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33 results for “nuclear ribosomal DNA”
FIGURE 1 in Identification and molecular phylogeny of agriculturally important spider mites (Acari: Tetranychidae) based on mitochondrial and nuclear ribosomal DNA sequences, with an emphasis on Tetranychus
FIGURE 1. Scatter plot for the number of transitions (s) and transversions (v) versus TN distance of COI gene in pairwise comparisons between spider mites, (a) all codon positions; (b) third codon position.
FIGURE 5 in Identification and molecular phylogeny of agriculturally important spider mites (Acari: Tetranychidae) based on mitochondrial and nuclear ribosomal DNA sequences, with an emphasis on Tetranychus
FIGURE 5. ML tree based on ITS2 sequences. Sequence data for the ITS2 was aligned from a total of 23 individuals from nine species. Demodex folliculorum and D. canis (GenBank nos. AM904564 and GU299785, respectively) were selected as the outgroups of ITS2 tree. Numbers on the branches indicate the percentage bootstrap values (>50) based on NJ bootstrapping with ML settings (1,000 replicates).
FIGURE 1 in Reinstatement of Alysicarpus pokleanus (Leguminosae, Papilionoideae: Desmodieae) based on ITS sequences of nuclear ribosomal DNA
FIGURE 1. Best ML tree obtained after analyzing 41 accessions from previous study (Gholami et al. 2017) including 3 outgroups using RaXML (Stamatakis 2014) on CIPRES Science gateway (Miller et al. 2010).
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: Ribosomal RNA gene repeats associate with the nuclear pore complex for maintenance after DNA damage
The ribosomal RNA genes (rDNA) comprise a highly repetitive gene cluster. The copy number of genes at this locus can readily change and is therefore one of the most unstable regions of the genome. DNA damage in rDNA occurs after binding of the replication fork blocking protein Fob1 in S phase, which triggers unequal sister chromatid recombination. However, the precise mechanisms by which such DNA double-strand breaks (DSBs) are repaired is not well understood. Here, we demonstrate that the conserved protein kinase Tel1 maintains rDNA stability after replication fork arrest. We show that rDNA associates with nuclear pores, which is dependent on DNA damage checkpoint kinases Mec1/Tel1 and replisome component Tof1. These findings suggest that rDNA-nuclear pore association is due to a replication fork block and subsequent DSB. Indeed, quantitative microscopy revealed that rDNA is relocated to the nuclear periphery upon induction of a DSB. Finally, rDNA stability was reduced in strains where this association with the nuclear envelope was prevented, which suggests its importance for avoiding improper recombination repair that could induce repeat instability.
Table 6 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes
<p><b>Table 6.</b> Number and proportion of shared short tandem repeats (STRs) in the rDNA of opalinids. For each species* the total number of STRs (T) and the proportion of STRs species specific (not shared with other sequences) (S)* STRs shared by species of the same genus (G)* and STRs shared by species of different genera (C) are given. Incomplete sequences (those lacking ≥100 bases at the 3 <i>ʹ</i> or 5 <i>ʹ</i> end) are shown in parentheses. Abbreviation: N/A* sequence not available.</p><table><tbody><tr><th><b>Species</b></th><th><b>SSU rDNA</b></th><th><b>ITS1</b></th><th><b>5.8S rDNA</b></th><th><b>ITS2</b></th><th><b>LSU rDNA</b></th></tr><tr><th><b>T</b></th><th><b>S</b></th><th><b>G</b></th><th><b>C</b></th><th><b>T</b></th><th><b>S</b></th><th><b>G</b></th><th><b>C</b></th><th><b>T</b></th><th><b>S</b></th><th><b>G</b></th><th><b>C</b></th><th><b>T</b></th><th><b>S</b></th><th><b>G</b></th><th><b>C</b></th><th><b>T</b></th><th><b>S</b></th><th><b>G</b></th><th><b>C</b></th></tr><tr><th>OPALINIDA</th></tr></tbody><tbody><tr><th>(<i>Protoopalina axonucleata</i>)</th><td>45</td><td>13.3</td><td>35.6</td><td>51.1</td><td>N/A</td><td></td><td></td><td></td><td>N/A</td><td></td><td></td><td></td><td>N/A</td><td></td><td></td><td></td><td>N/A</td><td></td><td></td><td></td></tr><tr><th>(<i>Protoopalina intestinalis</i>)</th><td>52</td><td>11.5</td><td>38.5</td><td>50.0</td><td>N/A</td><td></td><td></td><td></td><td>N/A</td><td></td><td></td><td></td><td>N/A</td><td></td><td></td><td></td><td>N/A</td><td></td><td></td><td></td></tr><tr><th><i>Protoopalina limnocharis</i></th><td>68</td><td>14.7</td><td>29.4</td><td>55.9</td><td>19</td><td>31.6</td><td>68.4</td><td>0</td><td>5</td><td>0.0</td><td>20.0</td><td>80.0</td><td>16</td><td>25.0</td><td>75.0</td><td>0.0</td><td>177</td><td>3.4</td><td>47.5</td><td>49.1</td></tr><tr><th><i>Protoopalina pingi</i></th><td>68</td><td>14.7</td><td>29.4</td><td>55.9</td><td>20</td><td>35.0</td><td>65.0</td><td>0</td><td>5</td><td>0.0</td><td>20.0</td><td>80.0</td><td>15</td><td>20.0</td><td>80.0</td><td>0.0</td><td>179</td><td>4.5</td><td>46.9</td><td>48.6</td></tr><tr><th><i>Zelleriella orientalis</i></th><td>95</td><td>0.0</td><td>41.0</td><td>59.0</td><td>22</td><td>0.0</td><td>95.5</td><td>4.5</td><td>9</td><td>0.0</td><td>33.3</td><td>66.7</td><td>23</td><td>0.0</td><td>91.3</td><td>8.7</td><td>203</td><td>3.5</td><td>23.6</td><td>72.9</td></tr><tr><th><i>Zelleriella</i> sp.</th><td>95</td><td>0.0</td><td>41.0</td><td>59.0</td><td>22</td><td>0.0</td><td>95.5</td><td>4.5</td><td>9</td><td>0.0</td><td>33.3</td><td>66.7</td><td>23</td><td>0.0</td><td>91.3</td><td>8.7</td><td>212</td><td>6.1</td><td>22.7</td><td>71.2</td></tr><tr><th><i>Opalina undulata</i></th><td>104</td><td>12.5</td><td>33.7</td><td>53.8</td><td>26</td><td>80.8</td><td>15.4</td><td>3.8</td><td>8</td><td>0.0</td><td>37.5</td><td>62.5</td><td>25</td><td>44.0</td><td>48.0</td><td>8.0</td><td>213</td><td>10.3</td><td>19.3</td><td>70.4</td></tr><tr><th><i>Opalina triangulata</i></th><td>103</td><td>11.6</td><td>34.0</td><td>54.4</td><td>24</td><td>79.1</td><td>16.7</td><td>4.2</td><td>8</td><td>0.0</td><td>37.5</td><td>62.5</td><td>26</td><td>46.2</td><td>46.2</td><td>7.6</td><td>207</td><td>7.7</td><td>19.8</td><td>72.5</td></tr><tr><th><i>Opalina obtrigonoidea</i></th><td>104</td><td>12.5</td><td>33.7</td><td>53.8</td><td>27</td><td>81.5</td><td>14.8</td><td>3.7</td><td>8</td><td>0.0</td><td>37.5</td><td>62.5</td><td>26</td><td>46.2</td><td>46.2</td><td>7.6</td><td>217</td><td>12.0</td><td>18.9</td><td>69.1</td></tr><tr><th><i>Opalina japonica</i></th><td>103</td><td>11.6</td><td>34.0</td><td>54.4</td><td>25</td><td>80.0</td><td>16.0</td><td>4.0</td><td>8</td><td>0.0</td><td>37.5</td><td>62.5</td><td>29</td><td>51.7</td><td>41.4</td><td>6.9</td><td>215</td><td>11.2</td><td>19.1</td><td>69.7</td></tr><tr><th><i>Opalina longa</i></th><td>105</td><td>13.4</td><td>33.3</td><td>53.3</td><td>20</td><td>75.0</td><td>20.0</td><td>5.0</td><td>8</td><td>0.0</td><td>37.5</td><td>62.5</td><td>25</td><td>44.0</td><td>48.0</td><td>8.0</td><td>213</td><td>10.3</td><td>19.3</td><td>70.4</td></tr><tr><th>PROTEROMONADIDA</th></tr><tr><th><i>Karotomorpha</i> sp. a*b</th><td>52</td><td>36.5</td><td></td><td>63.5</td><td>N/A</td><td></td><td></td><td></td><td>N/A</td><td></td><td></td><td></td><td>N/A</td><td></td><td></td><td></td><td>N/A</td><td></td><td></td><td></td></tr><tr><th><i>Proteromonas lacertae</i> b</th><td>56</td><td>41.1</td><td></td><td>58.9</td><td>N/A</td><td></td><td></td><td></td><td>N/A</td><td></td><td></td><td></td><td>N/A</td><td></td><td></td><td></td><td>N/A</td><td></td><td></td><td></td></tr></tbody></table><p><sup>aThe</sup> data presented correspond to the sequence with accession number DQ431242;the <i>Karotomorpha</i> sp. DQ431243 sequence is partial and has not been considered for this analysis.</p><p><sup>bData</sup> are available for only one species per genus;STRs are therefore considered in two categories* as species/genus specific* or as shared with other genera.</p>
Table 5 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes
<p><b>Table 5.</b> Types of short tandem repeats (STRs) found in the sequences from opalinids.</p><table><tbody><tr><th><b>Type</b></th><th><b>Characteristics</b></th><th><b>Example</b></th><th><b>Sequence (position)</b></th></tr></tbody><tbody><tr><th>Direct</th><td>Head to tail</td><td></td><td></td></tr><tr><th>Perfect</th><td>All units equal</td><td>TAATAATAATAATAA</td><td><i>Opalina undulata</i> MN 638758 (3423)</td></tr><tr><th>Imperfect</th><td>With substitutions and/or indels</td><td>AGTTT ATTTT AATTT</td><td><i>Zelleriella</i> sp. MN638763 (1762)</td></tr><tr><th>Overlapped</th><td>STR includes bases</td><td>TTTA[T ATTAT]/ [TAT TAT] TAT</td><td><i>Protoopalina limnocharis</i> MN 638759 (1493/1497)</td></tr><tr><th>Inverted</th><td>Head to head</td><td></td><td></td></tr><tr><th>Perfect</th><td>All units equal</td><td>TTTATAATATTT</td><td><i>Opalina triangulata</i> MN 638762 (470)</td></tr><tr><th>Imperfect</th><td>With substitutions and/or indels</td><td>TTATTATTATTATTTTTTTTATTA(-) TATTATT</td><td><i>Opalina japonica</i> MN 638764 (73)</td></tr></tbody></table>
Table 4. Posterior means and 95 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes
<p><b>Table 4.</b> Posterior means and 95% credibility intervals (CIs) of divergence times (DTs) of Opalinata lineages (in million years) inferred in the TimeTree analysis. Three groups of calibration time points were used to calibrate the molecular clock. Group A (‘sequence evolution’): calibration points with uniform distribution were assigned for the origin of Stramenopiles (1469.6–812.4 Mya) and Ciliophora (1344.0–627.3 Mya) and to the split of Apicomplexa and Dinoflagellata (1098.8–501.9 Mya). Group B (‘host class constraints’): the maximum bounds of the origin of Amphibia (355.7 Mya) and Sauropsida (322.4 Mya) were assigned to the nodes where <i>Karotomorpha</i> (parasite of amphibians) and <i>Proteromonas</i> (parasite of lizards) branched off* respectively. Group C (‘anuran family constraints’): a maximum bound was assigned to the nodes where <i>Protoopalina</i> * <i>Zelleriella</i> * and <i>Opalina</i> branched off* based on the estimated maximum time of emergence of the most ancient anuran family in which species of each genus have been cited (respectively: Ascaphidae * 204 Mya; Microhylidae * 116.3 Mya; Bombinatoridae and Alytidae * 196 Mya). Four scenarios were analysed by combining the groups of calibration time points.</p><table><tbody><tr><th></th><th><b>Scenario 1 (A)</b></th><th><b>Scenario 2 (A + B)</b></th><th><b>Scenario 3 (A + C)</b></th><th><b>Scenario 4 (A + B + C)</b></th></tr></tbody><tbody><tr><th></th><td><b>DT (95% CI)</b></td><td><b>DT (95% CI)</b></td><td><b>DT (95% CI)</b></td><td><b>DT (95% CI)</b></td></tr><tr><th>Opalinata</th><td>586.7 (304.6–1130.1)</td><td>515.7 (267.0–996.0)</td><td>586.7 (304.6–1129.8)</td><td>515.7 (267.0–996.1)</td></tr><tr><th><i>Karotomorpha</i></th><td>351.7 (165.2–748.8)</td><td>309.2 (178.8–355.7)</td><td>351.7 (165.6–746.9)</td><td>309.2 (178.8–355.7)</td></tr><tr><th>Opalinida</th><td>250.4 (110.7–566.5)</td><td>220.1 (119.3–286.8)</td><td>250.4 (112.2–558.6)</td><td>220.1 (119.3–286.8)</td></tr><tr><th><i>Protoopalina</i></th><td>119.4 (48.6–293.5)</td><td>105.0 (56.1–196.6)</td><td>119.4 (55.1–204.0)</td><td>105.0 (56.0–196.9)</td></tr><tr><th><i>Zelleriella – Opalina</i> split</th><td>49.7 (17.4–142.3)</td><td>43.7 (20.1–95.0)</td><td>49.7 (19.8–124.7)</td><td>43.7 (20.4–93.5)</td></tr></tbody></table>
Data from: Phylogenetic relationships of Agaric fungi based on nuclear large subunit ribosomal DNA sequences
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Data from: Ribosomal RNA gene repeats associate with the nuclear pore complex for maintenance after DNA damage
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Figure 6 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes
Figure 6. Cladogram showing the evolution of Opalinata* based on the proposed evolution of morphological traits (white circles; Delvinquier and Patterson 1993) and the characteristics of the rRNA genes (green circles). The relationships within Proteromonadida are not clear and are represented as a polytomy. Evolutionary steps are as follows. (1) Uninucleated cells develop cytoplasmic membranes with ridges or folds supported by a cortical cytoskeleton; few flagella* with a transitional helix in its structure; rRNA with secondary structure and GC content similar to that of outgroup taxons (i.e. Blastocystis). (2) Multiple flagella covering the cell surface; marginal falx. (3) Insertions made of short tandem repeats (STRs) in the expansion regions of rRNA; low GC in rRNA insertions and ITS1–ITS2 regions. (4) Binucleated (occasionally four-nucleated) cells. (5) Increase in number and length of rRNA insertions; very low GC content in rRNA insertions and ITS1–ITS2 regions. (6) Axial falx. (7) Multinucleate cells. (8) Partial loss of kineties. The position of Hegneriella* if valid* cannot be determined with available data.
FIGURE 4 in Identification and molecular phylogeny of agriculturally important spider mites (Acari: Tetranychidae) based on mitochondrial and nuclear ribosomal DNA sequences, with an emphasis on Tetranychus
FIGURE 4. ML tree based on ITS1 sequences. Sequence data for the ITS1 was aligned from a total of 23 individuals from nine species. The outgroups Neoseiulus swirskii and Typhlodromus pyri (GenBank nos. EU310505 and FM179376, respectively) were used to root the ITS1 tree. Numbers on the branches indicate the percentage bootstrap values (>50) based on NJ bootstrapping with ML settings (1,000 replicates).
FIGURE 3 in Identification and molecular phylogeny of agriculturally important spider mites (Acari: Tetranychidae) based on mitochondrial and nuclear ribosomal DNA sequences, with an emphasis on Tetranychus
FIGURE 3. Neighbor-joining (NJ) tree (a) and maximum likelihood (ML) tree (b) based on COI sequences. Twentythree of the COI sequences were obtained from the nine Chinese tetranychid species analyzed in this study. In addition, thirteen acarine COI sequences were obtained from the GenBank: the COI sequence (GenBank nos. DQ789590 and AY320029) from Brevipalpus obovatus and Cenopalpus pulcher were used as outgroups; the other COI sequences Tetranychus truncatus, T. turkestani, T. piercei, T. neocaledonicus, Panonychus citri, Pa. ulmi, Pa. mori, Amphitetranychus viennensis, A. quercivorus, Petrobia harti and P. tunisiae (GenBank nos. AB257317, AJ316604, AB257314, X80859, AB041252, AB041253, AB041256, X99875, X99873, EU487121 and EU487119 respectively) from GenBank also included into our phylogenetic analysis. Numbers adjacent to branches show the bootstrap values (> 50%) of 1000 replicates.
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