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152 results for “ITS2”
Data from: Host specificity of Symbiodinium variants revealed by an ITS2 metahaplotype approach
Analysis of the widely used ITS region is confounded by the presence of intragenomic variants (IGVs). In Symbiodinium, the algal symbionts of reef building corals, deep-sequencing analyses are used to characterise communities within corals, yet these analyses largely overlook IGVs. Here we consider that distinct ITS2 sequences could represent IGVs rather than distinct symbiont types and argue that symbionts can be distinguished by their proportional composition of IGVs, described as their ITS2 metahaplotype. Using our metahaplotype approach on Minimum Entropy Decomposition (MED) analysis of ITS2 sequences from the corals Acropora downingi, Cyphastrea microphthalma and Playgyra daedalea, we show the dominance of a single species-specific Symbiodinium C3 variant within each coral species. We confirm the presence of these species-specific symbionts using the psbA non-coding region. Our findings highlight the importance of accounting for IGVs in ITS2 analyses and demonstrate their capacity to resolve biological patterns that would otherwise be overlooked.
Data from: Application of ITS2 metabarcoding to determine the provenance of pollen collected by honey bees in an agroecosystem
Premise of the study: Melissopalynology, the identification of bee-collected pollen, provides insight into the flowers exploited by foraging bees. Information provided by melissopalynology could guide floral enrichment efforts aimed at supporting pollinators, but it has rarely been used because traditional methods of pollen identification are laborious and require expert knowledge. We approach melissopalynology in a novel way, employing a molecular method to study the pollen foraging of honey bees (Apis mellifera) in a landscape dominated by field crops, and compare these results to those obtained by microscopic melissopalynology. Methods: Pollen was collected from honey bee colonies in Madison County, Ohio, USA, during a two-week period in mid-spring and identified using microscopic methods and ITS2 metabarcoding. Results: Metabarcoding identified 19 plant families and exhibited sensitivity for identifying the taxa present in large and diverse pollen samples relative to microscopy, which identified eight families. The bulk of pollen collected by honey bees was from trees (Sapindaceae, Oleaceae, and Rosaceae), although dandelion (Taraxacum officinale) and mustard (Brassicaceae) pollen were also abundant. Discussion: For quantitative analysis of pollen, using both metabarcoding and microscopic identification is superior to either individual method. For qualitative analysis, ITS2 metabarcoding is superior, providing heightened sensitivity and genus-level resolution.
Data from: ITS all right mama: Investigating the formation of chimeric sequences in the ITS2 region by DNA metabarcoding analyses of fungal mock communities of different complexities
The formation of chimeric sequences can create significant methodological bias in PCR-based DNA metabarcoding analyses. During mixed-template amplification of barcoding regions, chimera formation is frequent and well documented. However, profiling of fungal communities typically uses the more variable rDNA region ITS. Due to a larger research community, tools for chimera detection have been developed mainly for the 16S/18S markers. However, these tools are widely applied to the ITS region without verification of their performance. We examined the rate of chimera formation during amplification and 454 sequencing of the ITS2 region from fungal mock communities of different complexities. We evaluated the chimera detecting ability of two common chimera-checking algorithms: Perseus and UCHIME. Large proportions of the chimeras reported were false positives. No false negatives were found in the dataset. Verified chimeras accounted for only 0.2% of the total ITS2 reads, which is considerably less than what is typically reported in 16S and 18S metabarcoding analyses. Verified chimeric "parent sequences" had significantly higher percent identity to one another than to random members of the mock communities. Community complexity increased the rate of chimera formation. GC content was higher around the verified chimeric break points, potentially facilitating chimera formation through base pair mismatching in the neighboring regions of high similarity in the chimeric region. We conclude that the hypervariable nature of the ITS region seem to buffer the rate of chimera formation in comparison to other, less variable barcoding regions, due to shorter regions of high sequence similarity.
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 1. The ITS2 in Anopheles (Kerteszia) lepidotus (Diptera: Culicidae), not the malaria vector we thought it was: Revised male and female morphology; larva, pupa, and male genitalia characters; and molecular verification
FIGURE 1. The ITS2 (rDNA) sequence alignments of Anopheles (Kerteszia) pholidotus (n = 3, Venezuela) and An. lepidotus (n = 5, Ecuador), using MAFFT (Katoh et al., 2002). A total of 343 nucleotides were identical; 45 transversions, 39 transitions, and 89 gaps were observed. Underlined bases show the ITS2 primers.
Fig. 6. ITS2 secondary structures showing significant variations between our isolate A in Funiculosone, a substituted dihydroxanthene-1,9-dione with two of its analogues produced by an endolichenic fungus Talaromyces funiculosus and their antimicrobial activity
Fig. 6. ITS2 secondary structures showing significant variations between our isolate A. Talaromyces sp. (MF927596.1*) and B. T. funiculosus (consensus), incompatible base pairs are highlighted in pale red and yellow colour based on their degrees of incompatibility; * indicating own isolate. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Figure 1. Bayesian inference tree built using COI, 16S rDNA and ITS2 in Integrated taxonomy reveals multiple species in the Dendrobaena byblica (Rosa, 1893) complex (Oligochaeta: Lumbricidae)
Figure 1. Bayesian inference tree built using COI, 16S rDNA and ITS2 sequences. The numbers indicate the posterior probabilities. The colours show the two main clades.
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. Variable positions in the ITS2 secondary structure of some Coelastrella sensu lato species. The ITS2 model of Coelastrella striolata strain CAUP H 3602 (JX513881) was used to map sequence differences. Variable positions of analyzed strains (GenBank numbers can be found in Table 3, 4 are given next to the main structure and are marked in bold. Hemi- Compensatory Base Changes in conservative regions are circled and Compensatory Base Change is contoured. Sequences of strains with GenBank numbers JX513879 (C. aeroterrestrica), JX513882 (C. terrestris), JX513884 (C. rubescens), MH176120 (C. rubescens var. oocystiformis), JX513880 (C. multistriata), JX513887 (C. oocystiformis) were used as representatives of Coelastrella species. The strains analyzed in this study are underlined. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE. Variable positions in the ITS2 secondary structure of some Coelastrella sensu lato species. The ITS2 model of Coelastrella striolata strain CAUP H 3602 (JX513881) was used to map sequence differences. Variable positions of analyzed strains (GenBank numbers can be found in Table 3, 4 are given next to the main structure and are marked in bold. Hemi- Compensatory Base Changes in conservative regions are circled and Compensatory Base Change is contoured. Sequences of strains with GenBank numbers JX513879 (C. aeroterrestrica), JX513882 (C. terrestris), JX513884 (C. rubescens), MH176120 (C. rubescens var. oocystiformis), JX513880 (C. multistriata), JX513887 (C. oocystiformis) were used as representatives of Coelastrella species. The strains analyzed in this study are underlined.
FIGURE 2. Optimal phylogenetic tree from Maximum Likelihood analyses for the nrITS1–5.8S–ITS2 in Morphology and molecular data of the species of Suillus (Suillaceae, Boletales) associated with Pinus sibirica at the European northeast of Russia
FIGURE 2. Optimal phylogenetic tree from Maximum Likelihood analyses for the nrITS1–5.8S–ITS2 Suillus data. Bootstrap values (BS ≥ 70%) is added to the left of a node as follows: nearest neighbour method / maximum likelihood method. Scale bar indicates expected changes per site. New sequences from the Komi Republic are marked with red blocks. The specimen GenBank accession numbers in parentheses follows the names.
Fig. 6 in A Tale of Two Setae: How Morphology and ITS2 Help Delimit a Cryptic Species Complex in Eulophidae (Hymenoptera: Chalcidoidea)
Fig. 6. Dorsal view of mesosomal color variation in Burkseus vittatus: (A) D4559, (B) D5320, (C) D5113, (D) D5101, (E) D4699, (F) D3640, (G) D4173, (H) D3665, (I) D3666, (J) D4177, (K) D3993, and (L) illustrated view. Scale bar = 0.2 mm.
Fig. 8 in A Tale of Two Setae: How Morphology and ITS2 Help Delimit a Cryptic Species Complex in Eulophidae (Hymenoptera: Chalcidoidea)
Fig. 8. Gaster color variation within females (A–E) and males (F–J) of the four Nearctic Burkseus species.
Fig. 5 in A Tale of Two Setae: How Morphology and ITS2 Help Delimit a Cryptic Species Complex in Eulophidae (Hymenoptera: Chalcidoidea)
Fig. 5. Mesosomal color variation. (A–H) Burkseus robustus: (A) D3674, (B) D3675, (C) D4591, (D) D4580, (E) D4581, (F) D4680, (G) D5326, (H) illustrated view. (I–L) B. sigillatus: (H) D5325, (I) D5324, (J) D4738, and (L) illustrated view. Scale bar = 0.2 mm.
Fig. 4 in A Tale of Two Setae: How Morphology and ITS2 Help Delimit a Cryptic Species Complex in Eulophidae (Hymenoptera: Chalcidoidea)
Fig. 4. Mesosomal color variation in Burkseus flavoviridis: (A) D4682, (B) D4741, (C) D3791 (specimen collapsed while drying), (D) D4593, (E) D4171, F) D4172, (G) D4679, (H) D4683, (I) D4176, (J) D4169, (K) D4175, and (L) illustrated view. Scale bar = 0.2 mm.
Fig. 9 in A Tale of Two Setae: How Morphology and ITS2 Help Delimit a Cryptic Species Complex in Eulophidae (Hymenoptera: Chalcidoidea)
Fig. 9. Habitus: (A) Burkseus elongatus (BMNH: NHMUK 10371836), (B) B. singa (MZH: UCRCENT 513243), (C) B. pinicolus (BMNH: NHMUK 10371840), (D) Cirrospilus curvineurus (MZH: UCRCENT 513242).
Fig. 2 in A Tale of Two Setae: How Morphology and ITS2 Help Delimit a Cryptic Species Complex in Eulophidae (Hymenoptera: Chalcidoidea)
Fig. 2. Fore wings, dorsal view: (A) Burkseus vittatus comb. n., (B) B. flavoviridis comb. n., (C) B. robustus n. sp., (D) B. sigillatus n. sp. The photographs of B. robustus and B. sigillatus were taken after DNA extraction, displaying how the dark colors on the submarginal vein setae (B. robustus and B. sigillatus), stigmal vein and uncus (B. robustus), and banding patterns (B. sigillatus) are resilient enough to remain visible after extraction. Scale bar = 0.5 mm. ams = admarginal setae, bsl = basal setal line, csl = cubital setal line, disc = fore wing disc, spc = speculum, smv = submarginal vein, stg = stigmal vein, unc = uncus.
Fig. 3 in A Tale of Two Setae: How Morphology and ITS2 Help Delimit a Cryptic Species Complex in Eulophidae (Hymenoptera: Chalcidoidea)
Fig. 3. Combined molecular and morphological maximum likelihood tree.The different symbols correspond with specimens collected at the same location. Each specimen of these groups was collected during the same collecting event, with the exception of D3665, D3666, and D3791, collected at the same location but 2 wk apart.
Fig. 1 in A Tale of Two Setae: How Morphology and ITS2 Help Delimit a Cryptic Species Complex in Eulophidae (Hymenoptera: Chalcidoidea)
Fig. 1. Morphological characters. (A–C) head: (A) Zagrammosoma mirum, (B) Burkseus flavoviridis, (C) Burkseus robustus. (D–G) dorsal view of mesosoma: (D) Cirrospilus sp. D3867, (E) Cirrospilus sp. D3865, (F) Zagrammosoma americanum, (G) Diglyphus begini. (H) Burkseus robustus hind leg. (I) Burkseus flavoviridis antennae. Scale bar in all photos = 0.2 mm. axl = axilla, bst = basitarsus, clv = clava, fu = funicular, mc = median carina, ms = malar sulcus, msc = mesoscutum, no = pronotum, not = notaulus, pdg = prodiscrimen groove, pl1 = propleura, ppd = propodeum, scp = scape, sct = mesoscutellum, set = setae (bristle-like setae), smg = submedian groove, sss = small scattered setae, tbs = tibial spur, vtx = vertex.
Figure 4. COI and ITS2 in Systematics and phylogeography of western Mediterranean tarantulas (Araneae: Theraphosidae)
Figure 4. COI and ITS2 gene trees inferred by BEAST with bars representing three species delimitation methods: ABGD, mPTP and GMYC, respectively. Each individual block represents a delimited unit. Split blocks within ABGD and mPTP analyses indicate incongruences among phylogenetic inference and species delimitation analysis. Circles indicate support levels for the corresponding split in mPTP: black> 0.60, grey = 0.59–0.20 and no circle <0.20.
FIGURE 7. Comparison concatenated tree ITS2 – 28S rDNA D2 in Description of two new species closely related to Doryctobracon areolatus (Szépligeti, 1911) (Hymenoptera, Braconidae), based on morphometric and molecular analyses
FIGURE 7. Comparison concatenated tree ITS2 – 28S rDNA D2 (UPGMA) produced from the nucleotide sequences (A), cluster analysis of the Mahalanobis distance (UPGMA) calculated from the shape of the wings components (B). (DAAP = Doryctobracon areolatus from Amapá, DAGO = D. areolatus from Goiás, DATO = D. areolatus from Tocantins, DASP = D. areolatus from São Paulo, YSAP = Doryctobracon whartoni sp. nov. (yellow stigma) from Amapá; BSAP = Doryctobracon adaimei sp. nov. (brown stigma) from Amapá, BSGO = D. adaimei sp. nov. from Goiás, BSTO = D. adaimei sp. nov. from Tocantins.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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