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22 results for “Mucorales”
Multiple sequence alignments: Detection and isolation of a new member of Burkholderiaceae‑related endofungal bacteria from Saksenaea boninensis sp. nov., a new thermotolerant fungus in Mucorales
<p><strong>Methods:</strong></p><p>Nucleotide sequences were aligned independently for each region using MAFFT v7.212 (Katoh and Standley, 2013). The obtained alignment blocks were subject to Gblocks 0.91b (Castresana, 2000) to remove poorly aligned positions with the relaxed selection setting described in Talavera & Castresana (2007) using the following parameters (-t = d -b2 = 9 -b3 = 10 -b4 = 5 -b5 = h). After automatically removing gaps, the alignment blocks were viewed using MEGA 6.06 software (Tamura et al., 2013) and poorly aligned positions at either end of the alignments were removed manually. Pairwise distances of the nucleotide sequences (ITS2, ITS1-5.8S-ITS2, LSU, and tef1) of the ex-type strains of seven <i>Saksenaea</i> spp. and the representative isolate <i>S. boninensis</i> Sak4 were calculated by MEGA 6.06 software (Tamura et al. 2013). Multiple sequence alignment of 16S rRNA gene of the family <i>Burkholderiaceae</i> was prepared for the phylogeny of a bacterial endosymbiont. Multiple sequence alignments of ITS, LSU, and tef1 genes of <i>Saksenaea</i> spp. (Mucorales) were separately prepared for the phylogeny of a fungal host. Concatenated dataset of these genes were also prepared. All nucleotide sequences were retrieved from GenBank (See "Sequence_ID.csv" and taxon names of each alignment). </p><p> </p><p><strong>Description of files:</strong></p><p><strong>A. Phylogeny of the family </strong><i><strong>Burkholderiaceae</strong></i><strong> (Bacterial endosymbiont):</strong></p><p>1. Burkholderiaceae_16S_RAW.fasta</p><p>Non-aligned dataset of 16S rRNA gene of the family <i>Burkholderiaceae</i>.</p><p> </p><p>2. Burkholderiaceae_16S_aligned.fasta</p><p>Aligned dataset of 16S rRNA gene of the family <i>Burkholderiaceae</i>.</p><p> </p><p><strong>B. Phylogenies of </strong><i><strong>Saksenaea</strong></i><strong> spp. (Fungal host):</strong></p><p>1. Sequence_ID_v2.csv</p><p>Taxon names, accession numbers, and sequence ID for the concatenated multiple sequence alignment are listed.</p><p> </p><p>2. Saksenaea_ITS_RAW_v2.fasta</p><p>Non-aligned dataset of ITS1-5.8S-ITS2 region of <i>Saksenaea</i> spp. </p><p> </p><p>3. Saksenaea_ITS_aligned_v2.fasta</p><p>Aligned dataset of ITS1-5.8S-ITS2 region of <i>Saksenaea</i> spp. Only used for ITS1-5.8S-ITS2 phylogeny.</p><p> </p><p>4. Saksenaea_LSU_RAW_v2.fasta</p><p>Non-aligned dataset of LSU gene region of <i>Saksenaea</i> spp. </p><p> </p><p>5. Saksenaea_LSU_aligned_v2.fasta</p><p>Aligned dataset of LSU gene region of <i>Saksenaea</i> spp. Only used for LSU phylogeny.</p><p> </p><p>6. Saksenaea_tef1_RAW_v2.fasta</p><p>Non-aligned dataset of tef1 gene region of <i>Saksenaea</i> spp. </p><p> </p><p>7. Saksenaea_tef1_aligned_v2.fasta</p><p>Aligned dataset of tef1 gene region of <i>Saksenaea</i> spp. Only used for tef1 phylogeny.</p><p> </p><p><strong><Concatenated dataset 1 (ITS2, LSU, tef1)></strong></p><p>8. Saksenaea_ITS2_for_concatenated_RAW_v2.fasta</p><p>Non-aligned dataset of ITS2 region of <i>Saksenaea</i> spp. used for preparation of a concatenated dataset 1.</p><p> </p><p>9. Saksenaea_ITS2_for_concatenated_aligned_v2.fasta</p><p>Aligned dataset of ITS2 region of <i>Saksenaea</i> spp. used for preparation of a concatenated dataset 1.</p><p> </p><p>10. Saksenaea_LSU_for_concatenated_RAW_v2.fasta</p><p>Non-aligned dataset of LSU gene region of <i>Saksenaea</i> spp. used for preparation of concatenated datasets 1 and 2.</p><p> </p><p>11. Saksenaea_LSU_for_concatenated_aligned_v2.fasta</p><p>Aligned dataset of LSU gene region of <i>Saksenaea</i> spp. used for preparation of concatenated datasets 1 and 2.</p><p> </p><p>12. Saksenaea_tef1_for_concatenated_RAW_v2.fasta</p><p>Non-aligned dataset of tef1 gene region of <i>Saksenaea</i> spp. used for preparation of concatenated datasets 1 and 2.</p><p> </p><p>13. Saksenaea_tef1_for_concatenated_aligned_v2.fasta</p><p>Aligned dataset of tef1 gene region of <i>Saksenaea</i> spp. used for preparation of concatenated datasets 1 and 2.</p><p> </p><p>14. Saksenaea_ITS2_LSU_tef1_concatenated_dataset1.fasta</p><p>Concatenated dataset of three multiple sequence alignments (9, 11, and 13). This concatenated dataset was used for the main phylogeny of <i>Saksenaea</i> spp.</p><p> </p><p><strong><Concatenated dataset 2 (ITS1-5.8S-ITS2, LSU, tef1)></strong></p><p>15. Saksenaea_ITS_for_concatenated_RAW_v2.fasta</p><p>Non-aligned dataset of ITS1-5.8S-ITS2 region of <i>Saksenaea</i> spp. used for preparation of a concatenated dataset 2.</p><p> </p><p>16. Saksenaea_ITS_for_concatenated_aligned_v2.fasta</p><p>Aligned dataset of ITS1-5.8S-ITS2 region of <i>Saksenaea</i> spp. used for preparation of a concatenated dataset 2.</p><p>Blank sequences were inserted for five isolates of <i>Saksenaea longicolla</i> after the alignment.</p><p> </p><p>17.Saksenaea_ITS_LSU_tef1_concatenated_dataset2.fasta</p><p>Concatenated dataset of three multiple sequence alignments (15, 11, and 13). This concatenated dataset was used for the main phylogeny of <i>Saksenaea</i> spp.</p><p> </p><p><strong>C. Pairwise distances of the ex-type strains of </strong><i><strong>Saksenaea</strong></i><strong> spp.</strong></p><p>1. Saksenaea_ITS_type_RAW.fasta</p><p>Non-aligned dataset of ITS1-5.8S-ITS2 region of the ex-type strains of <i>Saksenaea</i> spp.</p><p> </p><p>2. Saksenaea_ITS2_type_aligned.fasta</p><p>Aligned dataset of ITS2 region of the ex-type strains of <i>Saksenaea</i> spp.</p><p> </p><p>3.Saksenaea_ITS_type_aligned.fasta</p><p>Aligned dataset of ITS1-5.8S-ITS2 region of the ex-type strains of <i>Saksenaea</i> spp. without <i>Saksenaea longicolla</i>.</p><p> </p><p>4. Saksenaea_LSU_type_RAW.fasta</p><p>Non-aligned dataset of LSU gene region of the ex-type strains of <i>Saksenaea </i>spp.</p><p> </p><p>5. Saksenaea_LSU_type_aligned.fasta</p><p>Aligned dataset of LSU gene region of the ex-type strains of <i>Saksenaea</i> spp.</p><p> </p><p>6. Saksenaea_tef1_type_RAW.fasta</p><p>Non-aligned dataset of tef1 gene region of the ex-type strains of <i>Saksenaea</i> spp.</p><p> </p><p>7. Saksenaea_tef1_type_aligned.fasta</p><p>Aligned dataset of tef1 gene region of the ex-type strains of <i>Saksenaea</i> spp.</p>
Image 1 in Abradeosporangium, a new genus of Mucorales (Fungi: Zygomycetes) from India
Image 1. Abradeosporangium variosporum gen. et sp. nov.
FIGURE 2 in Cunninghamella verrucosa sp. nov. (Mucorales, Mucoromycota) from Guangdong Province in China
FIGURE 2. Morphologies of Cunninghamella verrucosa holotype CGMCC 3.16260. a, b. Colonies on PDA (a. obverse, b. reverse); c–e. Sporangiophores showing characteristic branching patterns with vesicles; f–h. Vesicles with broken pedicels; i. Sporangiola.—Scale bars: c–i. 10 μm.
FIGURE 1. A in Cunninghamella verrucosa sp. nov. (Mucorales, Mucoromycota) from Guangdong Province in China
FIGURE 1. A Maximum Likelihood (ML) phylogenetic tree of Cunninghamella based on ITS and LSU rDNA sequences, with two strains of Absidia glauca used as outgroup. The new species Cunninghamella verrucosa is in shade. ML bootstrap values (≥70%) / Maximum Parsimony (MP) bootstrap values (≥70%) / Bayesian Inference (BI) Posterior Probabilities (≥0.9) of each clade are indicated along branches. A scale bar in the upper left indicates substitutions per site.
FIGURE 2 in A new species of Mucor (Mucoromycotina, Mucorales) isolated from an enclave of Upland Atlantic Forest in the semi-arid region of Brazil
FIGURE 2. Phylogenetic tree of Mucoraceae constructed using the large subunit (LSU) rDNA sequences. Mortierella parvispora, Backusella lamprospora, B. grandis, Rhizopus microsporus, and Actinomucor elegans were used as outgroups. Sequences are labeled with their database accession numbers. Support values are from Bayesian inference and maximum likelihood analyses (values above and below the branches, respectively). The sequences obtained in this study are in boldface.
FIGURE 3 in A new species of Mucor (Mucoromycotina, Mucorales) isolated from an enclave of Upland Atlantic Forest in the semi-arid region of Brazil
FIGURE 3. Mucor septatum (holotype). A–D: branched multiseptate (arrows) sporangiophores; E–F: Unbranched multiseptate sporangiophores and columella; G: Unbranched septate sporangiophore with sporangium; H: sporangiospores.
FIGURE 1 in A new species of Mucor (Mucoromycotina, Mucorales) isolated from an enclave of Upland Atlantic Forest in the semi-arid region of Brazil
FIGURE 1. Phylogenetic tree of Mucor septatum and related species constructed using the ITS rDNA sequences. Mucor amphibiorum was used as an outgroup. Sequences are labeled with their database accession numbers. Support values are from Bayesian inference and maximum likelihood analyses (values above and below the branches, respectively). The sequences obtained in this study are in boldface.
FIGURE 3. Mucor pernambucoensis strain URM 7640 in Description Of Mucor Pernambucoensis (Mucorales, Mucoromycota), A New Species Isolated From The Brazilian Upland Rainforest
FIGURE 3. Mucor pernambucoensis strain URM 7640 (holotype): A. colony surface after five days at 25 ºC on MEA; B. sporangiophore repeatedly sympodially branched with globose sporangia; C. sporangiophore with globose sporangia; D. sporangiophore with sporangium and globose columella visible; E, F. sporangiophores with columellae; G. chlamydospores globose; H. sporangiospores
FIGURE 2 in Description Of Mucor Pernambucoensis (Mucorales, Mucoromycota), A New Species Isolated From The Brazilian Upland Rainforest
FIGURE 2. Phylogenetic tree of Mucor constructed using the ITS rDNA sequences. Mortierella parvispora was used as an outgroup. Sequences are labeled with their database accession numbers. Support values are from Bayesian inference and maximum likelihood analyses (values above and below of the branches, respectively). The sequence obtained in this study is annotated in boldface.
FIGURE 1 in Description Of Mucor Pernambucoensis (Mucorales, Mucoromycota), A New Species Isolated From The Brazilian Upland Rainforest
FIGURE 1. Phylogenetic tree of Mucor constructed using the large subunit (LSU) rDNA sequences. Mortierella parvispora, Backusella Iamprospora, B. grandis, Rhizopus microsporus and Actinomucor elegans were used as an outgroup. Sequences are labeled with their database accession numbers. Support values are from Bayesian inference and maximum likelihood analyses (values above and below of the branches, respectively). The sequence obtained in this study is annotated in boldface.
FIGURE 1 in Pilaira australis sp. nov. (Mucorales, Mucoromycota) isolated from emu faeces in Australia
FIGURE 1. Comparison of DNA sequences at two genetic loci supports P. australis as a distinct species with the Pilaira genus. (A) Phylogeny using the ITS by maximum likelihood based on the Tamura 3-parameter model. The tree with the highest log likelihood is shown (-2476.0688). (B) Phylogeny using the pyrG gene fragment by maximum likelihood method based on the Tamura 3-parameter model. The tree with the highest log likelihood is shown (-1674.0526). In both (A) and (B) the trees are drawn to scale, with branch lengths measured in the number of substitutions per site. The bootstraps values provided were generated with 1000 replicates.
FIGURE 2 in Pilaira australis sp. nov. (Mucorales, Mucoromycota) isolated from emu faeces in Australia
FIGURE 2. Morphological features of P. australis. Colonies growing on potato dextrose agar, becoming yellow in colour and emanating white sporangiophores that exhibit positive phototropism that collapse once several centimetres tall (A). The columella is visible at the base of the developing sporangium (B). Eventually the lower surface of the columella collapses inwards (C) to form a mature sporangium (D, F, G, H). Spores are elongated in shape (E, H, I). The outer surface of the sporangium is covered with small spikes (G and H). The spores lack surface ornamentation (H and I). B to D dissecting microscope, E DIC image from a compound microscope, F to I SEM images. Scales bares represent 300 μm B to D, 50 μm E, 100 μm F, 10 μm G, 20 μm H and 5 μm I.
FIGURE 2 in Cunninghamella saisamornae (Cunninghamellaceae, Mucorales), a new soil fungus from northern Thailand
FIGURE 2. Cunninghamella saisamornae (SDBR-CMU291, holotype). A–C. Colonies on three different agar media A. Czapek Dox agar. B. Potato dextrose agar. C. Modified synthetic Mucor agar. D. Vesicles. E−G. Sporangioles. H−J. Chlamydospores. Scale bars: A−C = 10 mm; D, F, G = 25 μm and E, H, I, J = 10 μm.
FIGURE 1 in Cunninghamella saisamornae (Cunninghamellaceae, Mucorales), a new soil fungus from northern Thailand
FIGURE 1. Phylogram derived from maximum likelihood analysis of 36 sequences of the combined ITS, LSU and tef-1 genes. Sequences of Absidia idahoensis and Rhizopus arrhizus were used as the outgroup. The numbers above branches represent maximum likelihood bootstrap percentages (left) and Bayesian posterior probabilities (right). Bootstrap values ≥ 75% and Bayesian posterior probabilities ≥ 0.90 are shown. The scale bar represents the expected number of nucleotide substitutions per site. Sequences of fungal species obtained in this study are in red. Type species are in bold.
Figure 4 from: Khuna S, Suwannarach N, Kumla J, Meerak J, Nuangmek W, Kiatsiriroat T, Lumyong S (2019) Apophysomyces thailandensis (Mucorales, Mucoromycota), a new species isolated from soil in northern Thailand and its solubilization of non-soluble minerals. MycoKeys 45: 75-92. https://doi.org/10.3897/mycokeys.45.30813
Figure 4 Apophysomycesthailandensis SDBR-CMUS26 (holotype). A colony on potato dextrose agar B Colony on malt extract agar C Colony on Czapek agar D Branched, aseptate hyphae E Funnel-shaped apophysis F Slightly trapezoidal sporangiospores. Scale bars: 10 mm (A–C), 10 µm (D–E), 20 µm (F).
Figure 3 from: Khuna S, Suwannarach N, Kumla J, Meerak J, Nuangmek W, Kiatsiriroat T, Lumyong S (2019) Apophysomyces thailandensis (Mucorales, Mucoromycota), a new species isolated from soil in northern Thailand and its solubilization of non-soluble minerals. MycoKeys 45: 75-92. https://doi.org/10.3897/mycokeys.45.30813
Figure 3 Solubilization index of the ability to solve non-soluble mineral by Apophysomycesthailandensis. Data are means of three replicates. Error bar at each point indicates ± SD. Different letters above each graph indicate that the means are significantly different by Tukey's test (P < 0.05)
Figure 2 from: Khuna S, Suwannarach N, Kumla J, Meerak J, Nuangmek W, Kiatsiriroat T, Lumyong S (2019) Apophysomyces thailandensis (Mucorales, Mucoromycota), a new species isolated from soil in northern Thailand and its solubilization of non-soluble minerals. MycoKeys 45: 75-92. https://doi.org/10.3897/mycokeys.45.30813
Figure 2 Solubilization of non-soluble minerals in agar media by Apophysomycesthailandensis SDBR-CMUS26 (holotype). A Ca3(PO4)2B CuCO3•Cu(OH)2C CuO D ZnCO3E FePO4F MnO G Feldspar H Kaolin. Scale bars: 10 mm. Fungal colonies in E and F were cut for the solubilization area (halo zone) observation.
Figure 1 from: Khuna S, Suwannarach N, Kumla J, Meerak J, Nuangmek W, Kiatsiriroat T, Lumyong S (2019) Apophysomyces thailandensis (Mucorales, Mucoromycota), a new species isolated from soil in northern Thailand and its solubilization of non-soluble minerals. MycoKeys 45: 75-92. https://doi.org/10.3897/mycokeys.45.30813
Figure 1 Phylogenetic tree derived from maximum likelihood analysis of a combined ITS, LSU, and H3 genes of 28 sequences. Saksenaeavasiformis and S.erythrospora were used as outgroup. Numbers above branches are the bootstrap statistics percentages (left) and Bayesian posterior probabilities (right). Branches with bootstrap values ≥ 50% are shown at each branch and the bar represents 0.1 substitutions per nucleotide position. The fungal isolates from this study are in bold. Superscript T = type species.
Mucorales PCR Screening in At-risk Hematology Patients
ClinicalTrials.gov study NCT05925660. IPD Sharing: NO. Countries: 1. Publications: 0.
Fig. 1 a–d in The use of compensatory base change analysis of ITS2 as a tool in the phylogeny of Mucorales, illustrated by the Mucor circinelloides complex
Fig. 1 a–d. Secondary structure and specific position of compensatory base changes (CBCs). a ITS2 secondary structure and sequence of strains CBS 526.68 and CBS 846.73, CBCs are highlighted in yellow. b ITS2 secondary structure and sequence of M. circinelloides f. griseocyanus, CBCs are highlighted in yellow. c ITS2 secondary structure and sequence of M. circinelloides; CBCs are highlighted in yellow. d Schematic consensus structure of ITS2 in M. circinelloides complex; CBC positions are shown in yellow and variable sites in brown
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