Myxomycete biosystematics: Some recent developments and future research opportunities

Collins, O’Neil Ray

doi:10.1007/bf02860855

Cited by 81 publications

(8 citation statements)

References 228 publications

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“…All reported attempts to make hyperamoebae strains fruit have failed, although amoebae were transferred from liquid cultures to agar plates (Dyková et al 2007;Karpov and Mylnikov 1997;Michel et al 2003). However, fruiting is a sexual process that involves fusion of two haploid, sexually compatible and thus, genetically diverse, amoeboflagellates in a diploid zygote which, under appropriate conditions, can differentiate into fruiting bodies (Collins 1979). Many myxogastrid strains are heterothallic, and cannot form fruiting bodies in clonal cultures because of the absence of the compatible mating type.…”

Section: Discussionmentioning

confidence: 99%

Invalidation of Hyperamoeba by Transferring its Species to Other Genera of Myxogastria

Fiore‐Donno¹,

Kamono²,

Chao³

et al. 2017

Preprint

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ABSTRACT. The genus Hyperamoeba Alexeieff, 1923 was established to accommodate an aerobic amoeba exhibiting three life stagesamoeba, flagellate, and cyst. As more species/strains were isolated, it became increasingly evident from small subunit (SSU) gene phylogenies and ultrastructure that Hyperamoeba is polyphyletic and its species occupy different positions within the class Myxogastria. To pinpoint Hyperamoeba strains within other myxogastrid genera we aligned numerous myxogastrid sequences: whole small subunit ribosomal (SSU or 18S rRNA) gene for 50 dark-spored (i.e. Stemonitida and Physarida) Myxogastria (including a new ''Hyperamoeba''/ Didymium sequence) and a $ 400-bp SSU fragment for 147 isolates assigned to 10 genera of the order Physarida. Phylogenetic analyses show unambiguously that the type species Hyperamoeba flagellata is a Physarum (Physarum flagellatum comb. nov.) as it nests among other Physarum species as robust sister to Physarum didermoides. Our trees also allow the following allocations: five Hyperamoeba strains to the genus Stemonitis; Hyperamoeba dachnaya, Pseudodidymium cryptomastigophorum, and three other Hyperamoeba strains to the genus Didymium; and two further Hyperamoeba strains to the family Physaridae. We therefore abandon the polyphyletic and redundant genus Hyperamoeba. We discuss the implications for the ecology and evolution of Myxogastria, whose amoeboflagellates are more widespread than previous inventories supposed, being now found in freshwater and even marine environments.

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Section: Discussionmentioning

confidence: 99%

Invalidation of Hyperamoeba by Transferring its Species to Other Genera of Myxogastria

Fiore‐Donno¹,

Kamono²,

Chao³

et al. 2017

Preprint

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“…Only, a minority of myxomycetes can be induced to fruit in culture. However, experiments with cultivable species, mostly Physarales, revealed groups of compatible strains (Collins, ) or so‐called biospecies. Empirical evidence of whether all morphospecies reflect true biospecies is lacking (reviewed in Clark & Haskins, ).…”

Section: Introductionmentioning

confidence: 99%

Genetic barcoding of dark‐spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies

Dahl

Brejnrod

Unterseher³

et al. 2017

Molecular Ecology Resources

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Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.

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“…lower surface of the plasmodium, while Liceida, Tri chiida, Echinostelida, and Physarida were subhypo thallic. Collins [7] based the characteristic of plasmo dia suggested the Physarida was the most primitive, possessing phaneroplasmodia, it was further divided into Echinostelida which has a protoplasmodium, Stemonitida with a phaneroplasmodium, Liceida with a protoplasmodium or phaneroplasmodium, and finally Trichiida, which has an intermediate between a aphaneroplasmodium and phaneroplasmodium.…”

Section: Introductionmentioning

confidence: 99%

Further resolving the phylogeny of Myxogastria (slime molds) based on COI and SSU rRNA genes

2015

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To date, molecular systematics of Myxogastria has been based primarily on small subunit riboso mal RNA (SSU rRNA) and elongation factor 1 alpha (EF 1α) genes. To establish a natural classification sys tem for the organisms, we examined phylogenetic relationships among myxogastrian species using cyto chrome c oxidase subunit I (COI) and SSU rRNA genes. Twenty new sequences were obtained, including 10 COI and 10 SSU rRNA sequences, were compared with sequences of related species from GenBank in order to construct phylogenic trees. The analysis of the two data sets supported the modern phylogeny of myxogastria: orders Liceida and Trichiida formed a sister group at the most basal clade, while orders Ste monitida and Physarida formed a close group, and order Echinostelida was a sister group to Stemonitida and Physarida. However, the partial COI sequences were too conserved to resolve of the branches in Stemonitida and Physarida. In addition, we also deemed the specific edited mRNA events of COI sequences in myxogas trian species.

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Myxomycete biosystematics: Some recent developments and future research opportunities

Cited by 81 publications

References 228 publications

Invalidation of Hyperamoeba by Transferring its Species to Other Genera of Myxogastria

Invalidation of Hyperamoeba by Transferring its Species to Other Genera of Myxogastria

Genetic barcoding of dark‐spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies

Further resolving the phylogeny of Myxogastria (slime molds) based on COI and SSU rRNA genes

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