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Two-gene phylogeny of bright-spored Myxomycetes (slime moulds, superorder Lucisporidia).

Fiore-Donno AM, Clissmann F, Meyer M, Schnittler M, Cavalier-Smith T - PLoS ONE (2013)

Bottom Line: We discuss possible evolutionary pathways.Our study fills a gap in the phylogeny of Amoebozoa and provides an extensive SSU rRNA sequence reference database for environmental sampling and barcoding.We report a new group I intron insertion site for Myxomycetes in one Licea.

View Article: PubMed Central - PubMed

Affiliation: Zoology Department, University of Oxford, Oxford, United Kingdom. afiore-donno6@infomaniak.ch

ABSTRACT
Myxomycetes, or plasmodial slime-moulds, are one of the largest groups in phylum Amoebozoa. Nonetheless, only ∼10% are in the database for the small subunit (SSU) ribosomal RNA gene, the most widely used gene for phylogenetics and barcoding. Most sequences belong to dark-spored Myxomycetes (order Fuscisporida); the 318 species of superorder Lucisporidia (bright-spored) are represented by only eleven genuine sequences. To compensate for this, we provide 66 new sequences, 37 SSU rRNA and 29 elongation factor 1-alpha (EF-1α), for 82% of the genera of Lucisporidia. Phylogenetic analyses of single- and two-gene alignments produce congruent topologies and reveal both morphological characters that have been overemphasised and those that have been overlooked in past classifications. Both classical orders, Liceida and Trichiida, and several families and genera are para/polyphyletic; some previously unrecognised clades emerge. We discuss possible evolutionary pathways. Our study fills a gap in the phylogeny of Amoebozoa and provides an extensive SSU rRNA sequence reference database for environmental sampling and barcoding. We report a new group I intron insertion site for Myxomycetes in one Licea.

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SSU rRNA gene tree of Lucisporidia derived by Bayesian inference of 1325 nucleotide positions of 51 sequences, with Ceratiomyxa fruticulosa as outgroup.Species names are followed by GenBank accession number, except for sequences obtained during this study (in bold), whose accession numbers and collection sites are in Table S1. Clades are highlighted and labelled according to current classification or as new. Bayesian posterior probabilities (BPP)/ML bootstrap replicates (MLB) are shown for each branch; dashes indicate a conflicting topology in the ML tree; a dot on the line indicates maximum support in both analyses. The scale bar indicates the fraction of substitutions per site. Credit photos: A, F, G, J–M: Michel Poulain; B–E, H, I, N–P: Alain Michaud.
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pone-0062586-g001: SSU rRNA gene tree of Lucisporidia derived by Bayesian inference of 1325 nucleotide positions of 51 sequences, with Ceratiomyxa fruticulosa as outgroup.Species names are followed by GenBank accession number, except for sequences obtained during this study (in bold), whose accession numbers and collection sites are in Table S1. Clades are highlighted and labelled according to current classification or as new. Bayesian posterior probabilities (BPP)/ML bootstrap replicates (MLB) are shown for each branch; dashes indicate a conflicting topology in the ML tree; a dot on the line indicates maximum support in both analyses. The scale bar indicates the fraction of substitutions per site. Credit photos: A, F, G, J–M: Michel Poulain; B–E, H, I, N–P: Alain Michaud.

Mentions: Readers unfamiliar with these taxa can find excellent illustrated descriptions [10], [11], [12] or consult the online searchable database of the eumycetozoan project at the University of Arkansas (http://slimemold.uark.edu/databaseframe.htm, last accessed: 19 Sep. 2012). We shall use only a few specialized terms, explained below. Differentiation of the plasmodium into a fruiting body (sporophore) forms three structures: peridium, capillitium, and spores. The peridium is the wall surrounding the fruiting body, and the capillitium is a system of threads interwoven throughout the spores (best seen in Fig. 1K). The sporophore is named according to its shape: most common are individual sporocarps or sporangia, stalked (Fig. 1 A, J, K, O) or sessile (Fig. 1 F, H, I, L, N). In the former, the ensemble of the spore mass, peridium and capillitium (the two latter facultative) is called the sporotheca, to differentiate the “fertile” part from the stalk. Large sporophores (>1 cm) are mostly a compound of multiple sporangia: if the sporangia are delimited, it is called a pseudoaethalium (Fig. 1 C, G), and an aethalium when it looks like a single mass (Fig. 1 B, D, E).


Two-gene phylogeny of bright-spored Myxomycetes (slime moulds, superorder Lucisporidia).

Fiore-Donno AM, Clissmann F, Meyer M, Schnittler M, Cavalier-Smith T - PLoS ONE (2013)

SSU rRNA gene tree of Lucisporidia derived by Bayesian inference of 1325 nucleotide positions of 51 sequences, with Ceratiomyxa fruticulosa as outgroup.Species names are followed by GenBank accession number, except for sequences obtained during this study (in bold), whose accession numbers and collection sites are in Table S1. Clades are highlighted and labelled according to current classification or as new. Bayesian posterior probabilities (BPP)/ML bootstrap replicates (MLB) are shown for each branch; dashes indicate a conflicting topology in the ML tree; a dot on the line indicates maximum support in both analyses. The scale bar indicates the fraction of substitutions per site. Credit photos: A, F, G, J–M: Michel Poulain; B–E, H, I, N–P: Alain Michaud.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3646832&req=5

pone-0062586-g001: SSU rRNA gene tree of Lucisporidia derived by Bayesian inference of 1325 nucleotide positions of 51 sequences, with Ceratiomyxa fruticulosa as outgroup.Species names are followed by GenBank accession number, except for sequences obtained during this study (in bold), whose accession numbers and collection sites are in Table S1. Clades are highlighted and labelled according to current classification or as new. Bayesian posterior probabilities (BPP)/ML bootstrap replicates (MLB) are shown for each branch; dashes indicate a conflicting topology in the ML tree; a dot on the line indicates maximum support in both analyses. The scale bar indicates the fraction of substitutions per site. Credit photos: A, F, G, J–M: Michel Poulain; B–E, H, I, N–P: Alain Michaud.
Mentions: Readers unfamiliar with these taxa can find excellent illustrated descriptions [10], [11], [12] or consult the online searchable database of the eumycetozoan project at the University of Arkansas (http://slimemold.uark.edu/databaseframe.htm, last accessed: 19 Sep. 2012). We shall use only a few specialized terms, explained below. Differentiation of the plasmodium into a fruiting body (sporophore) forms three structures: peridium, capillitium, and spores. The peridium is the wall surrounding the fruiting body, and the capillitium is a system of threads interwoven throughout the spores (best seen in Fig. 1K). The sporophore is named according to its shape: most common are individual sporocarps or sporangia, stalked (Fig. 1 A, J, K, O) or sessile (Fig. 1 F, H, I, L, N). In the former, the ensemble of the spore mass, peridium and capillitium (the two latter facultative) is called the sporotheca, to differentiate the “fertile” part from the stalk. Large sporophores (>1 cm) are mostly a compound of multiple sporangia: if the sporangia are delimited, it is called a pseudoaethalium (Fig. 1 C, G), and an aethalium when it looks like a single mass (Fig. 1 B, D, E).

Bottom Line: We discuss possible evolutionary pathways.Our study fills a gap in the phylogeny of Amoebozoa and provides an extensive SSU rRNA sequence reference database for environmental sampling and barcoding.We report a new group I intron insertion site for Myxomycetes in one Licea.

View Article: PubMed Central - PubMed

Affiliation: Zoology Department, University of Oxford, Oxford, United Kingdom. afiore-donno6@infomaniak.ch

ABSTRACT
Myxomycetes, or plasmodial slime-moulds, are one of the largest groups in phylum Amoebozoa. Nonetheless, only ∼10% are in the database for the small subunit (SSU) ribosomal RNA gene, the most widely used gene for phylogenetics and barcoding. Most sequences belong to dark-spored Myxomycetes (order Fuscisporida); the 318 species of superorder Lucisporidia (bright-spored) are represented by only eleven genuine sequences. To compensate for this, we provide 66 new sequences, 37 SSU rRNA and 29 elongation factor 1-alpha (EF-1α), for 82% of the genera of Lucisporidia. Phylogenetic analyses of single- and two-gene alignments produce congruent topologies and reveal both morphological characters that have been overemphasised and those that have been overlooked in past classifications. Both classical orders, Liceida and Trichiida, and several families and genera are para/polyphyletic; some previously unrecognised clades emerge. We discuss possible evolutionary pathways. Our study fills a gap in the phylogeny of Amoebozoa and provides an extensive SSU rRNA sequence reference database for environmental sampling and barcoding. We report a new group I intron insertion site for Myxomycetes in one Licea.

Show MeSH