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42 results for “ITS1”
ITS1 metabarcoding revealing Phytophthora diversity in anthropized and natural ecosystems in Sicily, Italy
<p>This dataset on Zenodo contains the raw sequencing data for: <a href="https://doi.org/10.3390/jof8040330">La Spada <em>et al.</em> (2022) DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing <em>Phytophthora</em> Diversity in Anthropized and Natural Ecosystems</a>.</p> <p>This a subset of 192 demultiplexed Illumina MiSeq raw sequencing samples run at the James Hutton Institute in January 2020, consisting of two 96-well plates labelled with the Illumina A and D multiplexing kits.</p> <p>There are 61 pairs of raw gzipped compressed FASTQ files (122 files), provided as a 930MB gzipped compressed tar-ball.</p> <p>From the D multiplexing kit, there are 27 Nature Reserve (<em>NR</em>) samples, 16 Botanical Garden (<em>BG</em>) samples, and 6 managed Citrus Orchard (<em>CO</em>) samples containing <em>Phytophthora</em> targeted ITS1 marker sequences, and 6 synthetic controls (prefix <em>GL1D</em>) which should have contained only four known synthetic sequences. Additionally included are the 6 synthetic controls (prefix <em>GL1A</em>) from the A multiplexing kit, which were clean.</p> <p>The filenames start with the sample name, followed by something like <em>DH03_S183_L001_R1_001.fastq.gz</em> where <em>DH03</em> indicates well <em>H03</em> on the 96-well plate labelled with the <em>D</em> multiplexing set, <em>S183</em> is the MiSeq sample number (from 1 to 192), and <em>R1</em> (or <em>R2</em>) indicate the Illumina forward (or reverse) paired read files.</p>
UNITE+INSD 2024 Fungal ITS, ITS1, and ITS2 Reference Sequences
<p>These datasets were created from the 2024 release (Abarenkov et al. 2024) of the UNITE+INSD database as reference sequences for and by dnabarcoder (Vu et al. 2022). The ITS1 and ITS2 sequences were extracted using ITSx (Bengtsson-Palme et al. 2013).</p>
Fig. 2. ITS1 in Wild chimpanzees are infected by Trypanosoma brucei
Fig. 2. ITS1-based dendogram of trypanosomes from primate tissue and fecal samples. Sequences generated in this study are marked as follows: T ‾ tissue samples of apes (TA) and monkeys (TM); F ‾ fecal samples of apes (FA); sequences retrieved from GenBank are labeled with Latin names (Trypanosoma sp. ex Wildebeest JN673403, for T. theileri JX178185, HQ664848, and HQ664849).
Fig. 1. ITS1 in Wild chimpanzees are infected by Trypanosoma brucei
Fig. 1. ITS1-based detection of trypanosomes in blood and feces of experimentally infected mice. (A‾D, I) detection in blood; (E‾H, J) detection in feces. (A, E) Trypanosoma b. brucei; (B, F) T. b. gambiense; (C, G) T. b. rhodesiense; (D, H) T. b. evansi; (I) blood from a non-infected mouse; (J) feces from a non-infected mouse; (K) negative control; (m) marker.
Fig. 3. Maximum likelihood tree constructed from 38 nuclear rDNA ITS1 and ITS2 sequences from Apiaceae genus Daucus and relatives using a in Molecular phylogeny of Daucus (Apiaceae): Evidence from nuclear ribosomal DNA ITS sequences
Fig. 3. Maximum likelihood tree constructed from 38 nuclear rDNA ITS1 and ITS2 sequences from Apiaceae genus Daucus and relatives using a transition/transversion rate ratio of 1.6. Branch lengths are proportional to the number of expected nucleotide substitutions per site.
Fig. 2. ITS1 in Diversity of trypanosomes in wildlife of the Kafue ecosystem, Zambia
Fig. 2. ITS1-PCR Gel analysis Gel image of the ITS-PCR-positive samples. The species were estimated by the band size. The expected sizes for each species are T. godfreyi: 220 bp, T. simiae: 331–343 bp, T. theileri: 269–350 bp, T. brucei: 415–431 bp, T. congolense: 560–705 bp (Gaithuma et al., 2019).
Fig. 4. Maximum likelihood tree generated using ITS1-5.8S-ITS2 in Morphological and molecular description of Pallisentis roparensis n. sp. (Acanthocephala: Quadrigyridae) infecting the freshwater cat fish Wallago attu from Ropar Wetland, Punjab, India
Fig. 4. Maximum likelihood tree generated using ITS1-5.8S-ITS2 gene sequence of Pallisentis roparensis and the sequences of related taxa downloaded from GenBank. Numbers near internal nodes show ML bootstrap clade frequencies.
UNITE+INSD 2024 Fungal ITS, ITS1, and ITS2 Reference Sequences and classification
<p>These datasets were created from the 2024 release (Abarenkov et al. 2024) of the UNITE+INSD database as reference sequences for and by dnabarcoder (Vu et al. 2022). The ITS1 and ITS2 sequences were extracted using ITSx (Bengtsson-Palme et al. 2013).</p>
Data from: Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae)
Premise of the Study The internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic relationships ranging from shallow to deep taxonomic levels. Despite several taxonomical revisions in Cassiinae, a stable phylogeny remains elusive at the molecular level, particularly concerning the delineation of species in the genera Cassia, Senna and Chamaecrista. This study addresses the comparative potential of ITS datasets (ITS1, ITS2 and concatenated) in resolving the underlying morphological disparity in the highly complex genera, to assess their discriminatory power as potential barcode candidates in Cassiinae. Methodology A combination of experimental data and an in-silico approach based on threshold genetic distances, sequence similarity based and hierarchical tree-based methods was performed to decipher the discriminating power of ITS datasets on 18 different species of Cassiinae complex. Lab-generated sequences were compared against those available in the GenBank using BLAST and were aligned through MUSCLE 3.8.31 and analysed in PAUP 4.0 and BEAST1.8 using parsimony ratchet, maximum likelihood and Bayesian inference (BI) methods of gene and species tree reconciliation with bootstrapping. DNA barcoding gap was realized based on the Kimura two-parameter distance model (K2P) in TaxonDNA and MEGA. Principal Findings Based on the K2P distance, significant divergences between the inter- and intra-specific genetic distances were observed, while the presence of a DNA barcoding gap was obvious. The ITS1 region efficiently identified 81.63% and 90% of species using TaxonDNA and BI methods, respectively. The PWG-distance method based on simple pairwise matching indicated the significance of ITS1 whereby highest number of variable (210) and informative sites (206) were obtained. The BI tree-based methods outperformed the similarity-based methods producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. Conclusion The reticulated phylogenetic hypothesis using the ITS1 region mainly supported the relationship between the species of Cassiinae established by traditional morphological methods. The ITS1 region showed a higher discrimination power and desirable characteristics as compared to ITS2 and ITS1 + 2, thereby concluding to be the locus of choice. Considering the complexity of the group and the underlying biological ambiguities, the results presented here are encouraging for developing DNA barcoding as a useful tool for resolving taxonomical challenges in corroboration with morphological framework.
Control samples for ITS1 Metabarcoding of the Cynomolgus Macaque Intestinal Mycobiome
<p>Library and Sequencing controls used for the Metabarcoding ITS1 analysis of intestinal content of the Cynomolgus Macaque</p> <p> </p>
Herbarium specimens reveal a cryptic invasion of polyploid Centaurea stoebe in Europe - ITS1 dataset
<h3>Description of the data and file structure</h3> <p>We genotyped the ITS1 locus of 178 herbarium specimens using protocol described in Suchan et al. (2018; https://doi.org/10.1111/1755-0998.12948) and processed using custom script. The specimens were chosen after morphological determination of their cytotypes (morphological determination accuracy: 97.8%). We choose this subsample (3.5% of the total number of specimens) to represent comparable distributional ranges and collection dates across both cytotypes, including specimens from both the native and expanded ranges of tetraploid <em>C. stoebe</em>. Genotyping of the ITS1 locus unambiguously identifies the cytotype, as all tetraploid samples exhibit a unique ribotype B, which has never been found in diploid samples (Mráz et al., 2012; https://doi.org/10.1016/j.ympev.2011.11.006).</p> <h4>Files and variables</h4> <p><strong>File: Centaurea_stoebe_ITS1_script.sh</strong></p> <p>Description: This file contains the script used for processing raw sequence data to obtain a table with the numbers of reads in each sample mapping to the obtained ITS1 variants. The software used was: PEAR v0.9.6, cutadapt v.3.2, vsearch v2.28.1</p> <p><strong>File: Centaurea_stoebe_sample_list.xlsx</strong></p> <p>Description: This file contains a list of analyzed herbarium specimens.</p> <p>Variables</p> <ul> <li>ID - sample ID</li> <li>Lab working no. - Identifier of the samples in the ITS1 analyses, specifically in the Centaurea_stoebe_ITS1_sequence_numbers.xlsx file</li> <li>Morphology-based estimation - ploidy of the sample estimated with morphology (2 - diploid, 4 - tetraploid)</li> <li>ITS seq based estimation - ploidy of the sample estimated using ITS1 sequencing (2 - diploid, 4 - tetraploid)</li> <li>Congruence(1)/mismatch(0) - congruence (1) or mismatch (0) between morphological and genetic policy estimation</li> <li>Country of origin</li> <li>Herbarium</li> <li>Herbarium coll. number</li> <li>Collector</li> <li>Collection year</li> <li>Locality</li> <li>Latitude</li> <li>Longitude</li> </ul> <p><strong>File: Centaurea_stoebe_ITS1_sequences.fasta</strong></p> <p>Description: This file contains sequences of the obtained ITS1 variants.</p> <p><strong>File: Centaurea_stoebe_ITS1_sequence_numbers.xlsx</strong></p> <p>Description: This file contains a table with the numbers of reads in each sample mapping to the obtained ITS1 variants.</p> <p>Variables</p> <ul> <li>OTU - ITS1 variant number</li> <li>size - number of sequences from the total data clustered to the variant</li> <li>next columns contain numbers of reads mapped to each ITS1 variant for each sample</li> </ul> <h3>Code/software</h3> <p>The code to process sequence data is included in Centaurea_stoebe_ITS1_script.sh file. The software used was: PEAR v0.9.6, cutadapt v.3.2, vsearch v2.28.</p>
Data from: Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae)
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Alignments of ITS1 gene sequences from Harpacticella inopinata
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FIGURE 9. Single most parsimonious tree for 28SD2, ITS1, ITS2 in A new species of Gonatocerus (Hymenoptera: Mymaridae) parasitic on proconiine sharpshooters (Hemiptera: Cicadellidae) in the New World
FIGURE 9. Single most parsimonious tree for 28SD2, ITS1, ITS2, COI and COII (length 885, c.i. 0.76, r.i. 0.83); outgroups pruned from tree. Bootstrap values indicated above branches. Table presents unambiguous base substitutions (minimum number) for branches numbered on tree in boldface.
FIGURE 7. Haplotype parsimony networks for ITS1 in A comparative study of populations of Ectopleura crocea and Ectopleura ralphi (Hydrozoa, Tubulariidae) from the Southwestern Atlantic Ocean
FIGURE 7. Haplotype parsimony networks for ITS1+5.8S (A) and COI (B) for the different populations of Ectopleura crocea and Ectopleura ralphi of the Southwestern Atlantic Ocean. Black circles for the Argentine haplotypes, white ones for Brazilian localities; the sizes of the circles are proportional to the number of localities sharing the haplotype; small black circles represent hypothetical or unsampled haplotypes. Lines connecting circles represent one substitution step. Note that A BO/MP samples differ from JU/PA/BO only by an indel of three base pairs (AAT/– – –). Locality codes are represented inside the circles as MA: Macaé, JU: Juréia, PA: Paraná, BO: Bombas, MP: Mar del Plata.
FIGURE 2. Phylogenetic results. A, Maximum likelihood tree from COI dataset rooted with Ophelia limacina. B, Maximum likelihood tree from ITS1 in Validation of three sympatric Thoracophelia species (Annelida: Opheliidae) from Dillon Beach, California using mitochondrial and nuclear DNA sequence data
FIGURE 2. Phylogenetic results. A, Maximum likelihood tree from COI dataset rooted with Ophelia limacina. B, Maximum likelihood tree from ITS1 dataset rooted according to the result for the COI dataset. Support values are shown as jackknife from parsimony analysis and bootstrap from maximum likelihood respectively separated by /. * indicates 100% values for each support measure.
FIGURE Phylogenetic relationships of the Coelastrella genus inferred from the 18S-ITS1-5.8S-ITS2 region. The Neighbor-Joining (NJ), Maximum Likelihood (ML) bootstrap values and Bayesian posterior probabilities (PP) are presented at the nodes (NJ/ML/PP). Only values above 75 are shown. Strains provided in this study are indicated in bold font. Authentic strains marked with asterisks. The scale bar represents the number of substitutions per site. The GenBank accession numbers of Coelastrella can be found in the Table 3. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE Phylogenetic relationships of the Coelastrella genus inferred from the 18S-ITS1-5.8S-ITS2 region. The Neighbor-Joining (NJ), Maximum Likelihood (ML) bootstrap values and Bayesian posterior probabilities (PP) are presented at the nodes (NJ/ML/PP). Only values above 75 are shown. Strains provided in this study are indicated in bold font. Authentic strains marked with asterisks. The scale bar represents the number of substitutions per site. The GenBank accession numbers of Coelastrella can be found in the Table 3.
FIGURE. TCS network inferred from ITS1 in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE. TCS network inferred from ITS1 Coelastrella sequences. The area of a circle is proportional to the number of Coelastrella sequences available in GenBank database. Mutational events between haplotypes are indicated by hatch marks at branches. The network was inferred using the algorithm described by Clement et al. (2002).
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).
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