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36 results for “SSU rDNA”
PR2_V9, a SSU V9 rDNA reference database with functional annotations.
<p>The present data set provides a tab separated text file compressed in a gzip archive. The file includes 63,401 18S V9 rDNA reference sequences for 44,084 unique eukaryotic taxa and 9,759 16S V9 rDNA references sequences for 9,661 unique prokaryotic taxa. It includes the following fields : sequence = nucleic acid sequence of reference; lineage = taxonomic path of the reference sequence; refs = original accession numbers corresponding to the reference sequence; name = reference sequence identifier; taxogroup = high-taxonomic level assignation of the reference sequence. The file also includes six categories of functional annotations: (1) chloroplast: yes, presence of permanent chloroplast; no, absence of permanent chloroplast ; NA, undetermined. (2) symbiont (small partner): parasite, the species is a parasite; commensal, the species is a commensal; mutualist, the species is a mutualist symbiont, most often a microalgal taxon involved in photosymbiosis; no the species is not involved in a symbiosis as small partner; NA, undetermined. (3) symbiont (host): photo, the host species relies on a mutualistic microalgal photosymbiont to survive (obligatory photosymbiosis); photo_falc, same as photo, but facultative relationship; photo_klep, the host species maintains chloroplasts from microalgal prey(s) to survive; photo_klep_falc, same as photo_klep, but facultative; Nfix, the host species must interact with a mutualistic symbiont providing N2 fixation to survive; Nfix_falc, same as Nfix, but facultative; no, the species is not involved in any mutualistic symbioses; NA, undetermined. (4) silicification; yes, the species has a silicified skeleton; no, it does not; NA, undetermined. (5) calcification; yes, the species has a calcified skeleton; no, it does not; NA, undetermined. (6) strontification; yes, the species has a skeleton made of strontium; no, it does not; NA, undetermined.</p>
Fig. 5 in Morphological Redescription and SSU rDNA-based Phylogeny of Two Freshwater Ciliates, Uronema nigricans and Lembadion lucens (Ciliophora, Oligohymenophorea), with Discussion on the Taxonomic Status of Uronemita sinensis
Fig. 5. Maximum likelihood (ML) tree inferred from SSU rDNA sequences, showing the position of Uronema nigricans and Lembadion lucens (red arrows). Numbers near branches denote ML bootstrap value/BI posterior probability. Asterisks (*) indicate topologies that differ between the ML and BI analyses. Fully supported (100%/1.00) branches are marked with solid circles. Question marks (?) in red color indicate that the two sequences are possibly misidentified. The scale bar corresponds to 5 substitutions per 100 nucleotide positions. All branches are drawn to scale. Systematic classification mainly follows Lynn (2008).
Fig. 4 in Morphological Redescription and SSU rDNA-based Phylogeny of Two Freshwater Ciliates, Uronema nigricans and Lembadion lucens (Ciliophora, Oligohymenophorea), with Discussion on the Taxonomic Status of Uronemita sinensis
Fig. 4. Photomicrographs of Lembadion lucens from life (A–D, with A in bright field illumination and others in DIC microscopy) and after protargol staining (E–K). (A, B) Ventral views of representative individuals, cell in B was slightly depressed. Arrow shows caudal cilia. (C) Dorsal view, arrowhead points to the contractile vacuole. (D) Apical view, revealing the shape of cross section. Arrow shows oral cilia. (E) Ventral view of a stained cell, showing the silverline system. (F, G) Ventral (F) and dorsal (G) view of a representative individual, to show the ciliature and nuclear apparatus. (H) Micronucleus (arrow) and macronucleus. (I) Ventral view of posterior portion. Arrows depict two basal body rows of caudal cilia. (J) Mid portion of dorsal view, illustrating the monokinetids and dikinetids. (K) Detailed view, arrows show the two separated pairs of basal bodies and arrowheads indicate the posterior ends of four gradually shortened outer rows of adoral membranelle. Scale bars: 30 μm.
Fig. 6 in Morphological Redescription and SSU rDNA-based Phylogeny of Two Freshwater Ciliates, Uronema nigricans and Lembadion lucens (Ciliophora, Oligohymenophorea), with Discussion on the Taxonomic Status of Uronemita sinensis
Fig. 6. Sequence comparison of the small subunit ribosomal RNA gene determined by BioEdit 7.0.5.2 (Hall 1999), showing the unmatched nucleotides of Uronema nigricans MF072399 and Lembadion lucens MF072398 with their sister sequences in the same clades, respectively (see Fig. 5). Nucleotide positions are given at the top of each column. Insertions and deletions are compensated by introducing alignment gaps (–). Numbers of unmatched sites (n) and sequence similarity percentages (%) compared with Uronema nigricans MF072399 and Lembadion lucens MF072398 are also supplied. The two sequences with question marks (?) are possibly misidentified. ID, identical; n, numbers of unmatched sites; %, sequence similarity percentages.
Fig. 3 in Morphological Redescription and SSU rDNA-based Phylogeny of Two Freshwater Ciliates, Uronema nigricans and Lembadion lucens (Ciliophora, Oligohymenophorea), with Discussion on the Taxonomic Status of Uronemita sinensis
Fig. 3. Photomicrographs of Uronema nigricans from life (A–E, in bright field illumination) and after protargol (F–M) staining. (A–C) Right ventrolateral views of representative individuals, with cell in C slightly depressed. Arrow in A shows contractile vacuole, while in C indicates macronucleus. (D) View of caudal portion of another cell, arrow points to caudal cilium. (E) Different body sizes, showing conspicuous apical plate. (F, G) Ventral views of stained individuals, indicating the structure of scutica. (H, I) Portion views of oral apparatus, revealing the number of kinety rows in M2 (two rows in H and three rows in I). (J, K) Ventral (J) and dorsal (K) view of a representative individual to show the ciliature and nuclear apparatus. Arrow in J points to basal body of caudal cilium, arrow in K indicating the apical plate. (L, M) Left ventrolateral (L) and right dorsolateral (M) view of another stained individual to show the ciliature and oral apparatus. Scale bars: 15 μm (A, B); 30 μm (E).
Fig. 1 in Morphological Redescription and SSU rDNA-based Phylogeny of Two Freshwater Ciliates, Uronema nigricans and Lembadion lucens (Ciliophora, Oligohymenophorea), with Discussion on the Taxonomic Status of Uronemita sinensis
Fig. 1. Map and sampling site. The yellow dots on the map and two corresponding photographs (A, B) show the collecting sites. (A) Fresh- water river in Shenzhen, southern China (22°32'19"N; 114°06'45"E). (B) Huguangyan Lake, an oligotrophic lake in Zhanjiang, southern China (21°08'38"N; 110°16'20"E).
FIGURE 3 Bayesian tree inferred from SSU gene rDNA sequences. Posterior probabilities exceeding 50 in A review of the genus Trischistoma Cobb, 1913 (Nematoda: Enoplida), with descriptions of four new species from New Zealand
FIGURE 3 Bayesian tree inferred from SSU gene rDNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species, GenBank numbers are listed for each taxon.
FIGURE 5 in Morphology and SSU rDNA sequences of four cyrtophorian ciliates from China, with description of a new species (Protista, Ciliophora, Phyllopharyngea)
FIGURE 5. Photomicrographs of Dysteria monostyla (A–E) and D. crassipes (F–I) from live (A, B, F, and G) and after protargol impregnation (C–E and H, I). A. Left lateral view of a representative individual, arrowheads show contractile vacuoles (CV). B. Cell surface, arrow refers to the transverse stripe, arrowhead shows bar-shaped ectosymbiotic bacteria. C. Left lateral view of ciliary pattern. D. Anterior part of cell. E. Ventral view of mid-body. F. Left lateral view of a representative individual, arrows point to contractile vacuoles. G. Rod-shaped ectosymbiotic bacteria attached on cell surface (arrowheads). H, I. Left lateral views of ciliature. Abbreviations: Co—circumoral kineties; EF—equatorial fragment; FvK—frontoventral kineties; Lfleft frontal kineties; LK—left kineties; Ma—macronucleus; Pr—preoral kinety; RK—right kineties; TF—terminal fragment. Scale bars: 30 μm (A, C, F and H).
FIGURE 4 in Morphology and SSU rDNA sequences of four cyrtophorian ciliates from China, with description of a new species (Protista, Ciliophora, Phyllopharyngea)
FIGURE 4. Photomicrographs of Chlamydodon bourlandi from life (A, D, and E in bright field, B, C, F, and G by differential interference contrast), after fluorescent staining (H), and after protargol staining (I–L). A, G. Ventral views of different individuals. B. Nematodesmal rods from a compressed cell, arrowheads indicate C-shaped clasps. C. Ventral view of part of a compressed cell showing macronucleus, arrow denotes the cross-striated band. D. Cortical granules on dorsal side, arrowhead marks the pigment spot. E. Cortical granules (arrowhead) on ventral side. F. Ventral view of cell, arrowheads indicate the pigment spot. H. Macronucleus. I. Ventral view of ciliature and macronucleus. J, K. Ventral view of the anterior part of ciliature showing oral structure. L. Dorsal view of the anterior body, arrowheads indicate the terminal fragments. Abbreviations: Cocircumoral kineties; Cs—cytostome; Ma—macronucleus; NR—nematodesmal rods; Pr—preoral kinety. Scale bars: 100 μm.
FIGURE 3 in Morphology and SSU rDNA sequences of four cyrtophorian ciliates from China, with description of a new species (Protista, Ciliophora, Phyllopharyngea)
FIGURE 3. Photomicrographs of Chlamydodon pararoseus sp. n. from life (A, D, and E by differential interference contrast, B, C, and F in bright field), after fluorescent staining (G), and after protargol staining (H–L). A, B. Ventral views of slightly compressed individuals, arrow in (A) marks the cytostome, and arrowheads indicate contractile vacuoles, and arrows in (B) refer to the sub-equatorial fossa. C, E. Dorsal views, arrow marks the cytostome, and arrowheads mark the pigment spot. D, F. Ventral views of individuals showing variations in body shape. G. Macronucleus. H. Ventral ciliature. I. Oral structure. J. Barren kinetosomes in oral area. K. Terminal fragment. L. Sub-equatorial fossa after protargol staining. Abbreviations: Co—circumoral kineties; Ks—barren kinetosomes; Ma—macronucleus; Pr—preoral kinety; TF—terminal fragment. Scale bars: 40 μm.
FIGURE 1 in Morphology and SSU rDNA sequences of four cyrtophorian ciliates from China, with description of a new species (Protista, Ciliophora, Phyllopharyngea)
FIGURE 1. Locations of the sample sites. A. Overview of locations. B. A mangrove wetland in Zhanjiang. C. A small puddle of the Dongpo Lake, Haikou. D, E. Intertidal zone in Qingdao, arrow indicates the sampling pool. E. The same tidal pool as shown by arrow in D.
FIGURE 6 in Morphology and SSU rDNA sequences of four cyrtophorian ciliates from China, with description of a new species (Protista, Ciliophora, Phyllopharyngea)
FIGURE 6. Phylogenetic tree of Maximum-likelihood (ML) based on small SSU rRNA gene sequences with Bayesian inference (BI) tapped on it. The four new sequences in the present paper are highlighted in bold. Numbers at nodes show ML bootstrap values and the BI posterior probabilities (ML/BI). Values with full support (ML/BI, 100/1.00) are marked with solid circle. The scale bar corresponds to 5 substitutions per 100 nucleotide positions. * Guangdong population of Chlamydodon bourlandi, ** misidentification, should be Chlamydodon bourlandi.
FIGURE 2 in Morphology and SSU rDNA sequences of four cyrtophorian ciliates from China, with description of a new species (Protista, Ciliophora, Phyllopharyngea)
FIGURE 2. Drawings of Chlamydodon pararoseus sp. n. from life (A–D) and after protargol staining (E–G). A. Ventral side of a representative individual. Dorsal (B) and ventral (C) views of a compressed individual, arrows denote the cross-striated band (CSB) and the arrowheads mark pigment spots. D. Cyrtos. E, F. Ventral (E) and dorsal (F) views of the same holotype specimen, arrow indicates the sub-equatorial fossa. G. Ventral view of anterior cell, arrow marks the suture, arrowheads denote barren kinetosomes. Abbreviations: Co—circumoral kineties; CSB—cross-striated band; LK—left kineties; Ma—macronucleus; NR—nematodesmal rods; PoK—postoral kineties; Pr—preoral kinety; RK—right kineties; TF—terminal fragments. Scale bars: 40 μm.
Supplementary material 3 from: Rajter Ľ, Dunthorn M (2021) Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. Metabarcoding and Metagenomics 5: e69602. https://doi.org/10.3897/mbmg.5.69602
File S3
Supplementary material 9 from: Rajter Ľ, Dunthorn M (2021) Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. Metabarcoding and Metagenomics 5: e69602. https://doi.org/10.3897/mbmg.5.69602
File S9
Supplementary material 1 from: Rajter Ľ, Dunthorn M (2021) Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. Metabarcoding and Metagenomics 5: e69602. https://doi.org/10.3897/mbmg.5.69602
File S1
Supplementary material 7 from: Rajter Ľ, Dunthorn M (2021) Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. Metabarcoding and Metagenomics 5: e69602. https://doi.org/10.3897/mbmg.5.69602
File S7
Supplementary material 21 from: Rajter Ľ, Dunthorn M (2021) Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. Metabarcoding and Metagenomics 5: e69602. https://doi.org/10.3897/mbmg.5.69602
Table S2
Supplementary material 8 from: Rajter Ľ, Dunthorn M (2021) Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. Metabarcoding and Metagenomics 5: e69602. https://doi.org/10.3897/mbmg.5.69602
File S8
Supplementary material 19 from: Rajter Ľ, Dunthorn M (2021) Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. Metabarcoding and Metagenomics 5: e69602. https://doi.org/10.3897/mbmg.5.69602
Figure S4
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