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Gromochytrium mamkaevae gen. & sp. nov. and two new orders: Gromochytriales and Mesochytriales (Chytridiomycetes).

Karpov SA, Kobseva AA, Mamkaeva MA, Mamkaeva KA, Mikhailov KV, Mirzaeva GS, Aleoshin VV - Persoonia (2014)

Bottom Line: During the last decade several new orders were established in the class Chytridiomycetes on the basis of zoospore ultrastructure and molecular phylogeny.Detailed investigation revealed that the zoospore ultrastructure of this strain has unique characters not found in any order of Chytridiomycetes: posterior ribosomal core unbounded by the endoplasmic reticulum and detached from the nucleus or microbody-lipid complex, and kinetosome composed of microtubular doublets.An isolated phylogenetic position of x-51 is further confirmed by the analysis of 18S and 28S rRNA sequences, and motivates the description of a new genus and species Gromochytrium mamkaevae.

View Article: PubMed Central - PubMed

Affiliation: Zoological Institute, Russian Academy of Sciences, St. Petersburg 198904, Russian Federation; ; Biological Faculty, St. Petersburg State University, St. Petersburg 198904, Russian Federation.

ABSTRACT
During the last decade several new orders were established in the class Chytridiomycetes on the basis of zoospore ultrastructure and molecular phylogeny. Here we present the ultrastructure and molecular phylogeny of strain x-51 CALU - a parasite of the alga Tribonema gayanum, originally described as Rhizophydium sp. based on light microscopy. Detailed investigation revealed that the zoospore ultrastructure of this strain has unique characters not found in any order of Chytridiomycetes: posterior ribosomal core unbounded by the endoplasmic reticulum and detached from the nucleus or microbody-lipid complex, and kinetosome composed of microtubular doublets. An isolated phylogenetic position of x-51 is further confirmed by the analysis of 18S and 28S rRNA sequences, and motivates the description of a new genus and species Gromochytrium mamkaevae. The sister position of G. mamkaevae branch relative to Mesochytrium and a cluster of environmental sequences, as well as the ultrastructural differences between Gromochytrium and Mesochytrium zoospores prompted us to establish two new orders: Gromochytriales and Mesochytriales.

No MeSH data available.


Related in: MedlinePlus

Bayesian phylogenetic tree based on concatenated rDNA sequences (18S, 5.8S, 28S). Node support values are given by Bayesian posterior probability (left of the vertical line) and Maximum Likelihood bootstrap support (right of the vertical line). Support values are omitted for nodes that score above 95 % in both analyses (edges drawn with thick lines) and nodes that score less than 50 % in both analyses (edges drawn with striated lines). The strain x-51 - Gromochytrium mamkaevae is highlighted with red. Two groups of nearly identical clones in the Mesochytriales clade are collapsed into single branches (represented by triangles).
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Figure 2: Bayesian phylogenetic tree based on concatenated rDNA sequences (18S, 5.8S, 28S). Node support values are given by Bayesian posterior probability (left of the vertical line) and Maximum Likelihood bootstrap support (right of the vertical line). Support values are omitted for nodes that score above 95 % in both analyses (edges drawn with thick lines) and nodes that score less than 50 % in both analyses (edges drawn with striated lines). The strain x-51 - Gromochytrium mamkaevae is highlighted with red. Two groups of nearly identical clones in the Mesochytriales clade are collapsed into single branches (represented by triangles).

Mentions: Ribosomal DNA sequences of x-51 were aligned with 113 OTUs from zoosporic fungi and closely related uncultured clones collected from the GenBank database. Sequences were selected based on the following scheme. First, all chytrid LSU genes that had sufficiently large length (> 2 000 bp) were added to the list of OTUs, and SSU genes were selected for all listed species. Second, all fragments of chytrid SSU and LSU rRNA genes were selected from cultured strains and environmental samples that occupied isolated positions on the distance tree. Third, all sequences of uncultured clones available in GenBank as of January 2013 were selected that grouped closely with x-51 CALU and Mesochytrium penetrans x-10 CALU. For environmental sample sequences that formed particularly long branches on the distance tree we performed an additional verification step that involved breaking the sequence into two or more non-overlapping fragments that were then used as independent OTUs for preliminary phylogenetic analysis (data not shown). This method identified seven sequences (accession numbers: EU162637, EF196798, EF196785, EF196773, EF196750, FJ592495, HQ191339) from three independent environmental samples as potentially chimaeric. The parts of sequences EU162637 and FJ592495 that presumably have fungal source were retained; the remainder and the other four sequences were excluded from the phylogenetic analysis. To minimise missing data a small number of sequences was assembled by fusing or constructing a consensus of sequences from different isolates of the same species or by fusing partial sequences that have a 98–100 % overlap identity. The full list of consensus and chimaeric sequences constructed for the purpose of phylogenetic analysis is presented in Table 1 and Fig. 2. The sequences of early-branching fungal taxa – Rozella allomycis and Amoeboaphelidium protococcarum were chosen as outgroup (James et al. 2006, Karpov et al. 2013). Alignments were generated with MUSCLE (Edgar 2004) and refined manually using BioEdit (Hall 1999). After discarding ambiguously aligned nucleotide positions and concatenating the alignments of 18S, 5.8S and 28S rRNA genes, the alignment consisted of 4 850 positions. Tree search for the concatenated alignment was performed using the Bayesian method implemented by MrBayes v. 3.1.2 (Ronquist & Huelsenbeck 2003). The tree reconstruction used GTR+G12+I model and partition by genes (18S, 5.8S, and 28S) with all parameters unlinked, except the topology and branch lengths. Four independent runs of eight Markov Chain Monte Carlo (MCMC) were performed to evaluate the convergence. Chains were run for 10 million generations sampling trees every 1 000 generations after discarding the first 8 million as burn-in. Sampled trees were used to generate a majority rule consensus tree with Bayesian posterior probabilities. Bootstrap support values for the consensus tree reconstructed by MrBayes were generated using RAxML v. 7.2.6 (Stamatakis 2006) on the basis of 1 000 replicates under the GTR+G+I model.


Gromochytrium mamkaevae gen. & sp. nov. and two new orders: Gromochytriales and Mesochytriales (Chytridiomycetes).

Karpov SA, Kobseva AA, Mamkaeva MA, Mamkaeva KA, Mikhailov KV, Mirzaeva GS, Aleoshin VV - Persoonia (2014)

Bayesian phylogenetic tree based on concatenated rDNA sequences (18S, 5.8S, 28S). Node support values are given by Bayesian posterior probability (left of the vertical line) and Maximum Likelihood bootstrap support (right of the vertical line). Support values are omitted for nodes that score above 95 % in both analyses (edges drawn with thick lines) and nodes that score less than 50 % in both analyses (edges drawn with striated lines). The strain x-51 - Gromochytrium mamkaevae is highlighted with red. Two groups of nearly identical clones in the Mesochytriales clade are collapsed into single branches (represented by triangles).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150072&req=5

Figure 2: Bayesian phylogenetic tree based on concatenated rDNA sequences (18S, 5.8S, 28S). Node support values are given by Bayesian posterior probability (left of the vertical line) and Maximum Likelihood bootstrap support (right of the vertical line). Support values are omitted for nodes that score above 95 % in both analyses (edges drawn with thick lines) and nodes that score less than 50 % in both analyses (edges drawn with striated lines). The strain x-51 - Gromochytrium mamkaevae is highlighted with red. Two groups of nearly identical clones in the Mesochytriales clade are collapsed into single branches (represented by triangles).
Mentions: Ribosomal DNA sequences of x-51 were aligned with 113 OTUs from zoosporic fungi and closely related uncultured clones collected from the GenBank database. Sequences were selected based on the following scheme. First, all chytrid LSU genes that had sufficiently large length (> 2 000 bp) were added to the list of OTUs, and SSU genes were selected for all listed species. Second, all fragments of chytrid SSU and LSU rRNA genes were selected from cultured strains and environmental samples that occupied isolated positions on the distance tree. Third, all sequences of uncultured clones available in GenBank as of January 2013 were selected that grouped closely with x-51 CALU and Mesochytrium penetrans x-10 CALU. For environmental sample sequences that formed particularly long branches on the distance tree we performed an additional verification step that involved breaking the sequence into two or more non-overlapping fragments that were then used as independent OTUs for preliminary phylogenetic analysis (data not shown). This method identified seven sequences (accession numbers: EU162637, EF196798, EF196785, EF196773, EF196750, FJ592495, HQ191339) from three independent environmental samples as potentially chimaeric. The parts of sequences EU162637 and FJ592495 that presumably have fungal source were retained; the remainder and the other four sequences were excluded from the phylogenetic analysis. To minimise missing data a small number of sequences was assembled by fusing or constructing a consensus of sequences from different isolates of the same species or by fusing partial sequences that have a 98–100 % overlap identity. The full list of consensus and chimaeric sequences constructed for the purpose of phylogenetic analysis is presented in Table 1 and Fig. 2. The sequences of early-branching fungal taxa – Rozella allomycis and Amoeboaphelidium protococcarum were chosen as outgroup (James et al. 2006, Karpov et al. 2013). Alignments were generated with MUSCLE (Edgar 2004) and refined manually using BioEdit (Hall 1999). After discarding ambiguously aligned nucleotide positions and concatenating the alignments of 18S, 5.8S and 28S rRNA genes, the alignment consisted of 4 850 positions. Tree search for the concatenated alignment was performed using the Bayesian method implemented by MrBayes v. 3.1.2 (Ronquist & Huelsenbeck 2003). The tree reconstruction used GTR+G12+I model and partition by genes (18S, 5.8S, and 28S) with all parameters unlinked, except the topology and branch lengths. Four independent runs of eight Markov Chain Monte Carlo (MCMC) were performed to evaluate the convergence. Chains were run for 10 million generations sampling trees every 1 000 generations after discarding the first 8 million as burn-in. Sampled trees were used to generate a majority rule consensus tree with Bayesian posterior probabilities. Bootstrap support values for the consensus tree reconstructed by MrBayes were generated using RAxML v. 7.2.6 (Stamatakis 2006) on the basis of 1 000 replicates under the GTR+G+I model.

Bottom Line: During the last decade several new orders were established in the class Chytridiomycetes on the basis of zoospore ultrastructure and molecular phylogeny.Detailed investigation revealed that the zoospore ultrastructure of this strain has unique characters not found in any order of Chytridiomycetes: posterior ribosomal core unbounded by the endoplasmic reticulum and detached from the nucleus or microbody-lipid complex, and kinetosome composed of microtubular doublets.An isolated phylogenetic position of x-51 is further confirmed by the analysis of 18S and 28S rRNA sequences, and motivates the description of a new genus and species Gromochytrium mamkaevae.

View Article: PubMed Central - PubMed

Affiliation: Zoological Institute, Russian Academy of Sciences, St. Petersburg 198904, Russian Federation; ; Biological Faculty, St. Petersburg State University, St. Petersburg 198904, Russian Federation.

ABSTRACT
During the last decade several new orders were established in the class Chytridiomycetes on the basis of zoospore ultrastructure and molecular phylogeny. Here we present the ultrastructure and molecular phylogeny of strain x-51 CALU - a parasite of the alga Tribonema gayanum, originally described as Rhizophydium sp. based on light microscopy. Detailed investigation revealed that the zoospore ultrastructure of this strain has unique characters not found in any order of Chytridiomycetes: posterior ribosomal core unbounded by the endoplasmic reticulum and detached from the nucleus or microbody-lipid complex, and kinetosome composed of microtubular doublets. An isolated phylogenetic position of x-51 is further confirmed by the analysis of 18S and 28S rRNA sequences, and motivates the description of a new genus and species Gromochytrium mamkaevae. The sister position of G. mamkaevae branch relative to Mesochytrium and a cluster of environmental sequences, as well as the ultrastructural differences between Gromochytrium and Mesochytrium zoospores prompted us to establish two new orders: Gromochytriales and Mesochytriales.

No MeSH data available.


Related in: MedlinePlus