Virtually all empirical ecological studies require species identification during data collection. DNA metabarcoding refers to the automated identification of multiple species from a single bulk ...sample containing entire organisms or from a single environmental sample containing degraded DNA (soil, water, faeces, etc.). It can be implemented for both modern and ancient environmental samples. The availability of next‐generation sequencing platforms and the ecologists’ need for high‐throughput taxon identification have facilitated the emergence of DNA metabarcoding. The potential power of DNA metabarcoding as it is implemented today is limited mainly by its dependency on PCR and by the considerable investment needed to build comprehensive taxonomic reference libraries. Further developments associated with the impressive progress in DNA sequencing will eliminate the currently required DNA amplification step, and comprehensive taxonomic reference libraries composed of whole organellar genomes and repetitive ribosomal nuclear DNA can be built based on the well‐curated DNA extract collections maintained by standardized barcoding initiatives. The near‐term future of DNA metabarcoding has an enormous potential to boost data acquisition in biodiversity research.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
The neotropical orchid genus Telipogon Kunth was established in 1815 and currently comprises more than 250 species. Representatives of this genus are generally epiphytic plants lacking pseudobulbs. ...The stem is either abbreviated or elongate and the leaves are conduplicate. Flowers are usually resupinate with small sepals and petals similar to the lip, but sometimes different. The gynostemium is covered by stiff or soft hairs. This monograph is a presentation of taxonomic diversity of the orchid genus Telipogon in Colombia and adjecent areas. Morphological characteristics of a total of 96 Telipogon species from Colombia are presented together with information about over 50 taxa found in neighboring countries. A brief discussion of an additional seven taxa described in Colombia, but insufficiently characterized, is also given. Illustrations of perianth segments of almost all national genus representatives are provided. Twenty-five species are described in this paper for the first time – Telipogon alinae, T. bicallosus, T. bugalagrandei, T. castanedoi, T. chimborazoensis, T. cocuyensis, T. cuatrecasasii, T. fassetti, T. fernandezii, T. flabellatus, T. garayi, T. hirsutus, T. huertasii, T. idroboi, T. killipi, T. kraenzlinianus, T. orozcoi, T. pasquillensis, T. schlimii, T. spathipetala, T. sumapazensis, T. tolimensis, T. trianae, T. trilabiatus, and T. verrucosus. Several morphologically consistent groups are distinguished to facilitate identification of Telipogon representatives. Keys for determination of species within each group are provided.
Dendrobium williamsonii and Dendrobium cariniferum (Orchidaceae) are endangered perennial herbs, and they are very similar in morphology. Chloroplast genome sequencing technology provides a powerful ...tool for molecular analysis to get more infomation for phylogenetic analysis and identification of Dendrobium species. In this study, the complete chloroplast genomes of Dendrobium williamsonii and Dendrobium cariniferum were assembled and characterized using Illumina NovaSeq 6000. The genome sizes are 159 695 and 159 479 bp, including pairs of inverted repeats (27 055 and 27 024 bp) each separated by small single-copy regions (18 451 and 18 488 bp) and large single-copy regions (87 134 and 86 943 bp). The chloroplast genome overall GC content was 37.11% and 37.13%, respectively. Each chloroplast genome encoded the same number (147) of genes, including 88 protein-coding genes, 51 tRNA genes, and 8 rRNA genes. Comparative analysis of chloroplast genomes revealed the high degree of divergence included accD-psaL and ycf4 -cemA. The phylogenetic tree showed the two Dendrobium species formed only one small clade. A pair of primers that could effectively identify the two Dendrobium species were also screened. This study will provide theoretical basis for species identification, genetic breeding, and evolution of Dendrobium.
The aim of this study was to assess potential candidate gene regions and corresponding universal primer pairs as secondary DNA barcodes for the fungal kingdom, additional to ITS rDNA as primary ...barcode. Amplification efficiencies of 14 (partially) universal primer pairs targeting eight
genetic markers were tested across > 1 500 species (1 931 strains or specimens) and the outcomes of almost twenty thousand (19 577) polymerase chain reactions were evaluated. We tested several well-known primer pairs that amplify: i) sections of the nuclear ribosomal RNA gene large subunit
(D1-D2 domains of 26/28S); ii) the complete internal transcribed spacer region (ITS1/2); iii) partial β-tubulin II (TUB2); iv) γ-actin (ACT); v) translation elongation factor 1-α (TEF1α); and vi) the second largest subunit of RNA-polymerase
II (partial RPB2, section 5-6). Their PCR efficiencies were compared with novel candidate primers corresponding to: i) the fungal-specific translation elongation factor 3 (TEF3); ii) a small ribosomal protein necessary for t-RNA docking; iii) the 60S L10 (L1) RP;
iv) DNA topoisomerase I (TOPI); v) phosphoglycerate kinase (PGK); vi) hypothetical protein LNS2; and vii) alternative sections of TEF1α. Results showed that several gene sections are accessible to universal primers (or primers universal for phyla) yielding
a single PCR-product. Barcode gap and multi-dimensional scaling analyses revealed that some of the tested candidate markers have universal properties providing adequate infra- and inter-specific variation that make them attractive barcodes for species identification. Among these gene sections,
a novel high fidelity primer pair for TEF1α, already widely used as a phylogenetic marker in mycology, has potential as a supplementary DNA barcode with superior resolution to ITS. Both TOPI and PGK show promise for the Ascomycota, while TOPI and LNS2
are attractive for the Pucciniomycotina, for which universal primers for ribosomal subunits often fail.
Summary
Species identification via DNA barcodes has recently become an important and routine task in many biodiversity projects using DNA sequence data.
Here, we present BarcodingR, an integrated ...software package that provides a comprehensive implementation of species identification methods, including artificial intelligence, fuzzy‐set, Bayesian and kmer‐based methods, that are not readily available in other packages.
BarcodingR additionally provides new functions for barcode evaluation, barcoding gap analysis, delimitation comparison analysis, species membership analysis and consensus identification.
Comparison with other barcoding methods using 11 empirical data sets indicates that on average, FZKMER (implemented in BarcodingR) and one extant barcoding method BRONX outperform all other methods examined in this study. Two other methods, BP and FZ (both implemented in BarcodingR), present similar performance as SVM and BLOG, respectively, and all display better performance than that of Jrip.
The software of BarcodingR is open source under GNU General Public License and freely available for all major operating systems.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Forensic point of origin testing is a key tool in identifying the provenance of a sample, whether it be for human remains, the food industry, or illegal wildlife trade. A variety of techniques – ...morphological, genetic and isotopic – have been developed to provide resolution on the origin of an individual or sample. Herein, we employed all three approaches to identify a reported case of food contamination. A consumer in New Jersey, USA reported finding a rodent in a beer can, which was bottled in Dallas-Fort Worth (DFW), Texas, USA. Photographs of the organism as well as biological material (muscle and hair) were evaluated to determine the species, location and ultimate source of the contamination. The rodent removed from the can was surprisingly intact and was identified belonging to the family Cricetidae and subfamily Neotominae, and likely of the genus Peromyscus spp. Sequencing of the COIII mitochondrial gene confirmed a species identification of P. leucopus. The analysis of δ2H and δ18O and subsequent probability assignment showed little support that the sample did not originate from the bottling facility (PDFW = 0.02 ± 0.02) but very high support that the mouse originated from New Jersey (PNew Jersey = 0.98 ± 0.02). Together, these results provide clear and consistent results that the mouse did not enter the food system at the bottling facility. This complimentary approach of morphological and molecular identification as well as point-of-origin assignment using stable isotope analysis yielded a highly cost-effective and probabilistic approach to assign origin of species that can be used by future forensic scientists.
•Point of origin testing is a key in wildlife forensics to determine the provenance of a sample.•Using morphological, genetic and isotopic analyses we identified the source of reported food contamination in a beer can.•We found that the mouse did not enter the food system at the bottling facility but from where the consumer was located.•This complimentary approach is cost-effective in assigning the origin of species an for future forensic scientists to use.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The precious Malagasy rosewood species of the genus Dalbergia have been listed in Appendix II of CITES due to illegal logging and timber trade. Accurate identification and proper delimitation are of ...paramount importance for endangered species regulated by CITES. One of the most accurate methods of identifying precious woods is DNA barcoding which is a technique for rapid and accurate species identification based on a short DNA sequence or a few DNA regions. Recent studies have shown that the ITS barcode can identify Malagasy Dalbergia species, but the number of species has been limited. In this research study, a total of 136 nuclear ribosomal internal transcribed spacer (nrITS) DNA sequences representing 41 species of Malagasy Dalbergia were used to assess the effectiveness of the ITS barcode in species identification. Each sequence was evaluated by genetic distance and tree-based methods. Using clustering analyses, estimating genetic distances, and comparing sequences of 136 samples, we were able to distinguish species. The interspecific distance was greater than the intraspecific distance, but no barcoding gap was observed. It was found that ITS has a very high discriminatory power for Malagasy Dalbergia species using both NJ and TaxonDNA methods. Considering the "Best Match" and "Best Close Match" analyses, the discrimination powers of ITS were 98.54% and 93.40%, respectively. Our research indicates that the use of ITS as a barcode enables the identification of Malagasy Dalbergia species and contributes to completing the reference library for controlling the trade in precious woods. These results are essential to ensure effective enforcement of regulations and promote the long-term conservation of these species.
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•Accurate identification and proper delimitation are essential for Dalbergia species which are regulated by CITES.•The use of ITS as a molecular barcode has enabled the identification of Malagasy Dalbergia species with high confidence.•The barcode reference library could be used as reliable identification tool for controlling these Madagascar's precious wood.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
This study evaluated MALDI-TOF mass spectrometry and a custom reference spectra expanded database for the identification of bovine-associated coagulase-negative staphylococci (CNS). A total of 861 ...CNS isolates were used in the study, covering 21 different CNS species. The majority of the isolates were previously identified by rpoB gene sequencing (n = 804) and the remainder were identified by sequencing of hsp60 (n = 56) and tuf (n = 1). The genotypic identification was considered the gold standard identification. Using a direct transfer protocol and the existing commercial database, MALDI-TOF mass spectrometry showed a typeability of 96.5% (831/861) and an accuracy of 99.2% (824/831). Using a custom reference spectra expanded database, which included an additional 13 in-house created reference spectra, isolates were identified by MALDI-TOF mass spectrometry with 99.2% (854/861) typeability and 99.4% (849/854) accuracy. Overall, MALDI-TOF mass spectrometry using the direct transfer method was shown to be a highly reliable tool for the identification of bovine-associated CNS.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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