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Transcriptome profile of Dictyostelium discoideum slugs in clonal and chimeric development

ABSTRACT: Transcriptome profile of Dictyostelium discoideum slugs in clonal and chimeric development

PROVIDER: PRJNA484366 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7641790_1.fastq.gz	Fastqsanger.gz
	SRR7641790_2.fastq.gz	Fastqsanger.gz
	SRR7641791_1.fastq.gz	Fastqsanger.gz
	SRR7641791_2.fastq.gz	Fastqsanger.gz
	SRR7641782_1.fastq.gz	Fastqsanger.gz

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Transcriptome profile of Dictyostelium discoideum slugs in clonal and chimeric development

Project description:Social interactions are typically characterised by conflict and competition. This antagonism can play a critical role in evolutionary processes, such as promoting diversity through maintenance of alternative strategies or driving accelerated evolution through arms-race like escalation. However, despite our sophisticated understanding of how conflict shapes social traits, we still have limited knowledge of how it impacts molecular evolution across the underlying ‘social genes’. To address this problem, we analysed the genome wide impact of social interactions in a microbe. To understand broad-scale processes shaping molecular evolution at social genes we have used four different, but complementary, approaches to identify sets of social genes. For ease, we have named these sets ‘sociality’, ‘chimerism’, ‘antagonism’ and ‘cheater’ genes. Chimerism genes are defined as those up-regulated in chimeric aggregations in comparison to clonal aggregations. This is based on the logic that chimeric development will be characterised by conflict, and hence these genes will show the signatures of conflict driven evolution. Using genome sequences from 67 Dictyostelium discoideum strains, we find that social genes often exhibit enhanced polymorphism and accelerated evolution. However, these patterns are not consistent with the expectation of conflict driven processes, but instead reflect relatively relaxed purifying selection. This pattern reflects the fact that social interactions are conditional, and therefore selection on genes expressed in social interactions is diluted by generations of inactivity. This results in the ‘Red King’ process, wherein dilution of selection by inactivity enhances the role of drift, resulting in increased polymorphism and accelerated evolution.

2019-05-09 | GSE118081 | GEO

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Dictyostelium discoideum O-Ser-fucome from WT and SPY-KO developing cells (slugs)

Project description:Dictyostelium discoideum O-Ser-fucosylated proteins from WT and SPY-KO developing cells (slugs) were immunoprecipitated using anti O-Ser fucose polyclonal antibodies in 3 Biological Replicates, with 3 Technical Replicates each, by comparing AX3 (WT strain) against SPY-KO (mutant, deficient in O-fucosylation).

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Dictyostelium discoideum O-Thr-fucome from WT and SPY-KO developing cells (slugs)

Project description:Dictyostelium discoideum O-Thr-fucosylated proteins from WT and SPY-KO developing cells (slugs) were immunoprecipitated using anti O-Thr fucose polyclonal antibodies in 3 Biological Replicates, with 3 Technical Replicates each, by comparing AX3 (WT strain) against SPY-KO (mutant, deficient in O-fucosylation).

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Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum [NC105.1_RFP_vs_NC85.2]

Project description:Dictyostelium discoideum, a microbial model for social evolution, is known to distinguish self from non-self and show genotype-dependent behavior during chimeric development. Aside from a small number of cell-cell recognition genes, however, little is known about the genetic basis of self/non-self recognition in this species. Based on the key hypothesis that there should be differential expression of genes if D. discoideum cells were interacting with non-clone mates, we performed transcriptomic profiling study in this species during clonal vs. chimeric development. Wild strains isolated from North Carolina, which have been shown to form a dominance hierarchy when co-developing in chimeras, were used. The transcriptomic profiles of D. discoideum cells in clones vs. different chimeras were compared at five different developmental stages using a customized microarray. Effects of chimerism on global transcriptional patterns associated with social interactions were observed. The chimera developmental program may also provide insights on behavioral changes associated with social conflicts in this species.

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Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum [NC105.1_RFP_vs_NC28.1]

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