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Alexander Kudryavtsev - One of the best experts on this subject based on the ideXlab platform.
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Mitochondrial Genome of Vannella croatica (Amoebozoa, Discosea, Vannellida).
The Journal of eukaryotic microbiology, 2018Co-Authors: Natalya Bondarenko, Alexander Kudryavtsev, Elena Nassonova, Olja Mijanovic, Anna Glotova, Oksana Kamyshatskaya, Alexey Masharsky, Dmitrii E. Polev, Alexey V. SmirnovAbstract:Mitochondrial genome sequence of Vannella croatica (Amoebozoa, Discosea, Vannellida) was obtained using pulse-field gel electrophoretic isolation of the circular mitochondrial DNA, followed by the next-generation sequencing. The mitochondrial DNA of this species has the length of 28,933 bp and contains 12 protein-coding genes, two ribosomal RNAs, and 16 transfer RNAs. Vannella croatica mitochondrial genome is relatively short compared to other known Amoebozoan mitochondrial genomes but is rather gene-rich and contains significant number of open reading frames.
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The complete mitochondrial genome of Vannella simplex (Amoebozoa, Discosea, Vannellida).
European journal of protistology, 2018Co-Authors: Natalya Bondarenko, Alexander Kudryavtsev, Elena Nassonova, Anna Glotova, Alexey Masharsky, Alexey V. SmirnovAbstract:Abstract Vannella simplex (Amoebozoa, Discosea, Vannellida) is one of the commonest freshwater free-living lobose amoebae, known from many locations worldwide. In the present study, we describe the complete mitochondrial genome of this species. The circular mitochondrial DNA of V. simplex has 34,145obp in length and contains 27 protein-coding genes, 2 ribosomal RNAs, 16 transfer RNAs and 4 open reading frames. Mitochondiral genome of V. simplex is one of the most gene compact due to overlapping genes and reduced intergenic space. It has much in common with its closest relative, mitochondrial genome of V. croatica GenBank number MF508648. In the same time, both of them show considerable differences in length and in gene order from the next close relative – that of Neoparamoeba pemaquidensis KX611830 (deposited as Paramoeba) and even more – from other sequenced Amoebozoan mitochondrial genomes. The present study confirms the opinion that the level of synteny between the mitochondrial genomes across the entire Amoebozoa clade is low. More or less considerable similarity yet was found only between members of the same clade of the genera or family level, but hardly — among more distant lineages.
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Two new species of Ripella (Amoebozoa, Vannellida) and unusual intragenomic variability in the SSU rRNA gene of this genus.
European journal of protistology, 2017Co-Authors: Alexander Kudryavtsev, Anna GladkikhAbstract:Two new species, Ripella decalvata and R. tribonemae (Amoebozoa, Vannellida), are described and the diversity of known strains assigned to the genus analyzed. Ripella spp. are closely similar to each other in the light microscopic characters and sequences of small-subunit (SSU) ribosomal RNA gene, but differences in the cell coat structure and cytochrome oxidase (COI) gene sequences are more prominent. SSU rRNA in R. platypodia CCAP1589/2, R. decalvata and R. tribonemae demonstrates an unusual pattern of intragenomic variation. Sequencing of multiple molecular clones of this gene produced numerous sequence variants in a number of specific sites. These sites were usually terminal parts of several variable helices in all studied strains. Analysis of all known Ripella strains shows that SSU rRNA sites differing between strains of different origin are mainly restricted to these areas of the gene. There are only two sites, which differ between strains, but not within genomes. This intragenomic variability of the SSU rRNA gene, seemingly characteristic of all Ripella spp., was never reported to be so extensive in Amoebozoa. The data obtained show another example of complex organization of rRNA gene cluster in protists and emphasize caution needed when interpreting the metagenomic data based on this marker.
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Multigene phylogeny resolves deep branching of Amoebozoa.
Molecular phylogenetics and evolution, 2014Co-Authors: Thomas Cavalier-smith, Alexander Kudryavtsev, Cédric Berney, Anna Maria Fiore-donno, Ema Chao, Elizabeth A. Snell, Rhodri LewisAbstract:Amoebozoa is a key phylum for eukaryote phylogeny and evolutionary history, but its phylogenetic validity has been questioned since included species are very diverse: amoebo-flagellate slime-moulds, naked and testate amoebae, and some flagellates. 18S rRNA gene trees have not firmly established its internal topology. To rectify this we sequenced cDNA libraries for seven diverse Amoebozoa and conducted phylogenetic analyses for 109 eukaryotes (17–18 Amoebozoa) using 60–188 genes. We conducted Bayesian inferences with the evolutionarily most realistic site-heterogeneous CAT-GTR-Γ model and maximum likelihood analyses. These unequivocally establish the monophyly of Amoebozoa, showing a primary dichotomy between the previously contested subphyla Lobosa and Conosa. Lobosa, the entirely non-flagellate lobose amoebae, are robustly partitioned into the monophyletic classes Tubulinea, with predominantly tube-shaped pseudopodia, and Discosea with flattened cells and different locomotion. Within Conosa 60/70-gene trees with very little missing data show a primary dichotomy between the aerobic infraphylum Semiconosia (Mycetozoa and Variosea) and secondarily anaerobic Archamoebae. These phylogenetic features are entirely congruent with the most recent major Amoebozoan classification emphasising locomotion modes, pseudopodial morphology, and ultrastructure. However, 188-gene trees where proportionally more taxa have sparser gene-representation weakly place Archamoebae as sister to Macromycetozoa instead, possibly a tree reconstruction artefact of differentially missing data.
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Squamamoeba japonica n. g. n. sp. (Amoebozoa): a deep-sea amoeba from the Sea of Japan with a novel cell coat structure.
Protist, 2012Co-Authors: Alexander Kudryavtsev, Jan PawlowskiAbstract:Squamamoeba japonica n. g. n. sp. was isolated and described from marine bottom sediments collected at a depth of ca. 2700 m in the Sea of Japan. Trophic amoebae of this species are elongated and flattened, with a wide anterior hyaloplasm producing numerous ventral subpseudopodia for adhesion to the substratum. The cell coat consists of flat oval scales tightly packed together to form a continuous layer separated from the plasma membrane. Amoebae can form cytoplasmic projections protruding through the scale layer and having tips covered only with the plasma membrane. Small subunit ribosomal RNA gene phylogeny shows that S. japonica forms a long branch in the Amoebozoan tree, robustly grouping with the marine strain ‘Pessonella’ sp. PRA-29. Morphological data available for the latter, although scarce, give additional support for the relatedness of both species. The resulting clade comprising the two taxa shows no close relationships to other Amoebozoa and seems to be a novel lineage that developed an ability to temporarily liberate local areas of the plasma membrane from the cell coat independently from Himatismenida, Trichosida, Pellitida and Dermamoeba.
Laura A. Katz - One of the best experts on this subject based on the ideXlab platform.
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Amoebozoans Are Secretly but Ancestrally Sexual: Evidence for Sex Genes and Potential Novel Crossover Pathways in Diverse Groups of Amoebae
Genome biology and evolution, 2017Co-Authors: Yonas I. Tekle, Laura A. Katz, Fiona C. Wood, Mario A Cerón-romero, Lydia A. GorfuAbstract:Sex is beneficial in eukaryotes as it can increase genetic diversity, reshuffle their genomes, and purge deleterious mutations. Yet, its evolution remains a mystery. The eukaryotic clade supergroup Amoebozoa encompasses diverse lineages of polymorphic amoeboid forms, including both free-living and parasitic lineages. The group is generally believed to be asexual, though recent studies show that some of its members are implicated in cryptic forms of sexual cycles. In this study, we conduct a comprehensive inventory and analysis of genes involved in meiosis and related processes, in order to investigate the evolutionary history of sex in the clade. We analyzed genomic and transcriptomic data of 39 Amoebozoans representing all major subclades of Amoebozoa. Our results show that Amoebozoa possess most of the genes exclusive to meiosis but lack genes encoding synaptonemal complex (SC). The absence of SC genes is discussed in the context of earlier studies that reported ultrastructural evidence of SC in some amoebae. We also find interclade and intrageneric variation in sex gene distribution, indicating diversity in sexual pathways in the group. Particularly, members of Mycetozoa engage in a novel sexual pathway independent of the universally conserved meiosis initiator gene, SPO11. Our findings strongly suggest that not only do Amoebozoans possess sex genes in their genomes, but also, based on the transcriptome evidence, the present sex genes are functional. We conclude that Amoebozoa is ancestrally sexual, contrary to the long held belief that most of its members are asexual. Thus, asexuality in Amoebozoa, if confirmed to be present, is a derived-trait that appeared later in their evolution.
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Phylogenomics of ‘Discosea’: A new molecular phylogenetic perspective on Amoebozoa with flat body forms
Molecular phylogenetics and evolution, 2016Co-Authors: Yonas I. Tekle, O. Roger Anderson, Laura A. Katz, Xyrus X. Maurer-alcalá, Mario Alberto Cerón Romero, Robert E. MolestinaAbstract:The majority of amoeboid lineages with flattened body forms are placed under a taxonomic hypothetical class 'Discosea' sensu Smirnov et al. (2011), which encompasses some of the most diverse morphs within Amoebozoa. However, its taxonomy and phylogeny is poorly understood. This is partly due to lack of support in studies that are based on limited gene sampling. In this study we use a phylogenomic approach including newly-generated RNA-Seq data and comprehensive taxon sampling to resolve the phylogeny of 'Discosea'. Our analysis included representatives from all orders of 'Discosea' and up to 550 genes, the largest gene sampling in Amoebozoa to date. We conducted extensive analyses to assess the robustness of our resulting phylogenies to effects of missing data and outgroup choice using probabilistic methods. All of our analyses, which explore the impact of varying amounts of missing data, consistently recover well-resolved and supported groups of Amoebozoa. Our results neither support the monophyly nor dichotomy of 'Discosea' as defined by Smirnov et al. (2011). Rather, we recover a robust well-resolved clade referred to as Eudiscosea encompassing the majority of discosean orders (seven of the nine studied here), while the Dactylopodida, Thecamoebida and Himatismenida, previously included in 'Discosea,' are non-monophyletic. We also recover novel relationships within the Eudiscosea that are largely congruent with morphology. Our analyses enabled us to place some incertae sedis lineages and previously unstable lineages such as Vermistella, Mayorella, Gocevia, and Stereomyxa. We recommend some phylogeny-based taxonomic amendments highlighting the new findings of this study and discuss the evolution of the group based on our current understanding.
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Multigene phylogenetic reconstruction of the Tubulinea (Amoebozoa) corroborates four of the six major lineages, while additionally revealing that shell composition does not predict phylogeny in the Arcellinida.
Protist, 2013Co-Authors: Daniel J. G. Lahr, Jessica R. Grant, Laura A. KatzAbstract:Tubulinea is a phylogenetically stable higher-level taxon within Amoebozoa, morphologically characterized by monoaxially streaming and cylindrical pseudopods. Contemporary phylogenetic reconstructions have largely relied on SSU rDNA, and to a lesser extent, on actin genes to reveal the relationships among these organisms. Additionally, the test (shell) forming Arcellinida, one of the most species-rich Amoebozoan groups, is nested within Tubulinea and suffers from substantial under-sampling of taxa. Here, we increase taxonomic and gene sampling within the Tubulinea, characterizing molecular data for 22 taxa and six genes (SSU rDNA, actin, α- and β-tubulin, elongation factor 2 and the 14-3-3 regulatory protein). We perform concatenated phylogenetic analyses using these genes as well as approximately unbiased tests to assess evolutionary relationships within the Tubulinea. We confirm the monophyly of Tubulinea and four of the six included lineages (Echinamoeboidea, Leptomyxida, Amoebida and Poseidonida). Arcellinida and Hartmanellidae, the remaining lineages, are not monophyletic in our reconstructions, although statistical testing does not allow rejection of either group. We further investigate more fine-grained morphological evolution of previously defined groups, concluding that relationships within Arcellinida are more consistent with general test and aperture shape than with test composition. We also discuss the implications of this phylogeny for interpretations of the Precambrian fossil record of testate amoebae.
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Trends in Supergroup Taxonomy
2013Co-Authors: Laura Wegener Parfrey, David J. Patterson, Debashish Bhattacharya, Erika Barbero, Elyse Lasser, Micah Dunthorn, Laura A. KatzAbstract:A comparison of three formal classifications illustrates trends within (A) “Amoebozoa” [7,45,47]; (B) “Excavata” [7,33,60]; (C) “Plantae” [2,6,7]; and (D) “Rhizaria” [6,7,33]. A majority of solid, horizontal lines would indicate temporal stability of supergroup classification. For visual simplicity we do not indicate groups newly included in the supergroups or taxonomic restructuring within subgroups. Asterisk indicates a newly introduced term. “Chromalveolata” and “Opisthokonta” are not included because only one formal taxonomy exists for both groups. See Figure 1 for further notes.
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Support for Membership and Supergroup Monophyly from “Amoebozoa”-Targeted Molecular Genealogies
2013Co-Authors: Laura Wegener Parfrey, David J. Patterson, Debashish Bhattacharya, Erika Barbero, Elyse Lasser, Micah Dunthorn, Laura A. KatzAbstract:Membership: • indicates the member taxon falls within the supergroup Amoebozoa; ○ indicates that the member taxon is excluded from the Amoebozoa clade, or no clade is formed. Papers below blank line survey eukaryotic diversity [33,49,115] and are included in all analyses. Member taxa: My, Mycetozoa; Dc, Dictyosteliids; Tu, Tubulinea (Lobosea, Gymnamoebea sensu stricto); Am, Acanthamoebidae; Fl, Flabellinea (Discosea, Glycostylea); Pe, Pelomyxa; Ma, Mastigamoebidae; En, Entamoebidae; Rs, residua; Br, Breviata, “Mastigamoeba invertans sensu NCBI.” Supergroup Monophyly, + indicates monophyly; − indicates group is para- or polyphyletic, and blank indicates insufficient data available. Supergroup definition based on Adl et al. 2005 [4]: A, Amoebozoa; C, Chromalveolata; E, Excavata; O, Opisthokonta; P, Plantae; R, Rhizaria. The position of Breviata, Br, was not considered when scoring the monophyly of Amoebozoa as this organism was misidentified and affiliations are unknown (see text). Some nodes were constrained in reference [97]. References cited in this figure are [25,33,45,48,49,84,97,114,115].
Daniel J. G. Lahr - One of the best experts on this subject based on the ideXlab platform.
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The integrin-mediated adhesome complex, essential to multicellularity, is present in the most recent common ancestor of animals, fungi, and amoebae
2020Co-Authors: Seungho Kang, Daniel J. G. Lahr, Alexander K. Tice, Courtney W. Stairs, Robert E Jones, Matthew W BrownAbstract:Integrins are transmembrane receptor proteins that activate signal transduction pathways upon extracellular matrix binding. The Integrin Mediated Adhesion Complex (IMAC), mediates various cell physiological process. The IMAC was thought to be an animal specific machinery until over the last decade these complexes were discovered in Obazoa, the group containing animals, fungi, and several microbial eukaryote lineages. Amoebozoa is the eukaryotic supergroup sister to Obazoa. Even though Amoebozoa represents the closest outgroup to Obazoa, little genomic-level data and attention to gene inventories has been given to the supergroup. To examine the evolutionary history of the IMAC, we examine gene inventories of deeply sampled set of 100+ Amoebozoa taxa, including new data from several taxa. From these robust data sampled from the entire breadth of known Amoebozoan clades, we show the presence of an ancestral complex of integrin adhesion proteins that predate the evolution of the Amoebozoa. Our results highlight that many of these proteins appear to have evolved earlier in eukaryote evolution than previously thought. Co-option of an ancient protein complex was key to the emergence of animal type multicellularity. The role of the IMAC in a unicellular context is unknown but must also play a critical role for at least some unicellular organisms.
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Comparative Genomics Supports Sex and Meiosis in Diverse Amoebozoa
Genome Biology and Evolution, 2018Co-Authors: Paulo G. Hofstatter, Matthew W Brown, Daniel J. G. LahrAbstract:Sex and reproduction are often treated as a single phenomenon in animals and plants, as in these organisms reproduction implies mixis and meiosis. In contrast, sex and reproduction are independent biological phenomena that may or may not be linked in the majority of other eukaryotes. Current evidence supports a eukaryotic ancestor bearing a mating type system and meiosis, which is a process exclusive to eukaryotes. Even though sex is ancestral, the literature regarding life cycles of amoeboid lineages depicts them as asexual organisms. Why would loss of sex be common in amoebae, if it is rarely lost, if ever, in plants and animals, as well as in fungi? One way to approach the question of meiosis in the "asexuals" is to evaluate the patterns of occurrence of genes for the proteins involved in syngamy and meiosis. We have applied a comparative genomic approach to study the occurrence of the machinery for plasmogamy, karyogamy, and meiosis in Amoebozoa, a major amoeboid supergroup. Our results support a putative occurrence of syngamy and meiotic processes in all major Amoebozoan lineages. We conclude that most Amoebozoans may perform mixis, recombination, and ploidy reduction through canonical meiotic processes. The present evidence indicates the possibility of sexual cycles in many lineages traditionally held as asexual.
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nad9 nad7 mitochondrial nicotinamide adenine dinucleotide dehydrogenase gene a new holy grail phylogenetic and dna barcoding marker for arcellinida Amoebozoa
European Journal of Protistology, 2017Co-Authors: Quentin Blandenier, Ferry Siemensma, Enrique Lara, Edward A. D. Mitchell, Daniel Maximo Correa Alcantara, Milcho Todorov, Daniel J. G. LahrAbstract:Molecular phylogeny is an indispensable tool for assessing evolutionary relationships among protists. The most commonly used marker is the small subunit ribosomal RNA gene, a conserved gene present in many copies in the nuclear genomes. However, this marker is not variable enough at a fine-level taxonomic scale, and intra-genomic polymorphism has already been reported. Finding a marker that could be useful at both deep and fine taxonomic resolution levels seemed like a utopic dream. We designed Amoebozoa-specific primers to amplify a region including partial sequences of two subunits of the mitochondrial nicotinamide adenine dinucleotide dehydrogenase gene (NAD9/NAD7). We applied them to arcellinids belonging to distantly related genera (Arcella, Difflugia, Netzelia and Hyalosphenia) and to Arcellinid-rich environmental samples to obtain additional Amoebozoa sequences. Tree topology was congruent with previous phylogenies, all nodes being highly supported, suggesting that this marker is well-suited for deep phylogenies in Arcellinida and perhaps Amoebozoa. Furthermore, it enabled discrimination of close-related taxa. This short genetic marker (ca. 250bp) can therefore be used at different taxonomic levels, due to a fast-varying intergenic region presenting either a small intergenic sequence or an overlap, depending on the species.
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NAD9/NAD7 (mitochondrial nicotinamide adenine dinucleotide dehydrogenase gene)-A new "Holy Grail" phylogenetic and DNA-barcoding marker for Arcellinida (Amoebozoa)?
European journal of protistology, 2016Co-Authors: Quentin Blandenier, Ferry Siemensma, Enrique Lara, Edward A. D. Mitchell, Daniel Maximo Correa Alcantara, Milcho Todorov, Daniel J. G. LahrAbstract:Molecular phylogeny is an indispensable tool for assessing evolutionary relationships among protists. The most commonly used marker is the small subunit ribosomal RNA gene, a conserved gene present in many copies in the nuclear genomes. However, this marker is not variable enough at a fine-level taxonomic scale, and intra-genomic polymorphism has already been reported. Finding a marker that could be useful at both deep and fine taxonomic resolution levels seemed like a utopic dream. We designed Amoebozoa-specific primers to amplify a region including partial sequences of two subunits of the mitochondrial nicotinamide adenine dinucleotide dehydrogenase gene (NAD9/NAD7). We applied them to arcellinids belonging to distantly related genera (Arcella, Difflugia, Netzelia and Hyalosphenia) and to Arcellinid-rich environmental samples to obtain additional Amoebozoa sequences. Tree topology was congruent with previous phylogenies, all nodes being highly supported, suggesting that this marker is well-suited for deep phylogenies in Arcellinida and perhaps Amoebozoa. Furthermore, it enabled discrimination of close-related taxa. This short genetic marker (ca. 250bp) can therefore be used at different taxonomic levels, due to a fast-varying intergenic region presenting either a small intergenic sequence or an overlap, depending on the species.
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Evolution of bacterial recombinase A (recA) in eukaryotes explained by addition of genomic data of key microbial lineages.
Proceedings of The Royal Society B: Biological Sciences, 2016Co-Authors: Paulo G. Hofstatter, Matthew W Brown, Seungho Kang, Alexander K. Tice, Daniel J. G. LahrAbstract:Recombinase enzymes promote DNA repair by homologous recombination. The genes that encode them are ancestral to life, occurring in all known dominions: viruses, Eubacteria, Archaea and Eukaryota. Bacterial recombinases are also present in viruses and eukaryotic groups (supergroups), presumably via ancestral events of lateral gene transfer. The eukaryotic recA genes have two distinct origins (mitochondrial and plastidial), whose acquisition by eukaryotes was possible via primary (bacteria–eukaryote) and/or secondary (eukaryote–eukaryote) endosymbiotic gene transfers (EGTs). Here we present a comprehensive phylogenetic analysis of the recA genealogy, with substantially increased taxonomic sampling in the bacteria, viruses, eukaryotes and a special focus on the key eukaryotic supergroup Amoebozoa, earlier represented only by Dictyostelium . We demonstrate that several major eukaryotic lineages have lost the bacterial recombinases (including Opisthokonta and Excavata), whereas others have retained them (Amoebozoa, Archaeplastida and the SAR-supergroups). When absent, the bacterial recA homologues may have been lost entirely (secondary loss of canonical mitochondria) or replaced by other eukaryotic recombinases. RecA proteins have a transit peptide for organellar import, where they act. The reconstruction of the RecA phylogeny with its EGT events presented here retells the intertwined evolutionary history of eukaryotes and bacteria, while further illuminating the events of endosymbiosis in eukaryotes by expanding the collection of widespread genes that provide insight to this deep history.
Michael Bonkowski - One of the best experts on this subject based on the ideXlab platform.
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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
The Journal of eukaryotic microbiology, 2020Co-Authors: Renato Cainelli, Michael Bonkowski, Myriam De Haan, Marianne Meyer, Anna Maria Fiore-donnoAbstract: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.
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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
Journal of Eukaryotic Microbiology, 2020Co-Authors: Renato Cainelli, Michael Bonkowski, Myriam De Haan, Marianne Meyer, Anna Maria FioredonnoAbstract: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.
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The Dancing Star: Reinvestigation of Artodiscus saltans (Variosea, Amoebozoa) Penard 1890.
Protist, 2019Co-Authors: Efthymia Ntakou, Michael Bonkowski, Ferry Siemensma, Kenneth DumackAbstract:Artodiscus saltans, first described by Penard (1890), has a unique morphology. Without genetic data it could not yet been reliably placed into a wider taxonomical context. We present morphological data for A. saltans from different aquatic habitats of four European countries. We subjected three cells of one strain from Germany to molecular analyses and, interestingly, obtained six different rDNA sequences. Phylogenetic analyses of these SSU rDNA sequences revealed that A. saltans branches close to the Amoebozoan Multicilia marina (Variosea, Amoebozoa).
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Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group
Biology direct, 2016Co-Authors: Alexander K. Tice, Stefan Geisen, Michael Bonkowski, Anna Maria Fiore-donno, Seungho Kang, Lora L. Shadwick, Gabriel A. Schuler, Frederick W. Spiegel, Katherine A. Wilkinson, Kenneth DumackAbstract:Acanthamoebidae is a “family” level Amoebozoan group composed of the genera Acanthamoeba, Protacanthamoeba, and very recently Luapeleamoeba. This clade of Amoebozoans has received considerable attention from the broader scientific community as Acanthamoeba spp. represent both model organisms and human pathogens. While the classical composition of the group (Acanthamoeba + Protacanthamoeba) has been well accepted due to the morphological and ultrastructural similarities of its members, the Acanthamoebidae has never been highly statistically supported in single gene phylogenetic reconstructions of Amoebozoa either by maximum likelihood (ML) or Bayesian analyses. Here we show using a phylogenomic approach that the Acanthamoebidae is a fully supported monophyletic group within Amoebozoa with both ML and Bayesian analyses. We also expand the known range of morphological and life cycle diversity found in the Acanthamoebidae by demonstrating that the Amoebozoans “Protostelium” arachisporum, Dracoamoeba jormungandri n. g. n. sp., and Vacuolamoeba acanthoformis n.g. n.sp., belong within the group. We also found that “Protostelium” pyriformis is clearly a species of Acanthamoeba making it the first reported sporocarpic member of the genus, that is, an amoeba that individually forms a walled, dormant propagule elevated by a non-cellular stalk. Our phylogenetic analyses recover a fully supported Acanthamoebidae composed of five genera. Two of these genera (Acanthamoeba and Luapeleameoba) have members that are sporocarpic. Our results provide high statistical support for an Acanthamoebidae that is composed of five distinct genera. This study increases the known morphological diversity of this group and shows that species of Acanthamoeba can include spore-bearing stages. This further illustrates the widespread nature of spore-bearing stages across the tree of Amoebozoa. This article was reviewed by Drs. Eugene Koonin, Purificacion Lopez-Garcia and Sandra Baldauf. Sandra Baldauf was nominated by Purificacion Lopez-Garcia, an Editorial Board member.
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Phylogeny of the Highly Divergent Echinosteliales (Amoebozoa).
The Journal of eukaryotic microbiology, 2016Co-Authors: Martin Kretzschmar, Michael Bonkowski, Andreas Kuhnt, Anna Maria Fiore-donnoAbstract:Myxomycetes or plasmodial slime molds are widespread and very common soil amoebae with the ability to form macroscopic fruiting bodies. Even if their phylogenetic position as a monophyletic group in Amoebozoa is well established, their internal relationships are still not entirely resolved. At the base of the most intensively studied dark-spored clade lies the order Echinosteliales, whose highly divergent small subunit ribosomal (18S) RNA genes represent a challenge for phylogenetic reconstructions. This is because they are characterized by unusually long variable helices of unknown secondary structure and a high inter- and infraspecific divergence. Current classification recognizes two families: the monogeneric Echinosteliaceae and the Clastodermataceae with the genera Barbeyella and Clastoderma. To better resolve the phylogeny of the Echinosteliales, we obtained three new small subunit ribosomal (18S) RNA gene sequences of Clastoderma and Echinostelium corynophorum. Our phylogenetic analyses suggested the polyphyly of the family Clastodermataceae, as Barbeyella was more closely related to Echinostelium arboreum than to Clastoderma, while Clastoderma debaryanum was the earliest branching clade in Echinosteliales. We also found that E. corynophorum was the closest relative of the enigmatic Semimorula liquescens, a stalkless-modified Echinosteliales. We discuss possible evolutionary pathways in dark-spored Myxomycetes and propose a taxonomic update.
Anna Maria Fiore-donno - One of the best experts on this subject based on the ideXlab platform.
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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
The Journal of eukaryotic microbiology, 2020Co-Authors: Renato Cainelli, Michael Bonkowski, Myriam De Haan, Marianne Meyer, Anna Maria Fiore-donnoAbstract: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.
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Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group
Biology direct, 2016Co-Authors: Alexander K. Tice, Stefan Geisen, Michael Bonkowski, Anna Maria Fiore-donno, Seungho Kang, Lora L. Shadwick, Gabriel A. Schuler, Frederick W. Spiegel, Katherine A. Wilkinson, Kenneth DumackAbstract:Acanthamoebidae is a “family” level Amoebozoan group composed of the genera Acanthamoeba, Protacanthamoeba, and very recently Luapeleamoeba. This clade of Amoebozoans has received considerable attention from the broader scientific community as Acanthamoeba spp. represent both model organisms and human pathogens. While the classical composition of the group (Acanthamoeba + Protacanthamoeba) has been well accepted due to the morphological and ultrastructural similarities of its members, the Acanthamoebidae has never been highly statistically supported in single gene phylogenetic reconstructions of Amoebozoa either by maximum likelihood (ML) or Bayesian analyses. Here we show using a phylogenomic approach that the Acanthamoebidae is a fully supported monophyletic group within Amoebozoa with both ML and Bayesian analyses. We also expand the known range of morphological and life cycle diversity found in the Acanthamoebidae by demonstrating that the Amoebozoans “Protostelium” arachisporum, Dracoamoeba jormungandri n. g. n. sp., and Vacuolamoeba acanthoformis n.g. n.sp., belong within the group. We also found that “Protostelium” pyriformis is clearly a species of Acanthamoeba making it the first reported sporocarpic member of the genus, that is, an amoeba that individually forms a walled, dormant propagule elevated by a non-cellular stalk. Our phylogenetic analyses recover a fully supported Acanthamoebidae composed of five genera. Two of these genera (Acanthamoeba and Luapeleameoba) have members that are sporocarpic. Our results provide high statistical support for an Acanthamoebidae that is composed of five distinct genera. This study increases the known morphological diversity of this group and shows that species of Acanthamoeba can include spore-bearing stages. This further illustrates the widespread nature of spore-bearing stages across the tree of Amoebozoa. This article was reviewed by Drs. Eugene Koonin, Purificacion Lopez-Garcia and Sandra Baldauf. Sandra Baldauf was nominated by Purificacion Lopez-Garcia, an Editorial Board member.
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Phylogeny of the Highly Divergent Echinosteliales (Amoebozoa).
The Journal of eukaryotic microbiology, 2016Co-Authors: Martin Kretzschmar, Michael Bonkowski, Andreas Kuhnt, Anna Maria Fiore-donnoAbstract:Myxomycetes or plasmodial slime molds are widespread and very common soil amoebae with the ability to form macroscopic fruiting bodies. Even if their phylogenetic position as a monophyletic group in Amoebozoa is well established, their internal relationships are still not entirely resolved. At the base of the most intensively studied dark-spored clade lies the order Echinosteliales, whose highly divergent small subunit ribosomal (18S) RNA genes represent a challenge for phylogenetic reconstructions. This is because they are characterized by unusually long variable helices of unknown secondary structure and a high inter- and infraspecific divergence. Current classification recognizes two families: the monogeneric Echinosteliaceae and the Clastodermataceae with the genera Barbeyella and Clastoderma. To better resolve the phylogeny of the Echinosteliales, we obtained three new small subunit ribosomal (18S) RNA gene sequences of Clastoderma and Echinostelium corynophorum. Our phylogenetic analyses suggested the polyphyly of the family Clastodermataceae, as Barbeyella was more closely related to Echinostelium arboreum than to Clastoderma, while Clastoderma debaryanum was the earliest branching clade in Echinosteliales. We also found that E. corynophorum was the closest relative of the enigmatic Semimorula liquescens, a stalkless-modified Echinosteliales. We discuss possible evolutionary pathways in dark-spored Myxomycetes and propose a taxonomic update.
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Multigene phylogeny resolves deep branching of Amoebozoa.
Molecular phylogenetics and evolution, 2014Co-Authors: Thomas Cavalier-smith, Alexander Kudryavtsev, Cédric Berney, Anna Maria Fiore-donno, Ema Chao, Elizabeth A. Snell, Rhodri LewisAbstract:Amoebozoa is a key phylum for eukaryote phylogeny and evolutionary history, but its phylogenetic validity has been questioned since included species are very diverse: amoebo-flagellate slime-moulds, naked and testate amoebae, and some flagellates. 18S rRNA gene trees have not firmly established its internal topology. To rectify this we sequenced cDNA libraries for seven diverse Amoebozoa and conducted phylogenetic analyses for 109 eukaryotes (17–18 Amoebozoa) using 60–188 genes. We conducted Bayesian inferences with the evolutionarily most realistic site-heterogeneous CAT-GTR-Γ model and maximum likelihood analyses. These unequivocally establish the monophyly of Amoebozoa, showing a primary dichotomy between the previously contested subphyla Lobosa and Conosa. Lobosa, the entirely non-flagellate lobose amoebae, are robustly partitioned into the monophyletic classes Tubulinea, with predominantly tube-shaped pseudopodia, and Discosea with flattened cells and different locomotion. Within Conosa 60/70-gene trees with very little missing data show a primary dichotomy between the aerobic infraphylum Semiconosia (Mycetozoa and Variosea) and secondarily anaerobic Archamoebae. These phylogenetic features are entirely congruent with the most recent major Amoebozoan classification emphasising locomotion modes, pseudopodial morphology, and ultrastructure. However, 188-gene trees where proportionally more taxa have sparser gene-representation weakly place Archamoebae as sister to Macromycetozoa instead, possibly a tree reconstruction artefact of differentially missing data.
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Myxomycetes in soil
Soil Biology and Biochemistry, 2011Co-Authors: Steven L Stephenson, Anna Maria Fiore-donno, Martin SchnittlerAbstract:Abstract The myxomycetes are a group of protists that form a monophyletic taxon in the phylum Amoebozoa. Evidence of their evolutionary success is the fact that they account for more species (ca. 900 are currently recognized) than the combined total for the rest of the Amoebozoa. Moreover, myxomycetes are present in every terrestrial environment investigated to date and also, as amoebae or flagellated cells, in aquatic environments where they cannot form fruiting bodies. Even if culture-based methods tend to underestimate their occurrence in soil, myxomycetes probably account for ∼50% of soil amoebae. The emergence of molecular-based methods has revolutionized our concepts of biodiversity, but myxomycetes are conspicuously absent from all environmental surveys. Herein we show that this is due to their highly diverging SSU rRNA gene sequences, which contain numerous Group I introns. Further proof comes from a recent study that used a massive sequencing approach without primer bias to amplify RNAs. The results obtained show that the mycetozoans (myxomycetes along with dictyostelids and protostelids) are indeed a dominant group of soil protozoans.