Phylogeny of Physarida (Amoebozoa, Myxogastria) Based on the Small‐Subunit Ribosomal RNA Gene, Redefinition of Physarum pusillum s. str. and Reinstatement of P. gravidum Morgan

Abstract

Myxomycetes (also called Myxogastria or colloquially, slime molds) are worldwide occurring soil amoeboflagellates. Among Amoebozoa, they have the notable characteristic to form, during their life cycle, macroscopic fruiting bodies, that will ultimately release spores. Some 1,000 species have been described, based on the macroscopic and microscopic characteristics of their fruiting bodies. We were interested in Physarum pusillum (Berk. & M.A. Curtis) G. Lister, a very common species described with two variants, each bearing such morphological differences that they could represent two distinct species. In order to test this, we observed key characters in a large selection of specimens attributed to P. pusillum, to its synonyms (in particular Physarum gravidum), and to related species. In addition, the small-subunit ribosomal RNA gene was obtained from seven of these specimens. Based on these data, we provide a comprehensive phylogeny of the order Physarida (Eukaryota: Amoebozoa: Conosa: Macromycetozoa: Fuscisporidia). Morphology and phylogeny together support the reinstatement of P. gravidum Morgan 1896 with a neotype here designated, distinct from P. pusillum, here redefined.

A Phylogenetic Approach to Structural Variation in Organization of Nuclear Group I Introns and Their Ribozymes

“…A phylogenetic tree obtained from maximum likelihood (ML) analysis based on 1575 aligned SSU rRNA positions from 72 taxa is shown in Supplementary Figure S5. The tree topology corrolates well to the current taxonomy of myxomycetes and more recently reported rDNA-based phylogeny [27][28][29][30]. However, we noted that the Lepidoderma tigrinum sequence (GenBank accession number DQ903678) appeared embedded within the Diderma cluster.…”

“…Multiple sequence alignments were generated using MAFFT version 7.450 [50,51] with default setting. The SSU dataset 1 (1575 bp) included sequences from all 72 taxa and was based on published information about myxomycete SSU rRNA [30,52] and evaluated and manually trimmed by excluding parts of variable regions that were not confidently aligned. SSU dataset 2 included 23 taxa and was made similar to dataset 1.…”

Structural Organization of S516 Group I Introns in Myxomycetes

“…Multiple sequence alignments were generated using MAFFT version 7.450 [ 40 , 41 ] with default settings. The SSU rDNA dataset 1 (1524 nt) and dataset 2 (1784 nt) alignments were manually adjusted according to published information about myxomycete SSU rDNA genes [ 42 , 43 ], excluding parts of variable regions that were not confidently aligned. Group I intron core sequences (143 bp) were manually aligned and strictly based on secondary structure features as described previously [ 6 , 8 , 11 ] using the Geneious prime ® software program.…”

<i>Lamproderma vietnamense</i>: a new species of myxomycetes with reticulate spores from Phia Oắc - Phia Đén National Park (northern Vietnam) supported by molecular phylogeny and morphological analysis

“…As in all hitherto published phylogenies of dark-spored myxomycetes (e.g. Fiore-Donno et al, 2012;Cainelli, de Haan, Meyer, Bonkowski, & Fiore-Donno, 2020), species of the genus Meriderma together with Collaria rubens (Lister) Nann.-Bremek. assumed a basal position.…”