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65 results for “Trebouxiophyceae”
FIGURE 3 in The polyphasic approach revealed new species of Chloroidium (Trebouxiophyceae, Chlorophyta)
FIGURE 3. Comparison of the conserved region of ITS-2 among the species of Chloroidium. Extraction of this region and translation into a number code for its usage as barcode (extracted bases highlighted with an asterisk). Number code for each base pair: 1 = A-U; 2 = U-A; 3 = G-C; 4 = C-G; 5 = G•U; 6 = U•G; 7 = mismatch; 8 = deletion, single or unpaired bases.
FIGURE 1 in The polyphasic approach revealed new species of Chloroidium (Trebouxiophyceae, Chlorophyta)
FIGURE 1. Molecular phylogeny of Chloroidium based on SSU and ITS rDNA sequence comparisons. The phylogenetic trees shown were inferred using the maximum likelihood method based on the data sets (2643 aligned positions of 58 taxa) using PAUP 4.0b10. For the analyses the best model was calculated by Modeltest 3.7. The setting of the best model was given as follows: GTR+I+G (base frequencies: A 0.2263, C 0.2597, G 0.2814, T 0.2326; rate matrix A-C 3.0220, A-G 3.2461, A-U 1.8828, C-G 1.0985, C-U 7.0041, G-U 1.0000) with the proportion of invariable sites (I = 0.7069) and gamma shape parameter (G = 0.6406). The branches in bold are highly supported in all analyses (Bayesian values> 0.95 calculated with PHASE and MrBayes; bootstrap values> 70% calculated with PAUP using maximum likelihood, neighbor-joining, maximum parsimony and RAxML using maximum likelihood). The taxa originally described as Parachloroidium were indicated by an asterisk. The ITS-2 haplotype designations as well as the geographical origins and habitats are given color-coded after the strain designations.
FIGURE 2 in The polyphasic approach revealed new species of Chloroidium (Trebouxiophyceae, Chlorophyta)
FIGURE 2. Molecular phylogeny of representatives belonging to the Watanabea clade based on rbcL and SSU rDNA sequence comparisons. The phylogenetic trees shown were inferred using the maximum likelihood method based on the data sets (23 taxa: 1790 aligned positions for SSU, 804 for rbcL) using PAUP 4.0b10. For the analyses the best model was calculated by Modeltest 3.7. The setting of the best model was given as follows: (SSU) TIM+I+G (base frequencies: A 0.2462, C 0.2339, G 0.2883, T 0.2316; rate matrix A-C 1.0000, A-G 2.2465, A-U 1.2966, C-G 1.2966, C-U 6.0538, G-U 1.0000) with the proportion of invariable sites (I = 0.5137) and gamma shape parameter (G = 0.6912); (rbcL) GTR+I+G (base frequencies: A 0.2606, C 0.2247, G 0.2899, T 0.2248; rate matrix A-C 2.3970, A-G 1.2715, A-U 0.7452, C-G 0.5103, C-U 6.8373, G-U 1.0000) with the proportion of invariable sites (I = 0.6386) and gamma shape parameter (G = 0.2501). The branches in bold are highly supported in all analyses (Bayesian values> 0.95 calculated with PHASE and MrBayes; bootstrap values> 70% calculated with PAUP using maximum likelihood, neighbor-joining, maximum parsimony and RAxML using maximum likelihood). The Bayesian analysis in PHASE was calculated using the dataset of all three codon bases (1206 bp) and the codon model YNH98 (Yang et al. 1998).
FIGURE 1 in The genus Jaagichlorella Reisigl (Trebouxiophyceae, Chlorophyta) and its close relatives: an evolutionary puzzle
FIGURE 1. Molecular phylogeny of representatives belonging to the Watanabea clade based on SSU rDNA sequence comparisons. The phylogenetic tree shown was inferred using the maximum likelihood method based on the data set (29 taxa: 1787 aligned positions for SSU) using PAUP 4.0b10. For the analyses the best model was calculated by Modeltest 3.7. The setting of the best model was given as follows: TIM+I+G (base frequencies: A 0.2413, C 0.2367, G 0.2935, T 0.2285; rate matrix A-C 1.0000, A-G 2.1970, A-U 1.2024, C-G 1.2024, C-U 5.128, G-U 1.0000) with the proportion of invariable sites (I = 0.4935) and gamma shape parameter (G = 0.6539); The branches in bold are highly supported in all analyses (Bayesian values> 0.95 calculated with PHASE and MrBayes; bootstrap values> 90% calculated with PAUP using maximum likelihood, neighbor-joining, maximum parsimony and RAxML using maximum likelihood). The authentic strains of species are marked with an asterisk.
FIGURE 7 in The genus Jaagichlorella Reisigl (Trebouxiophyceae, Chlorophyta) and its close relatives: an evolutionary puzzle
FIGURE 7. Morphology and phenotypic plasticity of Jaagichlorella sphaerica (UTEX 2485; A.–J.) and Kalinella apyrenoidosa var. japonica (SAG 2203; K.–R.); scale bar = 10 μm.
FIGURE 4 in The genus Jaagichlorella Reisigl (Trebouxiophyceae, Chlorophyta) and its close relatives: an evolutionary puzzle
FIGURE 4. Morphology and phenotypic plasticity of Jaagichlorella luteoviridis (SAG 211-2a; A.–I.) and J. africana (SAG 2213; H.–T.); scale bar = 10 μm.
FIGURE 3 in The genus Jaagichlorella Reisigl (Trebouxiophyceae, Chlorophyta) and its close relatives: an evolutionary puzzle
FIGURE 3. Comparison of the conserved region of ITS-2 among the species of Jaagichlorella and Kalinella. Extraction of this region and translation into a number code for its usage as barcode. The '/' indicated the position of the site loop in Helix III, which we excluded from the barcode. Number code for each base pair: 1 = A-U; 2 = U-A; 3 = G-C; 4 = C-G; 5 = G•U; 6 = U•G; 7 = pyrimidine-pyrimidine mismatch; 8 = deletion, single or unpaired bases. The phylogenetic tree shown was calculated using the neighbor-joining method based on the data set (69 number-coded positions of 11 haplotypes) using PAUP 4.0b10.
FIGURE 2 in The genus Jaagichlorella Reisigl (Trebouxiophyceae, Chlorophyta) and its close relatives: an evolutionary puzzle
FIGURE 2. Molecular phylogeny of Jaagichlorella and Kalinella based on SSU and ITS rDNA sequence comparisons. The phylogenetic tree shown was inferred using the maximum likelihood method based on the data set (2655 aligned positions of 23 taxa) using PAUP 4.0b10. For the analyses the best model was calculated by Modeltest 3.7. The setting of the best model was given as follows: GTR+I+G (base frequencies: A 0.2324, C 0.2449, G 0.2794, T 0.2433; rate matrix A-C 1.5591, A-G 2.0795, A-U 1.4741, C-G 0.5739, C-U 4.8359, G-U 1.0000) with the proportion of invariable sites (I = 0.3875) and gamma shape parameter (G = 0.4780). The branches in bold are highly supported in all analyses (Bayesian values 1.00 calculated with PHASE and MrBayes; bootstrap values 100% calculated with PAUP using maximum likelihood, neighbor-joining, maximum parsimony and RAxML using maximum likelihood).
FIGURE 8 in The genus Jaagichlorella Reisigl (Trebouxiophyceae, Chlorophyta) and its close relatives: an evolutionary puzzle
FIGURE 8. Molecular phylogeny of Jaagichlorella and Kalinella based on partial SSU rDNA sequence comparisons. The phylogenetic tree shown were inferred using the neighbor-joining method based on the data set (346 aligned positions of 24 taxa) using PAUP 4.0b10. The accession numbers of the partial sequences found in GenBank is given after the names of the isolates/clones. The letters after each sequence indicates their origin (A = aquatic; E = epiphytic; P = photobiont of lichen; S = epilithic on rocks or artificial hard substrates; U = unknown).
FIGURE 6 in The genus Jaagichlorella Reisigl (Trebouxiophyceae, Chlorophyta) and its close relatives: an evolutionary puzzle
FIGURE 6. Morphology and phenotypic plasticity of Jaagichlorella hainangensis (SAG 2360; A.–S.) and J. geometrica (SAG 2549; T.–J'.); scale bar = 10 μm.
FIGURE 5 in The genus Jaagichlorella Reisigl (Trebouxiophyceae, Chlorophyta) and its close relatives: an evolutionary puzzle
FIGURE 5. Morphology and phenotypic plasticity of Jaagichlorella roystonensis var. epilithica (SAG 2133; A.–H.) and J. roystonensis var. handai (SAG 2198; I.–G'.); scale bar = 10 μm.
FIGURE 3 in A case of taxonomic inflation in coccoid algae: Ellipsoidion parvum and Neocystis vischeri are conspecific with Neocystis (=Nephrodiella) brevis (Chlorophyta, Trebouxiophyceae)
FIGURE 3: Representative images of Neocystis mucosa (A–C) and Neocystis brevis (D–I) strains. A: CAUP D 801. B: KR 1989/14. C: SAG 40.88. D: CAUP D 802. E: ASIB BS 319. F: CCALA 393. G: CALA 341. H, I: SAG 40.86. Scale bar = 10 µm.
FIGURE 1 in A case of taxonomic inflation in coccoid algae: Ellipsoidion parvum and Neocystis vischeri are conspecific with Neocystis (=Nephrodiella) brevis (Chlorophyta, Trebouxiophyceae)
FIGURE 1: Comparison of the ITS2 sequences and predicted secondary structures of Neocystis brevis and Neocystis mucosa. Base numbering is indicated every 10 bases, and the four helices are numbered with Roman numerals. The structure shown corresponds to N. brevis; positions conserved in N. mucosa are portrayed in green, bases substituted in N. mucosa are shown by the structure and connected to the respective position by a short line, insertions and deletions are indicated with plus and minus symbols, respectively. The base pair marked in a grey box is a compensatory base change (CBC). The highly conserved U–U mismatch in the helix II and UGGU motif in the helix III (Schultz et al. 2005) are marked by arrows.
FIGURE 4 in A case of taxonomic inflation in coccoid algae: Ellipsoidion parvum and Neocystis vischeri are conspecific with Neocystis (=Nephrodiella) brevis (Chlorophyta, Trebouxiophyceae)
FIGURE 4: Unit-less centroid size values of strains of Neocystis spp. Boxplots with a full outline represent strains of N. mucosa. Boxplots with a dashed outline represent strains of N. brevis.
FIGURE 2 in A case of taxonomic inflation in coccoid algae: Ellipsoidion parvum and Neocystis vischeri are conspecific with Neocystis (=Nephrodiella) brevis (Chlorophyta, Trebouxiophyceae)
FIGURE 2: Morphometric characteristics of Neocystis strains. a) Visualisation of the multivariate regression model illustrating the relation of the shape and size of cells in the entire investigated dataset. b) The PCA ordination plot based on geometric morphometric data illustrating mean positions of individual strains and their standard deviations on PC1 (spanning 65.9% of the variation) and PC2 (23.2%). The theoretical cell shapes of marginal morphospace positions were reconstructed from the landmark coordinates of the original data.
Data from: Molecular phylogeny and symbiotic selectivity of the green algal genus Dictyochloropsis sensu lato (Trebouxiophyceae): a polyphyletic and widespread group forming photobiont-mediated guilds in the lichen family Lobariaceae
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Supplementary material 3 from: Cao S, Zhang F, Zheng H, Peng F, Liu C, Zhou Q (2018) Coccomyxa greatwallensis sp. nov. (Trebouxiophyceae, Chlorophyta), a lichen epiphytic alga from Fildes Peninsula, Antarctica. PhytoKeys 110: 39-50. https://doi.org/10.3897/phytokeys.110.26961
Table S3. Comparison of the closely related species :
Supplementary material 1 from: Cao S, Zhang F, Zheng H, Peng F, Liu C, Zhou Q (2018) Coccomyxa greatwallensis sp. nov. (Trebouxiophyceae, Chlorophyta), a lichen epiphytic alga from Fildes Peninsula, Antarctica. PhytoKeys 110: 39-50. https://doi.org/10.3897/phytokeys.110.26961
Table S1. Pairwise distance calculated using ITS rDNA sequences :
Supplementary material 2 from: Cao S, Zhang F, Zheng H, Peng F, Liu C, Zhou Q (2018) Coccomyxa greatwallensis sp. nov. (Trebouxiophyceae, Chlorophyta), a lichen epiphytic alga from Fildes Peninsula, Antarctica. PhytoKeys 110: 39-50. https://doi.org/10.3897/phytokeys.110.26961
Table S2. Pairwise distance calculated using SSU rDNA sequences :
Figure 3 from: Cao S, Zhang F, Zheng H, Peng F, Liu C, Zhou Q (2018) Coccomyxa greatwallensis sp. nov. (Trebouxiophyceae, Chlorophyta), a lichen epiphytic alga from Fildes Peninsula, Antarctica. PhytoKeys 110: 39-50. https://doi.org/10.3897/phytokeys.110.26961
Figure 3 The NJ tree based on ITS rDNA (a) and the ML tree based on SSU rDNA (b) sequences phylogenetic analyses. The sequences marked with Coccomyxa clade A–N referred after Malavasi et al. (2016).
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