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65 results for “Plant DNA barcoding”
Data from: Using a comprehensive DNA barcode library to detect novel egg and larval host plant associations in a Cephaloleia Rolled-leaf Beetle (Coleoptera: Chrysomelidae)
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Data from: Determining plant – leaf miner – parasitoid interactions: a DNA barcoding approach
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Data from: Seeing is believing? comparing plant-herbivore networks constructed by field co-occurrence and DNA barcoding methods for gaining insights into network structures
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Data from: Plant DNA-barcode library and community phylogeny for a semi-arid East African savanna
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Data from: Plant DNA barcodes and the influence of gene flow
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Data from: Applying plant DNA barcodes to identify species of Parnassia (Parnassiaceae)
DNA barcoding is a technique to identity species by using standardized DNA sequences. In the present study, a total of 105 samples, representing 30 Parnassia species were collected to test the effectiveness of four proposed DNA barcodes (rbcL, matK, trnH-psbA and ITS) for species identification. Our results demonstrated that all four candidate DNA markers have a maximum level of primer universality and sequencing success. As single DNA marker, ITS region provided the highest species resolution with 86.7%, followed by trnH-psbA with 73.3%. The combination of the core barcode, matK + rbcL, gave the lowest species identification success (63.3%) among any combination of multiple markers, and was found unsuitable as DNA barcode for Parnassia. The combination of ITS + trnH-psbA achieved the highest species discrimination with 90.0% resolution (27 out of 30 sampled species), equal to the four-marker combination; ITS combined with matK, rbcL or matK + rbcL did not improve species discrimination. Therefore, matK and rbcL should not be used as DNA barcode for species identification of Parnassia. Based on the overall performance, the combination of ITS + trnH-psbA, is proposed as the most suitable DNA barcode for identifying Parnassia species. DNA barcoding is a useful technique to providing a reliable and effective mean for the discrimination of Parnassia species, and in combination with morphology based taxonomy can be a robust approach for tackling taxonomically complex groups. In the light of our findings, we found among the three species not identified a possible cryptic speciation event in Parnassia.
Data from: Accelerating plant DNA barcode reference library construction using herbarium specimens: improved experimental techniques
A well-covered reference library is crucial for successful identification of species by DNA barcoding. The biggest difficulty in building such a reference library is the lack of materials of organisms. Herbarium collections are potentially an enormous resource of materials. In this study, we demonstrate that it is likely to build such reference libraries using the reconstructed (self-primed PCR amplified) DNA from the herbarium specimens. We used 179 rosaceous specimens to test the effects of DNA reconstruction, 420 randomly sampled specimens to estimate the usable percentage and another 223 specimens of true cherries (Cerasus, Rosaceae) to test the coverage of usable specimens to the species. The barcode rbcLb (the central four-sevenths of rbcL gene) and matK was each amplified in two halves and sequenced on Roche GS 454 FLX+. DNA from the herbarium specimens was typically shorter than 300 bp. DNA reconstruction enabled amplification fragments of 400–500 bp without bringing or inducing any sequence errors. About one-third of specimens in the national herbarium of China (PE) were proven usable after DNA reconstruction. The specimens in PE cover all Chinese true cherry species and 91.5% of vascular species listed in Flora of China. It is very possible to build well-covered reference libraries for DNA barcoding of vascular species in China. As exemplified in this study, DNA reconstruction and DNA-labelled next-generation sequencing can accelerate the construction of local reference libraries. By putting the local reference libraries together, a global library for DNA barcoding becomes closer to reality.
Figure 2 from: Mankga L, Kowiyou Y, Moteetee A, Daru B, van der Bank M (2013) Efficacy of the core DNA barcodes in identifying processed and poorly conserved plant materials commonly used in South African traditional medicine. ZooKeys 365: 215-233. https://doi.org/10.3897/zookeys.365.5730
Figure 2 - Evaluation of barcode gaps in matK, rbcLa and rbcLa + matK for commonly used medicinal plants of South Africa. A Boxplots indicate the genetic variation between interspecific distance and intraspecific distance; the boxplots clearly shows significant differences between inter- and intraspecific distances for all gene regions tested (P < 0.001; see text) B Lineplot of the barcode gap for the commonly used plants in South African medicine. For each gene region, the grey lines correspond to the furthest intraspecific distance (bottom of line value), and the closest interspecific distance (top of line value). The red lines show where this relationship is reversed, i.e. cases where there is no barcode gap.
Figure 1 from: Mankga L, Kowiyou Y, Moteetee A, Daru B, van der Bank M (2013) Efficacy of the core DNA barcodes in identifying processed and poorly conserved plant materials commonly used in South African traditional medicine. ZooKeys 365: 215-233. https://doi.org/10.3897/zookeys.365.5730
Figure 1 - Examples ofmedicinal herbs bought at Faraday muthi market in Johannesburg A different medicinal herbs in bags B Seeds of Entada rheedii (tindili) C mixed herbs (fembo) D A twig of Adenia gummifera (mphinde umshaye) E Barks of Vachellia sp. (umkhanya-kute) F Bulb of Boophane disticha (umqotho) G mixed herbs H Myrothamnus flabellifolius (vuka) I Barks of Vachellia sp. (umkhanya-kute) J Sarcostemma viminale (ube nam) K Plant of Clivia sp. (mayime) L Stangeria eriopus (imfingo) M mixed herbs (isihlalakahle) N Tuber (umbonsi) O Helichrysum sp. (impepo) and P Twigs of Synadenium cupulare (umdletshane). Names in brackets are vernacular names in isiZulu.
DNA barcoding of native Caucasus herbal plants: potentials and limitations in complex groups and implications for phylogeographic patterns
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Data from: Discriminating plants using the DNA barcode rbcLb: an appraisal based on a large data set
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Data from: Applying plant DNA barcodes to identify species of Parnassia (Parnassiaceae)
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Data from: Accelerating plant DNA barcode reference library construction using herbarium specimens: improved experimental techniques
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iBOL DNA barcode data for plants
<p>International Barcode of Life project (iBOL) Data Packages for Plants, releases 2.00-6.00</p>
Data from: DNA barcoding of invasive plants in China: a resource for identifying invasive plants
Invasive plants have aroused attention globally for causing ecological damage and having a negative impact on the economy and human health. However, it can be extremely challenging to rapidly and accurately identify invasive plants based on morphology because they are an assemblage of many different families and many plant materials lack sufficient diagnostic characteristics during border inspections. It is therefore urgent to evaluate candidate loci and build a reliable genetic library to prevent invasive plants from entering China. In this study, five common single markers (ITS, ITS2, matK, rbcL and trnH-psbA) were evaluated using 634 species (including 469 invasive plant species in China, 10 new records to China, 16 potentially invasive plant species around the world but not introduced into China yet and 139 plant species native to China) based on three different methods. Our results indicated that ITS2 displayed largest intra- and interspecific divergence (1.72% and 91.46%). Based on NJ tree method, ITS2, ITS, matK, rbcL and trnH-psbA provided 76.84%, 76.5%, 63.21%, 52.86% and 50.68% discrimination rates, respectively. The combination of ITS+matK performed best and provided 91.03% discriminatory power, followed by ITS2+matK (85.78%). For identifying unknown individuals, ITS+matK had 100% correct identification rate based on our database, followed by ITS/ITS2 (both 93.33%) and ITS2+matK (91.67%). Thus, we propose ITS/ITS2+matK as the most suitable barcode for invasive plants in China. This study also demonstrated that DNA barcoding is an efficient tool for identifying invasive species.
Figure 3 from: Mankga L, Kowiyou Y, Moteetee A, Daru B, van der Bank M (2013) Efficacy of the core DNA barcodes in identifying processed and poorly conserved plant materials commonly used in South African traditional medicine. ZooKeys 365: 215-233. https://doi.org/10.3897/zookeys.365.5730
Figure 3 - Continued.
Data from: DNA barcoding of invasive plants in China: a resource for identifying invasive plants
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FIGURES 73–77 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 73–77. Immature stages of South African Gracillariidae. 73, Amblyptila cynanchi, mines on Cynanchum obtusifolium (Asclepiadaceae), Western Cape, S. Mecenero leg. 74, Telamoptilia cordati sp. nov., mine on Syzygium cordatum (Myrtaceae), Limpopo Hoedspruit, A. & I. Sharp leg. 75, Leucocercops dasmophora, mine on Parinari capensis, (Chrysobalanaceae), Gauteng, Tshwane, A. Sharp leg. 76, Telamoptilia cordati sp. nov., larva on Syzygium cordatum (Myrtaceae), Limpopo Hoedspruit, A. & I. Sharp leg. 77, Leucocercops curatellifoliae sp. nov., larva on Parinari curatellifolia, Limpopo, Hoedspruit, A. & I. Sharp leg.
FIGURES 89–93 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 89–93. Habitats of Afrotropical Gracillariidae species. 89, Casketts farm, Limpopo, in spring. 90, Ian Sharp collecting leaf mines of the new species Phyllocnistis allisonae on Protea rubropilosa leaves at Mariepskop in the northern Drakensberg mountain range. 91, Casketts farm, Limpopo, in summer. 92, Mariepskop, type locality of Phyllocnistis allisonae. 93, Tshwane, the collecting area is situated in the Northern part of the Gauteng province at an altitude of about 1200 m.
FIGURES 52–55 in Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species
FIGURES 52–55. Male genitalia of South African Gracillariidae. 52-54, Phyllocnistis magalismontani sp. nov., holotype: 52, phallus (175 μm) (ae: aedeagus; an; anellus; be: bulbus ejaculatorius; de: ductus ejaculatorius; ma: manica; pb: phallobase; ve: vesica); 53, ventral view (175 μm); 54, segments VII and VIII in ventral view (190 μm); 55, Telamoptilia sp.: ventral view, phallus not visible, scale not available.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.