date, over 150,000 COI sequences for ~ 5600 described species of marine metazoan plankton (including holo- and meroplankton) are available via the MZGdb portal. This review uses the MZGdb as a resource for summaries of COI barcode data and metadata for important taxonomic groups of marine zooplankton and selected regions, including the North Atlantic, Arctic, North Pacific, and Southern Oceans. The MZGdb is designed to provide a foundation for analysis of species diversity of marine zooplankton based on DNA barcoding and metabarcoding for assessment of marine ecosystems and rapid detection of the impacts of climate change.

scholarly journals An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes

2021 ◽  
Author(s):  
Thomas K. F. Wong ◽  
Teng Li ◽  
Louis Ranjard ◽  
Steven Wu ◽  
Jeet Sukumaran ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Real Data ◽  
Reference Sequence ◽  
Nucleotide Polymorphisms ◽  
Data Set ◽  
Single Nucleotide ◽  
Short Read ◽  
Pooled Samples ◽  
Haplotype Information

AbstractA current strategy for obtaining haplotype information from several individuals involves short-read sequencing of pooled amplicons, where fragments from each individual is identified by a unique DNA barcode. In this paper, we report a new method to recover the phylogeny of haplotypes from short-read sequences obtained using pooled amplicons from a mixture of individuals, without barcoding. The method, AFPhyloMix, accepts an alignment of the mixture of reads against a reference sequence, obtains the single-nucleotide-polymorphisms (SNP) patterns along the alignment, and constructs the phylogenetic tree according to the SNP patterns. AFPhyloMix adopts a Bayesian model of inference to estimates the phylogeny of the haplotypes and their relative frequencies, given that the number of haplotypes is known. In our simulations, AFPhyloMix achieved at least 80% accuracy at recovering the phylogenies and frequencies of the constituent haplotypes, for mixtures with up to 15 haplotypes. AFPhyloMix also worked well on a real data set of kangaroo mitochondrial DNA sequences.

scholarly journals Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
F. A. Bastiaan von Meijenfeldt ◽  
Ksenia Arkhipova ◽  
Diego D. Cambuy ◽  
Felipe H. Coutinho ◽  
Bas E. Dutilh
Keyword(s):  
Dna Sequences ◽  
De Novo ◽  
Taxonomic Classification ◽  
Classification Method ◽  
Reference Database ◽  
Annotation Tool ◽  
Multiple Signals

Abstract Current-day metagenomics analyses increasingly involve de novo taxonomic classification of long DNA sequences and metagenome-assembled genomes. Here, we show that the conventional best-hit approach often leads to classifications that are too specific, especially when the sequences represent novel deep lineages. We present a classification method that integrates multiple signals to classify sequences (Contig Annotation Tool, CAT) and metagenome-assembled genomes (Bin Annotation Tool, BAT). Classifications are automatically made at low taxonomic ranks if closely related organisms are present in the reference database and at higher ranks otherwise. The result is a high classification precision even for sequences from considerably unknown organisms.

Characterization of equine cDNA sequences for αS1-, β- and κ-casein

2003 ◽  
Vol 70 (1) ◽  
pp. 29-36 ◽  
Author(s):  
Tina Lenasi ◽  
Irena Rogelj ◽  
Peter Dovc
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Genomic Region ◽  
Interspecies Comparison ◽  
Cryptic Exon ◽  
Conserved Sequence ◽  
Cdna Sequences ◽  
Sequence Identity ◽  
Lactating Mammary Gland

Here we report the entire cDNA sequences for equine αS1-, β- and κ-casein. Based on interspecies comparison, nine exons were found in equine β-casein and five in κ-casein. In equine αS1-casein cDNA the exon 5 was missing, which resulted in the total of 18 exons instead of 19 theoretically possible exons in αS1-casein cDNA. Comparison of DNA sequences representing exon 5 in other species with corresponding equine genomic region confirmed the presence of cryptic exon in horse genomic DNA. Equine αS1-casein mRNA was present in three forms in the lactating mammary gland and we showed that the two shorter forms were produced by skipping either the exon 8 or exon 15. In horse, as in some other mammals, β- and κ-casein are considerably more conserved (sequence identity 53% to 59% and 57% to 67%, respectively) than αS1-casein which appears as the most variable casein among species (sequence identity 40% to 54%). Interestingly, horse caseins resemble human much more than bovine caseins which may also explain the high dietetic value of mares' milk.

scholarly journals A Common Virulence Plasmid in Biotype 2 Vibrio vulnificus and Its Dissemination Aided by a Conjugal Plasmid

2007 ◽  
Vol 190 (5) ◽  
pp. 1638-1648 ◽  
Author(s):  
Chung-Te Lee ◽  
Carmen Amaro ◽  
Keh-Ming Wu ◽  
Esmeralda Valiente ◽  
Yi-Feng Chang ◽  
...  
Keyword(s):  
Animal Model ◽  
Human Serum ◽  
Dna Sequences ◽  
Vibrio Vulnificus ◽  
Bacterial Species ◽  
Virulence Plasmid ◽  
Virulence Plasmids ◽  
Sequence Identity ◽  
Loss Of Resistance ◽  
Novel Protein

ABSTRACT Strains of Vibrio vulnificus, a marine bacterial species pathogenic for humans and eels, are divided into three biotypes, and those virulent for eels are classified as biotype 2. All biotype 2 strains possess one or more plasmids, which have been shown to harbor the biotype 2-specific DNA sequences. In this study we determined the DNA sequences of three biotype 2 plasmids: pR99 (68.4 kbp) in strain CECT4999 and pC4602-1 (56.6 kb) and pC4602-2 (66.9 kb) in strain CECT4602. Plasmid pC4602-2 showed 92% sequence identity with pR99. Curing of pR99 from strain CECT4999 resulted in loss of resistance to eel serum and virulence for eels but had no effect on the virulence for mice, an animal model, and resistance to human serum. Plasmids pC4602-2 and pR99 could be transferred to the plasmid-cured strain by conjugation in the presence of pC4602-1, which was self-transmissible, and acquisition of pC4602-2 restored the virulence of the cured strain for eels. Therefore, both pR99 and pC4602-2 were virulence plasmids for eels but not mice. A gene in pR99, which encoded a novel protein and had an equivalent in pC4602-2, was further shown to be essential, but not sufficient, for the resistance to eel serum and virulence for eels. There was evidence showing that pC4602-2 may form a cointegrate with pC4602-1. An investigation of six other biotype 2 strains for the presence of various plasmid markers revealed that they all harbored the virulence plasmid and four of them possessed the conjugal plasmid in addition.

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