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43 results for “Internal transcribed spacer (ITS)”
Data from: Utility of internally transcribed spacer region of rDNA (ITS) and β-tubulin gene sequences to infer genetic diversity and migration patterns of Colletotrichum truncatum infecting Capsicum spp.
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Data from: Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio
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Extensive intragenomic variation in the internal transcribed spacer (ITS) region of fungi
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nrDNA internal and external transcribed spacer sequences for investigating the systematics of Dieteria
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Figure 4 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 4 Heatmap using Pearson's correlation coefficient between the OTUs generated from the ITS2 and LSU D1-D2 metabarcodes and the analysed beetle species and forest types. Rectangles indicate the strength of association between an OTU and beetle/forest (strongly negative, grey, to strongly positive, red). Fungal OTUs (on the horizontal axis) were classified to genus or species level where possible; they are shown in random order and cannot be linked taxonomically between both markers.
Supplementary material 1 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure S1. Length distribution of the ITS (grey) and LSU (orange) OTUs
Figure 7 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 7 Closed reference clustering of OTUs and phylogenetic trees at different thresholds A results from the closed reference clustering of OTUs at each clustering threshold against composite LSU/ITS2 reference sequences. LSU matches in green, ITS2 matches in blue, linked matches (for which both an ITS2 and LSUOTU were matched to a reference sequence of the same species) in yellow. Underlined taxa indicate new matches at each clustering threshold B phylogenetic tree of LSUOTUs under increasingly stringent clustering thresholds, with arrows marking newly added taxa as threshold values are increased.
Figure 3 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 3 NMDS ordination plot of all specimens sampled with ITS2 and LSU D1-D2, based on the fungal community composition of the individual beetles. Shapes represent forest types and colours represent beetle species. Stress for this graph fell within acceptable ranges (<0.2).
Figure 2 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 2 Top panel: The proportion of OTUs identified as members of a fungal Class determined by the ITS2 and LSU D1-D2 regions. For the spruce forest, only nine X. germanus and four X. saxesenii specimens were retained after rarefaction. Lower panel: The number of fungal OTUs per beetle specimen, separate for each beetle species and forest type, for ITS2 and LSU.
Figure 6 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 6 Order-level trees and splitting/lumping of OTUs at clustering A order-level ML trees with mixed OTU clustering thresholds (99% LSU D1-D2, 98% ITS2). Full tree in supplementary materials. Leotia lubrica was used as the outgroup (not pictured). Brackets indicate reference taxa linked to an ITS2 and/or LSUOTU, with colours indicating potential splitting/lumping (blue, splitting; green, lumping; orange, 1:1) B diagram illustrating the effects of splitting and lumping of an OTU in the fungal community on the tree inference. Four hypothetical species (A to D) in a community are treated under uniform clustering thresholds for ITS2 and LSU. This may result in deviation from the 1:1 ratio of OTUs expected if each species in the community is represented equally by both markers (species A). Threshold values may be too high, resulting in splitting of species into multiples OTUs, which is likely to affect the more variable ITS2 region (species B) or may be too low, resulting in lumping of multiple species into a single OTU, likely to affect the conservative LSU region (species C and D).
Supplementary material 4 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure S4. Binding site of ITS86 primer showing mismatched base pairs in Ophiostomatales
Figure 1 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 1 The proportion of fungi classified with IDTAXA, Protax-fungi and RDP from class to species level. "All" refers to the proportion of OTUs for which the three classifiers agreed in their classification.
Supplementary material 7 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Table S3. Number of OTUs assigned to each order based on RDP Bayesian classifier
Figure 5 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 5 ML tree of Sordariomycetes constructed from the reference sequence alignments and OTUs for both markers (clustering thresholds: 98% ITS2, 99% LSU D1-D2). Leotia lubrica (Leotiomycetes) was specified as the outgroup. The assignment of OTUs by each of the three classifiers (RDP, IDTAXA, Protax-fungi) is shown by coloured boxes. Terminals missing these boxes are the reference sequences. Coloured dots on the nodes of the tree indicate the hypothetical ancestor defining monophyletic groups corresponding to the various orders of Sordariomycetes. The extent of each order is indicated by the coloured inner ring. Note that the ancestor of an order is defined by the youngest node from which all reference sequences are descended; OTUs falling outside of the resulting clades appear as 'unassigned' by the phylogenetic analysis approach. The distribution of ITS2 (red squares) and LSU D1-D2 (blue bullets) relative to the reference set (yellow stars) on each of the tips of the tree. Note the limited presence of ITS sequences in the Ophiostomatales (in top right quadrant).
Figure 8 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 8 Proportion of OTUs assigned to each Order from metabarcoding with LSU (left panel) and ITS (right panel) markers based on the RDP classifier and the phylogenetic tree, under increasing threshold values.
Linked collectors and determiners for: Fungal Internal Transcribed Spacer RNA (ITS) RefSeq Targeted Loci Project.
Natural history specimen data linked to collectors and determiners held within, "Fungal Internal Transcribed Spacer RNA (ITS) RefSeq Targeted Loci Project". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/9baace02-10fe-4972-b3ec-2cb647c55194">https://bionomia.net/dataset/9baace02-10fe-4972-b3ec-2cb647c55194</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/9baace02-10fe-4972-b3ec-2cb647c55194">https://gbif.org/dataset/9baace02-10fe-4972-b3ec-2cb647c55194</a>. Formatted as a Frictionless Data package.
Supplementary material 1 from: {"en": "Kolter A, Gemeinholzer B (2021) Internal transcribed spacer primer evaluation for vascular plant metabarcoding. Metabarcoding and Metagenomics 5: e68155. https://doi.org/10.3897/mbmg.5.68155"}
Supplementary files
Figure 3 from: Sutton BD, Steck GJ, Norrbom AL, Rodriguez EJ, Srivastava P, Alvarado NN, Colque F, Landa EY, Sánchez JJL, Quisberth E, Peñaranda EA, Clavijo PAR, Alvarez-Baca JK, Zapata TG, Ponce P (2015) Nuclear ribosomal internal transcribed spacer 1 (ITS1) variation in the Anastrepha fraterculus cryptic species complex (Diptera, Tephritidae) of the Andean region. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 175-191. https://doi.org/10.3897/zookeys.540.6147
Figure 3 - Overall similarity inferred by UPGMA (unweighted pair group method with arithmetic mean) cluster analysis (Sneath and Sokal (1973) of Andean Anastrepha fraterculus ITS1 sequence types (489nt). Distances were computed by the maximum composite likelihood method (Tamura et al. (2004) in number of base substitutions per site with gaps eliminated.
Figure 2 from: Sutton BD, Steck GJ, Norrbom AL, Rodriguez EJ, Srivastava P, Alvarado NN, Colque F, Landa EY, Sánchez JJL, Quisberth E, Peñaranda EA, Clavijo PAR, Alvarez-Baca JK, Zapata TG, Ponce P (2015) Nuclear ribosomal internal transcribed spacer 1 (ITS1) variation in the Anastrepha fraterculus cryptic species complex (Diptera, Tephritidae) of the Andean region. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 175-191. https://doi.org/10.3897/zookeys.540.6147
Figure 2 - ITS1 polymorphic region sequences for Andean Anastrepha fraterculus; hypothetical alignment.
Figure 1 from: Rosenblad MA, Martín MP, Tedersoo L, Ryberg M, Larsson E, Wurzbacher C, Abarenkov K, Nilsson RH (2016) Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota). MycoKeys 13: 21-33. https://doi.org/10.3897/mycokeys.13.8579
Figure 1 - Schematic illustration of the fungal ITS region and neighboring rDNA genes. The subregions ITS1, 5.8S, and ITS2 of the ITS region are indicated along with the SRP RNA in the first part of the ITS1. The absolute positions of the subregions and the SRP RNA are provided in Suppl. material 2.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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