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40 results for “large subunit”
G-quadruplex in the gene of the large subunit of plant RNA polymerase II: billion years old story
<p><strong>Supplementary material to the journal article</strong></p> <p>Consist of:</p> <p>Supplementary material S1: Analyzed <em>RPB1 </em>sequences in 40 plant species together with detailed characteristics and G-quadruplex prediction using four different computational approaches.</p> <p>Supplementary material S2: G4 locus is the most conserved within the <em>RPB1</em> gene (40 bp long potential G4 locus is the most conserved site in the whole ~ 6000 bp long <em>RPB1</em> gene. See the histogram below the alignment: the position of the G4 locus is depicted, together with the horizontal red dashed line indicating relative nucleotide conservation among aligned sequences of<em> RPB1</em>)</p> <p>Supplementary material S3: Multiple alignment of G4 locus of <em>RPB1</em> paralogs in <em>Arabidopsis thaliana </em>centered to G4 locus of <em>RPB1 </em></p> <p>Supplementary material S4: Modelled 3D structure of G4 from <em>Bathycoccus prasinos</em> in PDB format</p> <p>Supplementary material S5: Gel electrophoresis and ThT staining of the selected G4-forming sequences</p> <p>Supplementary material S6: All analyzed <em>RPB1</em> sequences in FASTA format</p> <p>Supplementary material S7: Aligned <em>RPB1</em> sequences in FASTA format</p> <p>Supplementary material S8: <em>RPB1</em> paralogs in <em>Arabidopsis thaliana</em></p> <p>Supplementary material S9: Spectral composition of light used in the UV experiment. Analysis of emitted light was performed by Ocean Optics (HR4000CG-UV-NIR, USA) device.</p> <p>Supplementary material S10: Difference CD spectra - comparison without and with previous UV treatment</p>
Figure 3 in Phoronid phylogenetics (Brachiopoda; Phoronata): evidence from morphological cladistics, small and large subunit rDNA sequences, and mitochondrial cox1
Figure 3. Phoronid phylogeny. Most probable Bayesian likelihood tree (P = 0.68) from analysis of the 13tx alignment with clade credibility values from the majority rule consensus tree, which had the same topology. Where two clade credibility values are shown the first was from a run with the chiton as outgroup (not shown), and the second from a run with Phoronis ovalis as outgroup. MrBayes run commands were: charset coding_1st = 1-621\3; charset coding_2nd = 2-621\3; charset coding_3rd = 3-621\3; charset non-coding = 622-4515; partition all_4 = 4: coding_1st, coding_2nd, coding_3rd, non-coding; set partition = all_4; lset applyto=(all) nst = 6 rates = invgamma; databreaks 621 2386; unlink shape = all, pinvar = all, statefreq = all, revmat = all; prset ratepr = variable; mcmc ngen = 106 samplefreq = 100 printfreq = 5000 savebrlens = yes; plot match = all; sumt burnin = 2002. The tree shown was drawn in PAUP*4. The.con file was imported and displayed as a phylogram. Clade credibility values were added in a graphics editor.
Figure 2 in Phoronid phylogenetics (Brachiopoda; Phoronata): evidence from morphological cladistics, small and large subunit rDNA sequences, and mitochondrial cox1
Figure 2. Phoronid phylogeny. Maximum likelihood phylogram based on 24tx alignment of concatenated rDNA sequences, with selected bootstrap values (%, 100 pseudoreplicates).
Figure 1 in Phoronid phylogenetics (Brachiopoda; Phoronata): evidence from morphological cladistics, small and large subunit rDNA sequences, and mitochondrial cox1
Figure 1. Phoronid phylogeny. Reweighted parsimony cladogram (length = 36.75, consistency index = 0.907, retention index = 0.899) based on a 24-character morphological data matrix with bootstrap support (%; 500 pseudoreplicates; first figure unweighted, second figure reweighted).
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 10. Haplotype parsimonious networks constructed from cytochrome c oxidase subunit I in A new genus of large hydrothermal vent-endemic gastropod (Neomphalina: Peltospiridae)
Figure 10. Haplotype parsimonious networks constructed from cytochrome c oxidase subunit I sequences of 30 specimens of: A, Gigantopelta chessoia sp. nov.; B, Gigantopelta aegis sp. nov. Open circles are represented haplotypes, number inside the circles and sizes of the circles correspond to number of individuals sharing the haplotype. Filled circles are hypothesized intermediate haplotypes that are not represented by sequences.
Data from: Phylogenetic relationships of Agaric fungi based on nuclear large subunit ribosomal DNA sequences
Phylogenetic relationships of mushrooms and their relatives within the order Agaricales were addressed using nuclear large subunit ribosomal DNA sequences. Approximately 900 bases of the 5' end of the nucleus-encoded large subunit RNA gene (nLSU-rDNA) were sequenced for 154 selected taxa representing most families within the Agaricales. Several phylogenetic methods were used, including weighted and equally weighted parsimony (MP), maximum likelihood (ML), and distance methods (NJ). The starting tree for branch swapping in the ML analyses was the tree with the highest ML score among previously produced MP and NJ trees. A high degree of consensus was observed between phylogenetic estimates obtained through MP and ML. NJ trees differed according to the distance model that was used, however, all NJ trees still supported most of the same terminal groupings as MP and ML trees. NJ trees were always significantly suboptimal when evaluated against the best MP and ML trees, using both parsimony and likelihood tests. Our analyses suggest that weighted parsimony and ML provide the best estimates of Agaricales phylogeny. Similar support was observed between bootstrapping and jackknifing methods for evaluation of tree robustness. Phylogenetic analyses revealed many groups of agaricoid fungi that are supported by moderate to high bootstrap or jackknife levels or are consistent with morphology-based classification schemes. Analyzes also support separate placement of the boletes and russules, which are basal to the main core group of gilled mushrooms (the Agaricineae of Singer). Examples of monophyletic groups include the families Amanitaceae, Coprinaceae (excluding Coprinus comatus and subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and Strophariaceae pro parte (Stropharia, Pholiota, and Hypholoma); the mycorrhizal species of Tricholoma (including Leucopaxillus, also mycorrhizal); Mycena and Resinomycena; Termitomyces, Podabrella, and Lyophyllum; and Pleurotus with Hohenbuehelia. Several nonmonophyletic groups revealed by these data include the families Tricholomataceae, Cortinariaceae, and Hygrophoraceae and the genera Clitocybe, Omphalina, and Marasmius. This study provides a framework for future systematics studies in the Agaricales and suggestions for analyzing large molecular data sets.
Data from: SiSTL1, encoding a large subunit of ribonucleotide reductase, is crucial for plant growth, chloroplast biogenesis, and cell cycle progression in Setaria italica
The activity of ribonucleotide reductase (RNR), which catalyzes the transformation of four ribonucleoside diphosphates (NDPs) to their corresponding deoxyribonucleoside diphosphates (dNDPs), is the main determiner of the cellular concentration of dNTP pools and should be tightly coordinated with DNA synthesis and cell-cycle progression. Either constitutively increased or decreased RNR activity are indeed likely to interfere with DNA replication and lead to arrested cell cycle progression; however, the mechanisms underlying these disruptive effects in higher plants remain to be uncovered. In this study, we identified a RNR large subunit mutant, sistl1, in Setaria italica (foxtail millet), that exhibited growth retardation as well as striped leaf phenotype, i.e., irregularly reduced leaf vein distances and decreased chloroplast biogenesis. We determined that a Gly737 to Glu substitution occurrring in the C-terminus of the SiSTL1 protein slightly affected its optimal function, leading in turn to the reduced expression of genes variously involved in the assembly and activation of the DNA pre-replicative complex, elongation of replication forks and S phase entry. Our study provides new insight into how SiSTL1 regulates plant growth, chloroplast biogenesis, and cell cycle progression in Poaceae crops.
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
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