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152 results for “ITS2”
Tara Pacific ITS2 Symbiodiniaceae data release version 1
<p>This data is the result of the primary analysis of the Symbiodiniaceae ITS2 rDNA gene sequencing data collected from all islands as part of the Tara Pacific expedition.The analysis was conducted using SymPortal. A full README is contained within the data upload.</p>
Data from: ITS1 versus ITS2 as DNA metabarcodes for fungi
The nuclear ribosomal Internal Transcribed Spacer ITS region is widely used as a DNA metabarcoding marker to characterize the diversity and composition of fungal communities. In amplicon pyrosequencing studies of fungal diversity, one of the spacers ITS1 or ITS2 of the ITS region is normally used. In this methodological study we evaluate the usability of ITS1 vs. ITS2 as a DNA metabarcoding marker for fungi. We analyse three data sets: two comprising ITS1 and ITS2 sequences of known taxonomic affiliations and a third comprising ITS1 and ITS2 environmental amplicon pyrosequencing data. Clustering analyses of sequences with known taxonomy using the bioinformatics pipeline ClustEx revealed that a 97% similarity cut-off represent a reasonable threshold for estimating the number of known species in the data sets for both ITS1 and ITS2. However, no single threshold value worked well for all fungi at the same time within the curated UNITE database, and we found that the Operational Taxonomic Unit (OTU) concept is not easily translated into the level of species because many species are distributed over several clusters. Clustering analyses of the 134 692 ITS1 and ITS2 pyrosequences using a 97% similarity cut-off revealed a high similarity between the two data sets when it comes to taxonomic coverage. Although some groups are under- or unrepresented in the two data sets due to, e.g. primer mismatches, our results indicate that ITS1 and ITS2 to a large extent yield similar results when used as DNA metabarcodes for fungi.
Tara Pacific CDIV ITS2 Symbiodiniaceae data release
<p>This data is the result of the primary analysis of the ITS2 sequencing data associated with the Coral Diversity dataset collected from all islands as part of the Tara Pacific expedition. A full README is contained within the data upload.</p>
Fig. 6 in Constraints on Phylogenetic Interrelationships among Four Free-living Litostomatean Lineages Inferred from 18S rRNA gene-ITS Region sequences and Secondary Structure of the ITS2 molecule
Fig. 6. Consensus secondary structure of the ITS2 molecule of free-living litostomateans. The ITS2 molecule shows an internal loop, radiating two helices. There is an A-G bulge in the stem of helix III.
Fig. 4. Maximum parsimony consensus tree within Paromoionchis gen. nov., performed with ITS2 DNA sequences from 80 in A new genus and three new species of mangrove slugs from the Indo-West Pacific (Mollusca: Gastropoda: Euthyneura: Onchidiidae)
Fig. 4. Maximum parsimony consensus tree within Paromoionchis gen. nov., performed with ITS2 DNA sequences from 80 individuals (including 7 outgroups). Numbers by the branches are the bootstrap values (only numbers>50% are indicated). Numbers for each individual correspond to unique identifiers for DNA extraction. All sequences for specimens of Paromoionchis gen. nov. are new. Information on specimens can be found in the lists of material examined and in Table 1. The letter A corresponds to a clade referred to in the text. The color used for each (mitochondrial) unit is the same as that used in Figs 1–3 and 5–6.
FIGURE 59 continued. ITS2 in Cardicola Short, 1953 and Braya n. gen. Digenea: Sanguinicolidae) from five families of tropical Indo-Pacific fishes (
FIGURE 59 continued. ITS2 sequence alignment for putative species sequenced here.
Figure 8 from: Stahls G, Haarto A (2014) When mtDNA COI is misleading: congruent signal of ITS2 molecular marker and morphology for North European Melanostoma Schiner, 1860 (Diptera, Syrphidae). ZooKeys 431: 93-134. https://doi.org/10.3897/zookeys.431.7207
Figure 8 - Postgonite, lateral view. A Melanostoma scalare B Melanostoma certum C Melanostoma mellarium and D Melanostoma mellinum.
Figure 9 from: Stahls G, Haarto A (2014) When mtDNA COI is misleading: congruent signal of ITS2 molecular marker and morphology for North European Melanostoma Schiner, 1860 (Diptera, Syrphidae). ZooKeys 431: 93-134. https://doi.org/10.3897/zookeys.431.7207
Figure 9 - Postgonite, ventral view. A Melanostoma scalare B Melanostoma certum C Melanostoma mellarium and D Melanostoma mellinum.
Figure 6 from: Stahls G, Haarto A (2014) When mtDNA COI is misleading: congruent signal of ITS2 molecular marker and morphology for North European Melanostoma Schiner, 1860 (Diptera, Syrphidae). ZooKeys 431: 93-134. https://doi.org/10.3897/zookeys.431.7207
Figure 6 - Cerci and surstyli, dorsal view and surstyli, lateral view. A Melanostoma scalare B Melanostoma certum C Melanostoma mellarium and D Melanostoma mellinum.
Figure 5 from: Stahls G, Haarto A (2014) When mtDNA COI is misleading: congruent signal of ITS2 molecular marker and morphology for North European Melanostoma Schiner, 1860 (Diptera, Syrphidae). ZooKeys 431: 93-134. https://doi.org/10.3897/zookeys.431.7207
Figure 5 - Shape of male sterna 2–4. A Melanostoma scalare B Melanostoma certum C Melanostoma mellarium and D Melanostoma mellinum.
Figure 7 from: Stahls G, Haarto A (2014) When mtDNA COI is misleading: congruent signal of ITS2 molecular marker and morphology for North European Melanostoma Schiner, 1860 (Diptera, Syrphidae). ZooKeys 431: 93-134. https://doi.org/10.3897/zookeys.431.7207
Figure 7 - Postgonite and anterior part of hypandrium, lateral view. A Melanostoma scalare B Melanostoma certum C Melanostoma mellarium and D Melanostoma mellinum.
Figure 2 from: Stahls G, Haarto A (2014) When mtDNA COI is misleading: congruent signal of ITS2 molecular marker and morphology for North European Melanostoma Schiner, 1860 (Diptera, Syrphidae). ZooKeys 431: 93-134. https://doi.org/10.3897/zookeys.431.7207
Figure 2 - Strict consensus tree resulting from parsimony analysis of mtDNA COI gene. Filled circles denote unambiguous nucleotide changes, open circles ambiguous changes. Bootstrap support values indicated above branches.
Figure 3 from: Stahls G, Haarto A (2014) When mtDNA COI is misleading: congruent signal of ITS2 molecular marker and morphology for North European Melanostoma Schiner, 1860 (Diptera, Syrphidae). ZooKeys 431: 93-134. https://doi.org/10.3897/zookeys.431.7207
Figure 3 - Strict consensus tree resulting from parsimony analysis of nuclear ITS2 gene region. Filled circles denote unambiguous nucleotide changes, open circles ambiguous changes. Samples from Finland labelled with locality names, from elsewhere with country name (for more information see Table 1). Bootstrap support values indicated above branches.
Figure 14 from: Stahls G, Haarto A (2014) When mtDNA COI is misleading: congruent signal of ITS2 molecular marker and morphology for North European Melanostoma Schiner, 1860 (Diptera, Syrphidae). ZooKeys 431: 93-134. https://doi.org/10.3897/zookeys.431.7207
Figure 14 - Abdomen of female. A Melanostoma scalare B Melanostoma certum C Melanostoma mellarium D Melanostoma mellinum.
Figure 13 from: Stahls G, Haarto A (2014) When mtDNA COI is misleading: congruent signal of ITS2 molecular marker and morphology for North European Melanostoma Schiner, 1860 (Diptera, Syrphidae). ZooKeys 431: 93-134. https://doi.org/10.3897/zookeys.431.7207
Figure 13 - Dorsal view of female head. Position of posterior ocellus as compared to the hind eye line of female. A Melanostoma mellarium and B Melanostoma mellinum.
Figure 12 from: Stahls G, Haarto A (2014) When mtDNA COI is misleading: congruent signal of ITS2 molecular marker and morphology for North European Melanostoma Schiner, 1860 (Diptera, Syrphidae). ZooKeys 431: 93-134. https://doi.org/10.3897/zookeys.431.7207
Figure 12 - Shape of female sterna 2–4. A Melanostoma scalare, B and C Melanostoma certum D Melanostoma mellarium and E and F Melanostoma mellinum.
Figure 11 from: Stahls G, Haarto A (2014) When mtDNA COI is misleading: congruent signal of ITS2 molecular marker and morphology for North European Melanostoma Schiner, 1860 (Diptera, Syrphidae). ZooKeys 431: 93-134. https://doi.org/10.3897/zookeys.431.7207
Figure 11 - Hypandrium, ventral view, shape of postgonites A Melanostoma scalare B Melanostoma certum C Melanostoma mellarium and D Melanostoma mellinum.
Figure 10 from: Stahls G, Haarto A (2014) When mtDNA COI is misleading: congruent signal of ITS2 molecular marker and morphology for North European Melanostoma Schiner, 1860 (Diptera, Syrphidae). ZooKeys 431: 93-134. https://doi.org/10.3897/zookeys.431.7207
Figure 10 - Hypandrium, lateral view. A Melanostoma scalare B Melanostoma certum C Melanostoma mellarium and D Melanostoma mellinum.
Figures 1-3 from: Jürgenstein S, Kurina O, Põldmaa K (2015)) The Mycetophila ruficollis Meigen (Diptera, Mycetophilidae) group in Europe: elucidating species delimitation with COI and ITS2 sequence data. ZooKeys 508: 15-51. https://doi.org/10.3897/zookeys.508.9814
Figures 1-3 - Mycetophila ichneumonea Say, 1823, a typical member of the Mycetophila ruficollis group. 1 male habitus 2 head with maxillary palpi, closer view 3 male terminalia, closer view. Scale bar = 1 mm (1), 0.5 mm (2) and 0.2 mm (3). Abbreviations: plp = segments of maxillary palpus; gc = gonocoxite; gst d = dorsal branch of gonostylus; gst v = ventral branch of gonostylus.
Figures 27-32 from: Jürgenstein S, Kurina O, Põldmaa K (2015)) The Mycetophila ruficollis Meigen (Diptera, Mycetophilidae) group in Europe: elucidating species delimitation with COI and ITS2 sequence data. ZooKeys 508: 15-51. https://doi.org/10.3897/zookeys.508.9814
Figures 27-32 - Ventral branch of gonostylus, ventral view (27, 29, 31) and internal view (28, 30, 32). 27, 28 Mycetophila strobli 29, 30 Mycetophila suffusala 31, 32 Mycetophila uninotata. Scale bar = 0.05 mm.
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