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43 results for “Internal transcribed spacer (ITS)”
Fig. 3. Sequence variation among 4 internal transcribed spacer 2 in Population genetics of Oligonychus perseae (Acari: Tetranychidae) collected from avocados in Mexico and California
Fig. 3. Sequence variation among 4 internal transcribed spacer 2 (ITS2) genotypes identified from Oligonychus perseae populations in California,Mexico, and Costa Rica. Genotypes are named according to 3 genetic clusters identified from cytochrome oxidase subunit 1 (COI) haplotypes (see Fig. 2).
Fig. 3 Species diagnostic internal transcribed spacer 2 in Anopheles (Anopheles) petragnani Del Vecchio 1939-a new mosquito species for Germany
Fig. 3 Species diagnostic internal transcribed spacer 2 (ITS2) fragments from all An. petragnani (367 bp) and some An. claviger s.s. (269 bp) individuals found during this study (M, Quantitas DNA Marker 100 bp–1 kb, Biozym; lanes 1–5, An. petragnani; lanes 6–10, An. claviger s.s.; − negative control)
Fig. 2. Bayesian Inference tree constructed from Internal transcribed Spacer 2 in Ecological and geographical speciation in Lucilia bufonivora: The evolution of amphibian obligate parasitism
Fig. 2. Bayesian Inference tree constructed from Internal transcribed Spacer 2 (non-coding) sequence data. Each specimen is labelled with the species name and location abbreviation as indicated in Table 1. Green text corresponds to European samples of Lucilia bufonivora; red represents Lucilia elongata; purple represents Canadian L. bufonivora; orange represents Lucilia silvarum. Scale bar represents expected changes per site. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Data from: Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio
The recently developed environmental DNA (eDNA) analysis has been used to estimate the distribution of aquatic vertebrates by using mitochondrial DNA (mtDNA) as a genetic marker. However, mtDNA markers have certain drawbacks such as variable copy number and maternal inheritance. In this study, we investigated the potential of using nuclear DNA (ncDNA) as a more reliable genetic marker for eDNA analysis by using common carp (Cyprinus carpio). We measured the copy numbers of cytochrome b (CytB) gene region of mtDNA and internal transcribed spacer 1 (ITS1) region of ribosomal DNA of ncDNA in various carp tissues and then compared the detectability of these markers in eDNA samples. In the DNA extracted from the brain and gill tissues and intestinal contents, CytB was detected at 95.1 ± 10.7 (mean ± 1 standard error), 29.7 ± 1.59 and 24.0 ± 4.33 copies per cell, respectively, and ITS1 was detected at 1760 ± 343, 2880 ± 503 and 1910 ± 352 copies per cell, respectively. In the eDNA samples from mesocosm, pond and lake water, the copy numbers of ITS1 were about 160, 300 and 150 times higher than those of CytB, respectively. The minimum volume of pond water required for quantification was 33 and 100 mL for ITS1 and CytB, respectively. These results suggested that ITS1 is a more sensitive genetic marker for eDNA studies of C. carpio.
FIGURE. Comparison of the sequences of the internal transcribed spacer (ITS) region of Hedysarum sunhangii and Hedysarum nuratense. The variable region is shown in a red frame. in Hedysarum sunhangii (Fabaceae, Hedysareae), a new species from Pamir-Alay (Babatag Ridge - Uzbekistan)
FIGURE. Comparison of the sequences of the internal transcribed spacer (ITS) region of Hedysarum sunhangii and Hedysarum nuratense. The variable region is shown in a red frame.
Supplementary material 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
Table S2. Class level identification of OTUs showing the number of OTUs produced with ITS2 and LSU and the proportion of the total OTU set on the rarefied data
Supplementary material 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
Table S1. Accession numbers corresponding with the reference sequences used to build the phylogenetic trees
Supplementary material 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 S3. Maximum-likelihood tree constructed in IQ-Tree2 based on three-gene (LSU D1-D2, SSU, ITS2) reference sequence alignments and OTUs for both markers (clustering thresholds: 99% LSU D1-D2 and 98% ITS2)
Supplementary material 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 S2. Species accumulation curves of the OTUs generated from the ITS (panel right) and LSU (panel left) metabarcodes
FIGURE 2 in Molecular Phylogeny of Ethiopian Artemisia (Asteraceae) Species Based on Nuclear External Transcribed Spacer (ETS) and Internal Transcribed Spacer (ITS)
FIGURE 2. The maximum likelihood (ML) tree inferred from 1000 replicates is taken to represent the evolutionary history of the combined nuclear datasets (ITS and ETS). Contrary to this, the branches corresponding to partitions reproduced in less than 50% bootstrap replicates were collapsed. The values indicated above and below branches are the Bootstrap values (> 50%) obtained from ML and MP analysis respectively with 1000 replicates. The species names are colored according to their subgeneric affiliation.
FIGURE 1 in Molecular Phylogeny of Ethiopian Artemisia (Asteraceae) Species Based on Nuclear External Transcribed Spacer (ETS) and Internal Transcribed Spacer (ITS)
FIGURE 1. Map of Ethiopia indicating the geographic distribution of Artemisia samples included in this study.
Supplementary material 4 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
SRP RNA multiple sequence alignment : Explanation note: Multiple sequence alignment with the SRP RNA sequences of Dumesic et al. (2015; Stereum hirsutum, Heterobasidion irregulare, and Heterobasidion annosum) aligned to our newly generated ITS sequences of Russula and Lactarius.
Supplementary material 3 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
ITS/SRP RNA multiple sequence alignment : Explanation note: Multiple sequence alignment comprising the 63 public ITS1 sequences with SRP RNA found in them, the three newly generated sequences, and the SRP RNA sequences from Dumesic et al. (2015) (Stereum hirsutum, Heterobasidion irregulare, and Heterobasidion annosum).
Supplementary material 2 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
ITS multiple sequence alignment : Explanation note: A multiple sequence alignment in the NEXUS format (Maddison et al. 1997) comprising all 63 matching ITS sequences, plus the three newly generated ones (KU356730, KU356731, and KU356732). The alignment was produced in MAFFT without manual adjustment (Katoh and Standley 2013). The alignment is composed of partial nSSU (bases 1-34 in the alignment), the full ITS1 (bases 35-678), the full 5.8S (bases 679-838), the full ITS2 (bases 839-1395), and partial nLSU (bases 1396-end). The SRP RNA occupies position 203-474 in the alignment. The alignment is provided for overview purposes only; the two-order nature of the taxa (Boletales and Russulales) coupled with the high variability of the ITS region jointly mean that the alignment will not be suited for phylogenetic inference.
Supplementary material 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
Output from cmsearch and primers used : Explanation note: A) The output from cmsearch showing all 63 relevant matches to the three ectomycorrhizal lineages. B) Detail of the primers used to re-amplify the specimens.
Fig. 2 in Using compensatory base change analysis of internal transcribed spacer 2 secondary structures to identify three new species in Paramacrobiotus (Tardigrada)
Fig. 2 Phylogenetic tree topol- ogies and sampling locations. a Neighbor-joining tree obtained by ProfDistS and supporting bootstrap values (1,000 repli- cates) shown in black; CBC tree obtained by CBCanalyzer in dark grey; corresponding sampling locations indicated by arrows. b Numbers of CBCs distinguishing three species classified within Paramacrobiotus; grey ovals correspond to those in Fig. 2a and indicate the species groups that can be identified on the basis of CBCs
Figure 3. Maximum likelihood topologies. A, cytochrome oxidase 1 fragments. B, internal transcribed spacer fragment. C, combined data set. Bootstrap supports over 75 in Integrative taxonomy of Parasabella and Sabellomma (Sabellidae: Annelida) from Australia: description of new species, indication of cryptic diversity, and translocation of some species out of their natural distribution range
Figure 3. Maximum likelihood topologies. A, cytochrome oxidase 1 fragments. B, internal transcribed spacer fragment. C, combined data set. Bootstrap supports over 75% shown on nodes. Scale bar, average of nucleotide substitutions per site.
Extensive intragenomic variation in the internal transcribed spacer (ITS) region of fungi
<p>Fungi are among the most biodiverse organisms in the world. Accurate species identification is imperative for studies on fungal ecology and evolution. The internal transcribed spacer (ITS) rDNA region has been widely accepted as the universal barcode for fungi. However, several recent studies have uncovered intragenomic sequence variation within the ITS in multiple fungal species. Here, we mined the genome of 2414 fungal species to determine the prevalence of intragenomic variation and found that the genomes of 641 species, about one-quarter of the 2414 species examined, contained multiple ITS copies. Of those 641 species, 419 (~65%) contained variation among copies revealing that intragenomic variation is common in fungi. We proceeded to show how these copies could result in the erroneous description of hundreds of fungal species and skew studies evaluating eDNA especially when making diversity estimates. Additionally, many genomes were found to be contaminated, especially those of unculturable fungi.</p>
Sequences of nuclear ribosomal internal transcribed spacer (ITS) for five Toxicodendron vernicifluum individuals
<p>This dataset includes the aligned sequences of nuclear ribosomal internal transcribed spacer (ITS) for five <em>Toxicodendron vernicifluum</em> individuals sampled from China.</p>
FIGURE 1. MrBayes phylogram inferred from incomplete internal transcribed spacer rDNA sequence data. Choiromyces meandriformis and C in A new species of Tuber (Tuberaceae, Pezizales) from Inner Mongolia, China
FIGURE 1. MrBayes phylogram inferred from incomplete internal transcribed spacer rDNA sequence data. Choiromyces meandriformis and C. alveolatus were used to root the tree. The same outcome was shown via Maximum Likelihood. On each branch, Bayesian posterior probability values (PP> 0.75) and maximum likelihood bootstrap values (MLbs> 75%) are displayed. The new species sequences are denoted by an asterisk (*). Different colours are used to represent the six primary Tuber phylogroups. Our findings establish T. mongolicum sp. nov. based on phylogenetic studies as well as morphological observations.
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