Root of Dictyostelia based on 213 universal proteins

Sheikh, Sanea; Gloeckner, Gernot; Kuwayama, Hidekazu; Schaap, Pauline; Urushihara, Hideko; Baldauf, Sandra L.

doi:10.1016/j.ympev.2015.05.017

Cited by 17 publications

(17 citation statements)

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“…2a,b). Firstly, as in the published multi-protein phylogenies [18, 19], the root is no longer positioned between groups 1 and 2, but separates two branches containing groups 1 and 2 and groups 3 and 4. Additionally, the group-intermediate species Dcar changed position from the base of the clade comprising groups 3 and 4 to the base of group 2, while Aell which was previously sister to clade 2B is now branching at the base of the clade composed of 2A and 2B.…”

Section: Resultsmentioning

confidence: 99%

“…Due to the repositioned root, groups 1 and 2 are now separate sister groups, while group 4 remains in a clade with group 3. We included the obligate parasite Ehis in the initial phylogeny, but as also found previously [18, 19], most Ehis genes are either absent or very divergent from those in other Amoebozoa. Because this could lead to long-branch attraction errors, Ehis was omitted from further analysis.…”

Section: Resultsmentioning

confidence: 99%

“…For Dictyostelia, the relationships between the four major groups were well defined previously from multi-locus phylogenies [18, 19], but the positions of early diverging species that occupy intermediate outgroup positions to the major groups were poorly resolved. Their position is however of crucial importance to identify the molecular changes that triggered the phenotypic diversification of the major groups.…”

Section: Discussionmentioning

confidence: 99%

“…D. lacteum in group 3 [15], Polyspondylium pallidum in group 2, clade 2B [16], Acytostelium subglobosum in group 2 clade 2A [17] and D. fasciculatum in group 1 [16]. The sequenced genomes enabled phylogenetic inference from multiple concatenated protein sequences and these efforts, using respectively 32 [18] and 213 protein sequences [19], both repositioned the root from a location between groups 1 and 2 to a location that separated the four groups into two branches, with branch I containing groups 1 and 2 and branch II, groups 3 and 4. Since no genome sequences for group-intermediate species were available, their positions remained unresolved.…”

Section: Introductionmentioning

confidence: 99%

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A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group

2016

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BackgroundDictyostelia are a well-studied group of organisms with colonial multicellularity, which are members of the mostly unicellular Amoebozoa. A phylogeny based on SSU rDNA data subdivided all Dictyostelia into four major groups, but left the position of the root and of six group-intermediate taxa unresolved. Recent phylogenies inferred from 30 or 213 proteins from sequenced genomes, positioned the root between two branches, each containing two major groups, but lacked data to position the group-intermediate taxa. Since the positions of these early diverging taxa are crucial for understanding the evolution of phenotypic complexity in Dictyostelia, we sequenced six representative genomes of early diverging taxa.ResultsWe retrieved orthologs of 47 housekeeping proteins with an average size of 890 amino acids from six newly sequenced and eight published genomes of Dictyostelia and unicellular Amoebozoa and inferred phylogenies from single and concatenated protein sequence alignments. Concatenated alignments of all 47 proteins, and four out of five subsets of nine concatenated proteins all produced the same consensus phylogeny with 100% statistical support. Trees inferred from just two out of the 47 proteins, individually reproduced the consensus phylogeny, highlighting that single gene phylogenies will rarely reflect correct species relationships. However, sets of two or three concatenated proteins again reproduced the consensus phylogeny, indicating that a small selection of genes suffices for low cost classification of as yet unincorporated or newly discovered dictyostelid and amoebozoan taxa by gene amplification.ConclusionsThe multi-locus consensus phylogeny shows that groups 1 and 2 are sister clades in branch I, with the group-intermediate taxon D. polycarpum positioned as outgroup to group 2. Branch II consists of groups 3 and 4, with the group-intermediate taxon Polysphondylium violaceum positioned as sister to group 4, and the group-intermediate taxon Dictyostelium polycephalum branching at the base of that whole clade. Given the data, the approximately unbiased test rejects all alternative topologies favoured by SSU rDNA and individual proteins with high statistical support. The test also rejects monophyletic origins for the genera Acytostelium, Polysphondylium and Dictyostelium. The current position of Acytostelium ellipticum in the consensus phylogeny indicates that somatic cells were lost twice in Dictyostelia.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0825-7) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group

2016

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“…Even the correct positioning of nucleosomes seems to be influenced by the ability of DD to form multicellular structures [5]. A molecular phylogeny based on rRNA and nuclear encoded protein sequences subdivides all known Dictyostelia into two main branches each containing two major and some minor groupings, with DD residing in group 4 [6–8] (Fig. 1).…”

Section: Introductionmentioning

confidence: 99%

A set of genes conserved in sequence and expression traces back the establishment of multicellularity in social amoebae

et al. 2016

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BackgroundThe developmental cycle of Dictyostelid amoebae represents an early form of multicellularity with cell type differentiation. Mutant studies in the model Dictyostelium discoideum revealed that its developmental program integrates the actions of genes involved in signal transduction, adhesion, motility, autophagy and cell wall and matrix biosynthesis. However, due to functional redundancy and fail safe options not required in the laboratory, this single organism approach cannot capture all essential genes.To understand how multicellular organisms evolved, it is essential to recognize both the conserved core features of their developmental programs and the gene modifications that instigated phenotypic innovation. For complex organisms, such as animals, this is not within easy reach, but it is feasible for less complex forms, such as the Dictyostelid social amoebas.ResultsWe compared global profiles of gene expression during the development of four social amoebae species that represent 600 mya of Dictyostelia evolution, and identified orthologous conserved genes with similar developmental up-regulation of expression using three different methods. For validation, we disrupted five genes of this core set and examined the phenotypic consequences.ConclusionAt least 71 of the developmentally regulated genes that were identified with all methods were likely to be already present in the last ancestor of all Dictyostelia. The lack of phenotypic changes in null mutants indicates that even highly conserved genes either participate in functionally redundant pathways or are necessary for developmental progression under adverse, non-standard laboratory conditions. Both mechanisms provide robustness to the developmental program, but impose a limit on the information that can be obtained from deleting single genes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3223-z) contains supplementary material, which is available to authorized users.

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Evolution of Signalling and Morphogenesis in the Dictyostelids

Schilde

2023

The Mycota

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Root of Dictyostelia based on 213 universal proteins

Cited by 17 publications

References 46 publications

A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group

A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group

A set of genes conserved in sequence and expression traces back the establishment of multicellularity in social amoebae

Evolution of Signalling and Morphogenesis in the Dictyostelids

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