Find research datasets worth reusing

Figure 5 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Figure 5. Phylogenetic relations of the ITS1–5.8S rDNA–ITS2–LSU rDNA sequences of Opalinida by the maximum likelihood (ML) method. The numbers at the nodes represent* respectively* the bootstrap support as computed from 1000 replicates for ML and maximum parsimony methods* and the posterior probability values of the Bayesian analysis. The tree is rooted considering the Protoopalina sequences at the basal position according to the results obtained in the phylogenetic analysis of the SSU rDNA sequences. New sequences are noted in bold.

Figure 4 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Figure 4. Opalinata subtree showing the results of the TimeTree analysis inferred by applying the RelTime method to the SSU rDNA phylogenetic tree calculated by the maximum parsimony method. Three sets of calibrations including a total of seven time points were combined to obtain the TimeTree (set A* 'sequence evolution'* included three calibration points with uniform distributions; set B* 'host class constraints'* included two maximum time calibration points; and set C* 'host family constraints'* included two maximum time calibration points; see main text for further details); diamonds indicate calibration points included within the Opalinata subtree. Divergence time estimates and their 95% credibility intervals (magenta bars) are indicated in each node. Images showing the evolution of continents are from Scotese (2016).

Figure 3. A in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Figure 3. A* phylogenetic relationships of the SSU rDNA sequences of Opalinata by maximum likelihood (ML) method. The Salpingoeca infusorium AF100941 sequence was used as an outgroup. The number at the nodes represent* respectively* the bootstrap support as computed from 1000 replicates for ML and maximum parsimony methods* and the posterior probability values of the Bayesian analysis. Dashes (–) indicate a different tree topology. The tree is drawn to scale* with branch lengths measured in the number of substitutions per site. New sequences are noted in bold. B* phylogenetic relationships of the SSU rDNA sequences of Opalinata by Bayesian inference; only the subtree corresponding to Opalinata is presented* showing the differences in the branching pattern with respect to the trees obtained by ML and maximum parsimony methods. The numbers at the nodes represent posterior probability values; the probabilities for the nodes without numbers are given in Figure 3A.

Figure 2. Proposed general secondary structure model for the ITS1–5.8S rDNA–ITS2 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Figure 2. Proposed general secondary structure model for the ITS1–5.8S rDNA–ITS2–LSU rDNA of Opalinida* The expansion segments (ES#L) containing helices (in red) where there are important differences between genera are annotated. Colour code: yellow* ITS1 region; blue* 5.8S rRNA; magenta* ITS2 region; grey* LSU rRNA.

Figure 1 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Figure 1. Proposed general secondary structure model for the SSU rRNA of Opalinata (Proteromonadida and Opalinida). The expansion segments (ES#S) containing helices (in red) where there are important differences between genera are annotated.

Table 2 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Table 2. Primers used for PCRs and sequencing (F* forward; R* reverse).<table><tbody><tr><th>Primer</th><th>Sequence</th><th>Reference</th></tr></tbody><tbody><tr><th>MedlinA (F)</th><td>5 ʹ -AACCTGGTTGATCCTGCCAGT-3%</td><td>Medlin et al. (1988)</td></tr><tr><th>MedlinB (R)</th><td>5 ʹ -TGATCCTTCTGCAGGTTCACCTAC-3%</td><td>Medlin et al. (1988)</td></tr><tr><th>SSU-LSU-F (F)</th><td>5 ʹ -TCGCACCTACCGATTGGATG-3%</td><td>This study</td></tr><tr><th>SSU-LSU-R (R)</th><td>5 ʹ -GAAAAGATAACTCTTCCTAG-3%</td><td>This study</td></tr><tr><th>M28S-F (F)</th><td>5 ʹ -TAGCCCTGAAAATGGATGGCGCT-3%</td><td>This study</td></tr><tr><th>28S-4R (R)</th><td>5 ʹ -TTCTGACTTAGAGGCGTTCAG-3%</td><td>Moreira et al. (2007)</td></tr></tbody></table>

Table 1 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Table 1. Opalinid species investigated in the present study. All localities are from China. Morphological identification of each species was carried out in the articles indicated in the ‘reference’ column.<table><tbody><tr><th>Species</th><th>Host</th><th>Prevalence</th><th>Locality</th><th>Reference</th></tr></tbody><tbody><tr><th>Opalina undulata Nie* 1935</th><td>Fejervarya limnocharis (Gravenhorst* 1829) Iskandar* 1998</td><td>7.7% (22/285)</td><td>Diaocha Lake* Hubei Province</td><td>Li et al. (2018)</td></tr><tr><th>Opalina triangulata Metcalf* 1923</th><td>F. limnocharis</td><td>21.5% (9/42)</td><td>Diaocha Lake* Hubei Province</td><td>Wang et al. (2019)</td></tr><tr><th>Opalina japonica Sugiyama* 1920</th><td>Rana chensinensis David * 1875</td><td>33.3% (4/12)</td><td>Xinbin County* Liaoning Province</td><td>Unpublished</td></tr><tr><th>Opalina obtrigonoidea Metcalf* 1923</th><td>Duttaphrynus melanostictus (Schneider* 1799) Frost et al. * 2006</td><td>31.4% (11/35)</td><td>Yubei City* Chongquin Province</td><td>Zhao et al. (2020)</td></tr><tr><th>Opalina longa Bezzenberger* 1904 (= Cepedea longa)a</th><td>F. limnocharis</td><td>35.8% (76/ 212)</td><td>Honghu Lake* Hubei Province</td><td>Li et al. (2017a)</td></tr><tr><th>Protoopalina limnocharis Nie * 1932</th><td>F. limnocharis</td><td>25.6% (32/125)</td><td>Meishan County* Sichuan Province</td><td>Zou et al. (2018)</td></tr><tr><th>Protoopalina pingi Nie* 1935</th><td>Pelophylax nigromaculatus (Hallowell* 1861) Fei et al. * 2005</td><td>40.4% (42/104)</td><td>Honghu Lake* Hubei Province</td><td>Li et al. (2014)</td></tr><tr><th>Zelleriella orientalis Nie* 1935</th><td>Microhyla ornate (Duméril & Bibron* 1841) Boulenger* 1882</td><td>16.2% (6/37)</td><td>Nanning City* Guangxi Province</td><td>Unpublished</td></tr><tr><th>Zelleriella sp.</th><td>Hyla chinensis Gunther * 1858</td><td>11.1% (2/18)</td><td>Sanming City* Fujian Province</td><td>Unpublished</td></tr></tbody></table>aThe initial identification of this species as Cepedea longa followed the proposal by Metcalf (1923). See Discussion section for the justification of the change.

Table 3 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Table 3. List of sequences used in the present study. Sequences lacking>100 bases at the 5 ʹ or 3 ʹ ends are shown in parentheses. New sequences are marked in bold.<table><tbody><tr><th>Sequence/species</th><th>Accession sequence</th></tr><tr><th>Number</th><th>Length</th><th>GC%</th><th>Source</th></tr><tr><th>SSU rDNA</th></tr><tr><th>STRAMENOPILES</th></tr><tr><th>OPALINATA</th></tr><tr><th>Opalinida</th></tr><tr><th>(Protoopalina intestinalis (Stein* 1856) Metcalf* 1923)</th></tr></tbody><tbody><tr><th></th><td>AY576545</td><td>1409</td><td>33.6</td><td>Kostka et al. (2004)</td></tr><tr><th>(Protoopalina axonucleata Metcalf * 1923a)</th><td>AB175929</td><td>1263</td><td>32.5</td><td>Nishi et al. (2005)</td></tr><tr><th>Protoopalina limnocharis</th><td>MN625264</td><td>1829</td><td>32.2</td><td>This study</td></tr><tr><th>Protoopalina pingi</th><td>MN625266</td><td>1830</td><td>32.4</td><td>This study</td></tr><tr><th>Zelleriella orientalis</th><td>MN625263</td><td>2143</td><td>26.4</td><td>This study</td></tr><tr><th>Zelleriella sp.</th><td>MN625265</td><td>2143</td><td>26.4</td><td>This study</td></tr><tr><th>Opalina undulata</th><td>MF434114</td><td>2167</td><td>26.8</td><td>Li et al. (2018)</td></tr><tr><th>Opalina triangulata</th><td>MK872804</td><td>2166</td><td>26.8</td><td>Wang et al. (2019)</td></tr><tr><th>Opalina obtrigonoidea</th><td>MK970648</td><td>2167</td><td>26.8</td><td>Zhao et al. (2020)</td></tr><tr><th>Opalina japonica</th><td>MN625267</td><td>2170</td><td>26.0</td><td>This study</td></tr><tr><th>Opalina longa</th><td>MN625268</td><td>2171</td><td>27.7</td><td>This study</td></tr><tr><th>Proteromonadida</th></tr><tr><th>Karotomorpha sp.</th><td>DQ431242</td><td>1858</td><td>44.1</td><td>Kostka et al. (2007)</td></tr><tr><th>(Karotomorpha sp.)</th><td>DQ431243</td><td>1424</td><td>46.2</td><td>Kostka et al. (2007)</td></tr><tr><th>Proteromonas lacertae Grassé * 1879</th><td>U37108</td><td>1743</td><td>37.4</td><td>Leipe et al. (1996)</td></tr><tr><th>BLASTOCYSTIDA</th></tr><tr><th>Blastocystis cycluri Singh et al. * 1996</th><td>AY266474</td><td>1848</td><td>35.6</td><td>Yoshikawa et al. (2004)</td></tr><tr><th>Blastocystis lapemi Teow et al. * 1991 Blastocystis pythoni Singh et al. * 1996</th><td>AY266471 AY266472</td><td>1840 1794</td><td>36.7 39.1</td><td>Yoshikawa et al. (2004) Yoshikawa et al. (2004)</td></tr><tr><th>Blastocystis hominis (Swaine & Britain* 1849) Brumpt* 1912</th><td></td><td></td><td></td></tr><tr><th>Blastocystis ratti Chen et al. * 1997 PLACIDIDA</th><td>AB023499 AY590114</td><td>1740 1730</td><td>43.6 40.3</td><td>Arisue et al. (2002) Noel et al. (2005)</td></tr><tr><th>Placidia cafeteriopsis Moriya et al. * 2002</th><td>JF834161</td><td>1775</td><td>49.4</td><td>Chan YF* Chen CW* Tsai AY* Chiang KP* unpublished</td></tr><tr><th>Suigetsumonas clinomigrationis Okamura & Kondo * 2015</th><td></td><td></td><td></td></tr><tr><th>Wobblia lunata Moriya et al. * 2000 BICOSOECIDA</th><td>AB976561 AB032606</td><td>1769 1726</td><td>52.0 49.1</td><td>Okamura and Kondo (2015) Moriya et al. (2000)</td></tr><tr><th>Bicosoeca petiolata (Stein* 1878) Prinsheim* 1946</th><td></td><td></td><td></td></tr><tr><th></th><td>AY520444</td><td>1809</td><td>48.6</td><td>Cavalier-Smith and Chao (2006)</td></tr><tr><th>Cafeteria roenbergensis Fenchel & Patterson * 1988</th><td></td><td></td><td></td></tr><tr><th></th><td>AF174364</td><td>1695</td><td>47.1</td><td>Atkins et al. (2000)</td></tr><tr><th>ALVEOLATA</th></tr><tr><th>APICOMPLEXA</th></tr><tr><th>Babesia gibsoni (Patton* 1910)</th><td>KC461261</td><td>1665</td><td>45.5</td><td>Mandal et al. (2015)</td></tr><tr><th>Eimeria necatrix Johnson * 1930</th><td>KT184349</td><td>1763</td><td>46.8</td><td>Ogedengbe et al. (2016)</td></tr><tr><th>DINOFLAGELLATA</th></tr><tr><th>Blastodinium contortum Chatton * 1908</th><td>DQ317537</td><td>1799</td><td>44.8</td><td>Skovgaard et al. (2007)</td></tr><tr><th>Prorocentrum arenarium Faust * 1994</th><td>Y16234</td><td>1788</td><td>46.4</td><td>Grzebyk et al. (1998)</td></tr><tr><th>CILIOPHORA</th></tr><tr><th>LItonotus paracygnus Song* 1994</th><td>EU242509</td><td>1635</td><td>42.0</td><td>Gao et al. (2008)</td></tr><tr><th>Paramecium buestchlii van As et al. * 1998</th><td>KM091234</td><td>1703</td><td>44.2</td><td>Krenek et al. (2015)</td></tr><tr><th>AMORPHEA</th></tr><tr><th>CHOANOZOA</th></tr><tr><th>Salpingoeca infusionum Kent * 1880</th><td>AF100941</td><td>1978</td><td>49.6</td><td>Collins (1998)</td></tr><tr><th>ITS region (OPALINATA)</th><td></td><td></td><td></td><td></td></tr><tr><th>Protoopalina limnocharis</th><td>MN630239</td><td></td><td></td><td>This study</td></tr><tr><th>ITS1</th><td></td><td>231</td><td>2.2</td><td></td></tr><tr><th>5.8S</th><td></td><td>154</td><td>35.7</td><td></td></tr><tr><th>ITS2</th><td></td><td>229</td><td>4.4</td><td></td></tr><tr><th>Protoopalina pingi</th><td>MN630241</td><td></td><td></td><td>This study</td></tr><tr><th>ITS1</th><td></td><td>237</td><td>2.1</td><td></td></tr><tr><th>5.8S</th><td></td><td>154</td><td>36.4</td><td></td></tr><tr><th>ITS2</th><td></td><td>218</td><td>4.6</td><td></td></tr><tr><th>Zelleriella orientalis</th><td>MN630236</td><td></td><td></td><td>This study</td></tr><tr><th>ITS1</th><td></td><td>291</td><td>2.8</td><td></td></tr><tr><th>5.8S</th><td></td><td>167</td><td>26.4</td><td></td></tr><tr><th>ITS2</th><td></td><td>285</td><td>2.5</td><td></td></tr><tr><th>Zelleriella sp.</th><td>MN630237</td><td></td><td></td><td>This study</td></tr><tr><th>ITS1</th><td></td><td>290</td><td>2.8</td><td></td></tr><tr><th>5.8S</th><td></td><td>166</td><td>26.5</td><td></td></tr><tr><th>ITS2</th><td></td><td>279</td><td>2.5</td><td></td></tr><tr><th>Opalina undulata</th><td>MG816209</td><td></td><td></td><td>Li et al. (2018)</td></tr><tr><th>ITS1</th><td></td><td>325</td><td>1.5</td><td></td></tr><tr><th>5.8S</th><td></td><td>167</td><td>24.0</td><td></td></tr><tr><th>ITS2</th><td></td><td>290</td><td>2.4</td><td></td></tr><tr><th>Opalina triangulata</th><td>MK872803</td><td></td><td></td><td>Wang et al. (2019)</td></tr><tr><th>ITS1</th><td></td><td>292</td><td>1.7</td><td></td></tr><tr><th>5.8S</th><td></td><td>167</td><td>24.6</td><td></td></tr><tr><th>ITS2</th><td></td><td>284</td><td>1.8</td><td></td></tr><tr><th>Opalina obtrigonoidea</th><td>MK973090</td><td></td><td></td><td>Zhao et al. (2020)</td></tr><tr><th>ITS1</th><td></td><td>323</td><td>1.6</td><td></td></tr><tr><th>5.8S</th><td></td><td>167</td><td>24.6</td><td></td></tr><tr><th>ITS2</th><td></td><td>287</td><td>1.7</td><td></td></tr><tr><th>Opalina japonica</th><td>MN630238</td><td></td><td></td><td>This study</td></tr><tr><th>ITS1</th><td></td><td>357</td><td>1.7</td><td></td></tr><tr><th>5.8S</th><td></td><td>167</td><td>24.6</td><td></td></tr><tr><th>ITS2</th><td></td><td>358</td><td>2.5</td><td></td></tr><tr><th>Opalina longa</th><td>MN630240</td><td></td><td></td><td>This study</td></tr><tr><th>ITS1</th><td></td><td>283</td><td>1.8</td><td></td></tr><tr><th>5.8S</th><td></td><td>167</td><td>24.6</td><td></td></tr><tr><th>ITS2</th><td></td><td>261</td><td>2.3</td><td></td></tr><tr><th>LSU rDNA (OPALINATA)</th><td></td><td></td><td></td><td></td></tr><tr><th>Protoopalina limnocharis</th><td>MN638759</td><td>3652</td><td>26.7</td><td>This study</td></tr><tr><th>Protoopalina pingi</th><td>MN638761</td><td>3647</td><td>26.9</td><td>This study</td></tr><tr><th>Zelleriella orientalis</th><td>MN638760</td><td>4064</td><td>23.0</td><td>This study</td></tr><tr><th>Zelleriella sp.</th><td>MN638763</td><td>4102</td><td>22.8</td><td>This study</td></tr><tr><th>Opalina undulata</th><td>MN638758</td><td>4108</td><td>22.8</td><td>This study</td></tr><tr><th>Opalina triangulata</th><td>MN638762</td><td>4043</td><td>23.9</td><td>This study</td></tr><tr><th>Opalina obtrigonoidea</th><td>MW504710</td><td>4122</td><td>22.5</td><td>This study</td></tr><tr><th>Opalina japonica</th><td>MN638764</td><td>4120</td><td>22.4</td><td>This study</td></tr><tr><th>Opalina longa</th><td>MN638765</td><td>4096</td><td>23.6</td><td>This study</td></tr></tbody></table>aNishi et al. (2005: 701–702) indicated that ‘the four sequences from Protoopalina sp. were all identical* although they were isolated at different geographical locations.Futhermore* the genus Protoopalina is presently restricted to the host species Rana nigromaculata in Japan.They commonly retain four relatively large nuclei* show similar morphological characters (Table 1)* and are classified as P.japonica (Hara 1934) ’. However* the work by Hara (1934) is on the cell morphology and microtubular structures of Protoopalina axonucleata * and he did not mention any other species in his work.According to the statements by Nishi et al. (2005) * their isolates corresponded to the same species studied by Hara (1934) and should be identified as P.axonucleata. The name Protoopalina japonica is a nomen nudum because this species has never been described.

Table 7 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Table 7. List of nomenclatural acts.<table><tbody><tr><th>Taxon nameb</th><th>Previous name</th><th>Comments</th></tr><tr><th>Opalina Purkinje & Valentin * 1835 (= Cepedea Metcalf * 1920)</th></tr></tbody><tbody><tr><th>Opalina acuta (Delvinquier* Markus & Passmore* 1993) comb. nov.</th><td>Cepedea acuta Delvinquier * Markus & Passmore* 1992</td><td></td></tr><tr><th>Opalina affinis Nazaretskaja * 1922</th><td>Cepedea affinis (Nazaretskaja* 1922) Walton* 1964</td><td></td></tr><tr><th>Opalina africana (Tuzet & Zuber-Vogeli* 1954) comb. nov.</th><td>Cepedea africana Tuzet & Zuber-Vogeli * 1954</td><td>Proposed as synonym of Opalina affinis by Delvinquier et al. (1993)</td></tr><tr><th>Opalina amygdala (Boisson* 1965) Delvinquier et al. * 1991</th><td>Cepedea amygdala Boisson * 1965</td><td>Proposed as synonym of Opalina foliacea by Affa’a and Lynn (1994)</td></tr><tr><th>Opalina baudinii (Metcalf* 1923) comb. nov.</th><td>Cepedea baudini Metcalf * 1923</td><td></td></tr><tr><th>Opalina boissoni (Tuzet & Knoepffler* 1968) comb. nov.</th><td>Cepedea boissoni Tuzet & Knoepffler * 1968</td><td>Proposed as synonym of Opalina affinis by Delvinquier et al. (1993)</td></tr><tr><th>Opalina borneonensis (Metcalf* 1923) comb. nov.</th><td>Cepedea borneonensis Metcalf * 1923</td><td></td></tr><tr><th>Opalina buergeri (Metcalf* 1923) comb. nov.</th><td>Cepedea buergeri Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina brumpti (Cordero* 1928) comb. nov.</th><td>Cepedea brumpti Cordero * 1928</td><td></td></tr><tr><th>Opalina cantabrigensis (Metcalf* 1923)</th><td>Cepedea cantabrigensis Metcalf * 1923</td><td></td></tr><tr><th>Opalina celebensis (Metcalf* 1923) comb. nov.</th><td>Cepedea celebensis Metcalf * 1923</td><td></td></tr><tr><th>Opalina ciliata (Metcalf* 1940) comb. nov.</th><td>Cepedea ciliata Metcalf * 1940</td><td></td></tr><tr><th>Opalina crispata (Boisson* 1965) comb. nov.</th><td>Cepedea crispata Boisson * 1965</td><td>Proposed as synonym of Opalina affinis by Delvinquier et al. (1993)</td></tr><tr><th>Opalina daloalensis (Tuzet & Zuber-Vogeli* 1954) comb. nov.</th><td>Cepedea daloalensis Tuzet & Zuber-Vogeli * 1954</td><td></td></tr><tr><th>Opalina dimidiata Stein * 1860</th><td>Cepedea dimidiata (Stein* 1860) Metcalf* 1923</td><td></td></tr><tr><th>Opalina dolichosoma (Metcalf* 1923) comb. nov.</th><td>Cepedea dolichosoma Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina dracuncula (Boisson* 1957) comb. nov.</th><td>Cepedea dracuncula Boisson * 1957</td><td></td></tr><tr><th>Opalina elongata Gourvitsch * 1926</th><td>Cepedea elongata (Gourvitsch* 1926) Banina* 1962</td><td></td></tr><tr><th>Opalina flava Stokes * 1884</th><td>Cepedea flava (Stokes* 1884) Metcalf* 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina floridensis (Metcalf* 1923) comb. nov.</th><td>Cepedea floridensis Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina foliacea (Boisson* 1959) Delvinquier et al. * 1991</th><td>Cepedea foliacea Boisson * 1959</td><td></td></tr><tr><th>Opalina formosae (Metcalf* 1923) comb. nov.</th><td>Cepedea formosae Metcalf * 1923</td><td></td></tr><tr><th>Opalina fujiensis (Metcalf* 1923) comb. nov.</th><td>Cepedea fujiensis Metcalf * 1923</td><td></td></tr><tr><th>Opalina fusiformis (Tuzet & Knoepffler* 1968) comb. nov.</th><td>Cepedea fusiformis Tuzet & Knoepfler * 1968</td><td>Proposed as synonym of Opalina affinis by Delvinquier et al. (1993)</td></tr><tr><th>Opalina globosa (Metcalf* 1923) comb. nov.</th><td>Cepedea globosa Metcalf * 1923</td><td></td></tr><tr><th>Opalina gracilis (Banina* 1952) comb. nov.</th><td>Cepedea gracilis Banina * 1952</td><td></td></tr><tr><th>Opalina hasseltii (Metcalf* 1940) comb. nov.</th><td>Cepedea hasseltii Metcalf * 1940</td><td></td></tr><tr><th>Opalina hispanica (Metcalf* 1923) comb. nov.</th><td>Cepedea hispanica Metcalf * 1923</td><td>Proposed as synonym of Opalina longa by Metcalf (1940)</td></tr><tr><th>Opalina hosei (Metcalf* 1940) comb. nov.</th><td>Cepedea hosei Metcalf * 1940</td><td></td></tr><tr><th>Opalina hylae (Khan* 1962) comb. nov.</th><td>Cepedea hylae Khan * 1962</td><td></td></tr><tr><th>Opalina lemuriae (Metcalf* 1940) comb. nov.</th><td>Cepedea lemuriae Metcalf * 1940</td><td></td></tr><tr><th>Opalina longa Bezzenberger * 1904</th><td>Cepdea longa (Bezzenberger* 1904) Metcalf* 1923</td><td></td></tr><tr><th>Opalina luzonensis (Metcalf* 1940) comb. nov.</th><td>Cepedea luzonensis Metcalf * 1940</td><td></td></tr><tr><th>Opalina macronucleata (Banina* 1952) comb. nov.</th><td>Cepedea macronucleata Banina * 1952</td><td></td></tr><tr><th>Opalina madagascariensis (Metcalf* 1923) comb. nov.</th><td>Cepedea madagascariensis Metcalf * 1923</td><td>Considered in part as synonym of Opalina affinis by Delvinquier et al. (1993)</td></tr><tr><th>Opalina magna (Metcalf* 1923) comb. nov.</th><td>Cepedea magna Metcalf * 1923</td><td>(= Opalina sudafricana Fantham * 1923) (following Delvinquier et al. 1993)</td></tr><tr><th>Opalina marginata (Amaro* 1964) comb. nov.</th><td>Cepedea marginata Amaro * 1964</td><td></td></tr><tr><th>Opalina metcalfi (Bhatia & Gulati* 1927) comb. nov.</th><td>Cepedea metcalfi Bhatia & Gulati * 1927</td><td></td></tr><tr><th>Opalina mexicana (Metcalf* 1923) comb. nov.</th><td>Cepedea mexicana Metcalf * 1923</td><td></td></tr><tr><th>Opalina microhylae (Metcalf* 1940) comb. nov.</th><td>Cepedea microhylae Metcalf * 1940</td><td></td></tr><tr><th>Opalina minor (Metcalf* 1923) comb. nov.</th><td>Cepedea minor Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina mogyana Carini * 1937</th><td>Cepedea mogyana (Carini* 1937) Metcalf* 1940</td><td></td></tr><tr><th>Opalina multiformis (Metcalf* 1923) comb. nov.</th><td>Cepedea multiformis Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina obovoidea (Metcalf* 1923) comb. nov.</th><td>Cepedea obovoidea Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina obtrigonoidea Metcalf * 1923</th><td>Cepedea obtrigonoidea (Metcalf* 1923) Affa’a & Lynn* 1994</td><td></td></tr><tr><th>Opalina occidentalis (Metcalf* 1923) comb. nov.</th><td>Cepedea occidentalis Metcalf * 1923</td><td></td></tr><tr><th>Opalina ophis (Metcalf* 1923) comb. nov.</th><td>Cepedea ophis Metcalf * 1923</td><td></td></tr><tr><th>Opalina parva (Lu* 1945) comb. nov.</th><td>Cepedea parva Lu * 1945</td><td></td></tr><tr><th>Opalina philauti (Uttangi* 1952) comb. nov.</th><td>Cepedea philauti Uttangi * 1952</td><td></td></tr><tr><th>Opalina philippensis (Metcalf* 1940) comb. nov.</th><td>Cepedea philippensis Metcalf * 1940</td><td></td></tr><tr><th>Opalina phrynomantidis (Metcalf* 1923) comb. nov.</th><td>Cepedea phrynomantidis Metcalf * 1923</td><td>Proposed as synonym of Opalina magna by Delvinquier et al. (1993)</td></tr><tr><th>Opalina plata (Metcalf* 1940) comb. nov.</th><td>Cepedea plata Metcalf * 1940</td><td></td></tr><tr><th>Opalina pulchra (Metcalf* 1923) comb. nov.</th><td>Cepedea pulchra Metcalf * 1923</td><td></td></tr><tr><th>Opalina punjagbensis (Bhatia & Gulati* 1927) comb. nov.</th><td>Cepedea punjagbensis Bhatia & Gulati * 1927</td><td></td></tr><tr><th>Opalina rubra Carini * 1937</th><td>Cepedea rubra (Carini* 1937) Metcalf* 1940</td><td></td></tr><tr><th>Opalina rugosa Carini * 1937</th><td>Cepedea rugosa (Carini* 1937) Metcalf* 1940</td><td></td></tr><tr><th>Opalina saharana (Metcalf* 1923) comb. nov.</th><td>Cepedea saharana Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina scalpriformis Ghosh * 1918</th><td>Cepedea scalpriformis (Ghosh* 1918) Metcalf* 1940</td><td></td></tr><tr><th>Opalina segmentata (Metcalf* 1923) comb. nov.</th><td>Cepedea segmentata Metcalf * 1923</td><td></td></tr><tr><th>Opalina seychellensis (Metcalf* 1923) comb. nov.</th><td>Cepedea seychellensis Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina sialkoti (Bathia & Gulati* 1927) comb. nov.</th><td>Cepedea sialkoti Bathia & Gulati * 1927</td><td></td></tr><tr><th>Opalina siamensis (Metcalf* 1940) comb. nov.</th><td>Cepedea siamensis Metcalf * 1940</td><td></td></tr><tr><th>Opalina spinifera (Metcalf* 1923) comb. nov.</th><td>Cepedea spinifera Metcalf * 1923</td><td></td></tr><tr><th>Opalina subcylindrica (Mello* 1932) comb. nov.</th><td>Cepedea subcylindrica Mello * 1932</td><td></td></tr><tr><th>Opalina sudafricana Fantham * 1923</th><td>Cepedea sudafricana (Fantam* 1923) Affa’a & Lynn* 1994</td><td></td></tr><tr><th>Opalina thiagi (Mello* 1931) comb. nov.</th><td>Cepedea thiagi Mello * 1931</td><td></td></tr><tr><th>Opalina vanniekerkae (Delvinquier* Markus & Passmore* 1993)</th><td>Cepedea vanniekerkae Delvinquier * Markus & Passmore* 1993</td><td></td></tr><tr><th>Opalina virgula Dobell * 1910</th><td>Cepedea virgula (Dobell* 1910) Metcalf* 1940</td><td></td></tr><tr><th>Opalina virguloidea Metcalf * 1923</th><td>Cepedea virguloidea (Metcalf* 1923) Affa’a & Lynn* 1994</td><td></td></tr><tr><th>Protoopalina Metcalf * 1918 (= Bezzenbergeria Earl * 1973)</th><td></td><td></td></tr><tr><th>Protoopalina lanceolata Bezzenberger* 1904</th><td>Bezzenbergeria lanceolata [(Bezzenberger* 1904) Metcalf* 1923] Earl* 1973 Cepedea lanceolata (Bezzenberger* 1904) Metcalf* 1923</td><td></td></tr><tr><th>Protoopalina axoucleata Metcalf * 1923</th><td>Protoopalina japonica Nishi et al. * 2005</td><td>Nomem nudum</td></tr></tbody></table>aThe species Cepedea lanceolatum was listed by Delvinquier and Patterson (1993)* citing Evans et al. (1977) * but without specifying the author and publication year.We have been unable to obtain a copy of the paper by Evans et al. (1977) in order to search for a description or the reference to the original source.Therefore* we have not included this species in the list.If it were to be included* the correct species name would be Opalina lanceolata.bEarl (1973) proposed the suppression of 88 species/subspecies of Opalinida because he deemed them inadequately described:certain characteristics were absent from the original descriptions (such as the length of the falx)* and the descriptions were based on type specimens rather than on populations.

FIGURE 6 in Phylogenetic analysis of the Prionini (Coleoptera: Cerambycidae: Prioninae) from China based on mitochondrial ribosomal RNA genes and Cytochrome oxidase I gene

FIGURE 6. Phylogeny of the Chinese Prionini based on combined sequences of 12S rRNA and 16S rRNA. A: Bootstrap 50% majority-rule consensus tree of distance method by PAUP* with bootstrap values (%), Wtd. S.S. = 0.0496, APSD = 3.764, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; B: Bootstrap 50% majority-rule consensus tree of maximum likelihood method by PAUP* with bootstrap values (%), -Ln likelihood = 4527.5195, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; C: Bootstrap 50% majority-rule consensus tree of parsimony method by PAUP* with bootstrap values (%), tree length = 792, CI = 0.7109, RI = 0.3639, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; D: Bayesian tree by MrBayes with Bayesian posterior probabilities (%), the scale bar in the bottom left corner of the tree meaning 0.1 nucleotide substitutions per site.

FIGURE 4 in Phylogenetic analysis of the Prionini (Coleoptera: Cerambycidae: Prioninae) from China based on mitochondrial ribosomal RNA genes and Cytochrome oxidase I gene

FIGURE 4. Phylogeny of the Chinese Prionini based on partial sequences of 16S rRNA (excluding Priotyrannus closteroides)

FIGURE 3 in Phylogenetic analysis of the Prionini (Coleoptera: Cerambycidae: Prioninae) from China based on mitochondrial ribosomal RNA genes and Cytochrome oxidase I gene

FIGURE 3. Phylogeny of the Chinese Prionini based on partial sequences of 16S rRNA. A: Bootstrap 50% majority-rule consensus tree of distance method by PAUP* with bootstrap values (%), Wtd. S.S. = 0.1041, APSD = 5.454, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; B: Bootstrap 50% majority-rule consensus tree of maximum likelihood method by PAUP* with bootstrap values (%), -Ln likelihood = 1754.1334, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; C: Bootstrap 50% majority-rule consensus tree of parsimony method by PAUP* with bootstrap values (%), tree length = 280, CI = 0.7429, RI = 0.4586, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; D: Bayesian tree by MrBayes with Bayesian posterior probabilities (%), the scale bar in the bottom left corner of the tree meaning 0.1 nucleotide substitutions per site.

FIGURE 2 in Phylogenetic analysis of the Prionini (Coleoptera: Cerambycidae: Prioninae) from China based on mitochondrial ribosomal RNA genes and Cytochrome oxidase I gene

FIGURE 2. Phylogeny of the Chinese Prionini based on partial sequences of 12S rRNA (excluding Priotyrannus closteroides). A: Bootstrap 50% majority-rule consensus tree of distance method by PAUP* with bootstrap values, Wtd. S.S. = 0.0266, APSD = 3.139, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; B: Bootstrap 50% majority-rule consensus tree of maximum likelihood method by PAUP* with bootstrap values, -Ln likelihood = 2474.8359, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; C: Bootstrap 50% majority-rule consensus tree of parsimony method by PAUP* with bootstrap values, tree length =431, CI = 0.7425, RI = 0.4158, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; D: Bayesian tree by MrBayes with Bayesian posterior probabilities, the scale bar in the bottom left corner of the tree meaning 0.1 nucleotide substitutions per site.

FIGURE 1 in Phylogenetic analysis of the Prionini (Coleoptera: Cerambycidae: Prioninae) from China based on mitochondrial ribosomal RNA genes and Cytochrome oxidase I gene

FIGURE 1. Phylogeny of the Chinese Prionini based on partial sequences of 12S rRNA. A: Bootstrap 50% majority-rule consensus tree of distance method by PAUP* with bootstrap values, Wtd. S.S. = 0.0787, APSD = 4.741, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; B: Bootstrap 50% majority-rule consensus tree of maximum likelihood method by PAUP* with bootstrap values, -Ln likelihood = 2748.8839, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; C: Bootstrap 50% majority-rule consensus tree of parsimony method by PAUP* with bootstrap values, tree length = 499, CI = 0.7054, RI = 0.3849, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; D: Bayesian tree by MrBayes with Bayesian posterior probabilities, the scale bar in the bottom left corner of the tree meaning 0.1 nucleotide substitutions per site.

FIGURE 7 in Phylogenetic analysis of the Prionini (Coleoptera: Cerambycidae: Prioninae) from China based on mitochondrial ribosomal RNA genes and Cytochrome oxidase I gene

FIGURE 7. Phylogeny of the Chinese Prionini based on combined sequences of 12S rRNA and 16S rRNA (excluding Priotyrannus closteroides). A: Bootstrap 50% majority-rule consensus tree of distance method by PAUP* with bootstrap values (%), Wtd. S.S. = 0.0251, APSD = 3.047, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; B: Bootstrap 50% majority-rule consensus tree of maximum likelihood method by PAUP* with bootstrap values (%), -Ln likelihood = 4077.7392, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; C: Bootstrap 50% majority-rule consensus tree of parsimony method by PAUP* with bootstrap values (%), tree length =682, CI = 0.7405, RI = 0.3723, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; D: Bayesian tree by MrBayes with Bayesian posterior probabilities (%), the scale bar in the bottom left corner of the tree meaning 0.1 nucleotide substitutions per site.

publicDec 2015View details →

dryad32/100

Data from: The evolutionary dynamics of ribosomal genes, histone H3, and transposable Rex elements in the genome of Atlantic snappers

Open the record for dataset details and reuse information.

dryad28/100

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.

opencc-zeroDec 2018View details →

zenodo28/100

Fig. 3 in Karyotype characterization of Mugil incilis Hancock, 1830 (Mugiliformes: Mugilidae), including a description of an unusual co-localization of major and minor ribosomal genes in the family

Fig. 3. Metaphase plates of Mugil incilis after FISH with 45SrDNA (a) and 5SrDNA (c), respectively (b and d) DAPI counterstained. Arrows indicate chromosome pair number 1.

opencc-by-4.0Feb 2011View details →

zenodo28/100

Table 6 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Table 6. 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 ʹ or 5 ʹ end) are shown in parentheses. Abbreviation: N/A* sequence not available.<table><tbody><tr><th>Species</th><th>SSU rDNA</th><th>ITS1</th><th>5.8S rDNA</th><th>ITS2</th><th>LSU rDNA</th></tr><tr><th>T</th><th>S</th><th>G</th><th>C</th><th>T</th><th>S</th><th>G</th><th>C</th><th>T</th><th>S</th><th>G</th><th>C</th><th>T</th><th>S</th><th>G</th><th>C</th><th>T</th><th>S</th><th>G</th><th>C</th></tr><tr><th>OPALINIDA</th></tr></tbody><tbody><tr><th>(Protoopalina axonucleata)</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>(Protoopalina intestinalis)</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>Protoopalina limnocharis</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>Protoopalina pingi</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>Zelleriella orientalis</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>Zelleriella 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>Opalina undulata</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>Opalina triangulata</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>Opalina obtrigonoidea</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>Opalina japonica</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>Opalina longa</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>Karotomorpha 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>Proteromonas lacertae 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>aThe data presented correspond to the sequence with accession number DQ431242;the Karotomorpha sp. DQ431243 sequence is partial and has not been considered for this analysis.bData 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.

zenodo28/100

Table 5 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Table 5. Types of short tandem repeats (STRs) found in the sequences from opalinids.<table><tbody><tr><th>Type</th><th>Characteristics</th><th>Example</th><th>Sequence (position)</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>Opalina undulata MN 638758 (3423)</td></tr><tr><th>Imperfect</th><td>With substitutions and/or indels</td><td>AGTTT ATTTT AATTT</td><td>Zelleriella sp. MN638763 (1762)</td></tr><tr><th>Overlapped</th><td>STR includes bases</td><td>TTTA[T ATTAT]/ [TAT TAT] TAT</td><td>Protoopalina limnocharis 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>Opalina triangulata MN 638762 (470)</td></tr><tr><th>Imperfect</th><td>With substitutions and/or indels</td><td>TTATTATTATTATTTTTTTTATTA(-) TATTATT</td><td>Opalina japonica MN 638764 (73)</td></tr></tbody></table>