Related Experiment Video
Updated: May 13, 2026
06:47
High-throughput Measurement of Dictyostelium discoideum Macropinocytosis by Flow Cytometry
Published on: September 10, 2018
Comparative genomics of the dictyostelids
1Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA. loomis@biomail.ucsd.edu
Methods in Molecular Biology (Clifton, N.J.)
|March 16, 2013
Summary
Comparative genomics of four dictyostelid species reveals their evolutionary history and unique genetic pathways. This study uncovers key differences in signaling molecules like GABA and cytokinins, impacting intercellular communication and development in these social amoebas.
Area of Science:
- Genomics and Evolutionary Biology
- Molecular Biology
- Biochemistry
Background:
- The complete genomes of four dictyostelid species (Dictyostelium discoideum, Dictyostelium purpureum, Polysphondylium pallidum, and Dictyostelium fasciculatum) have been sequenced.
- Comparative analysis of these genomes provides insights into the evolutionary relationships and genetic makeup of these social amoebas.
Purpose of the Study:
- To compare the predicted proteomes of four dictyostelid species.
- To infer evolutionary pathways and divergence times among these species.
- To identify species-specific gene content and functional differences, particularly in signaling pathways.
Main Methods:
- Whole-genome sequencing of four Dictyostelium and Polysphondylium species.
- Comparative proteomic analysis against databases of bacterial, plant, fungal, and animal proteins.
- Phylogenetic analysis based on clusters of orthologous proteins to estimate divergence times.
- Identification and comparison of genes involved in signal transduction and secondary metabolite synthesis.
Main Results:
- Dictyostelids form a monophyletic group, diverging from the animal lineage before fungi, with four major clades.
- Polysphondylium pallidum (group 2) and Dictyostelium fasciculatum (group 1) diverged from Dictyostelium discoideum and Dictyostelium purpureum (group 4) around 600-800 million years ago.
- P. pallidum and D. fasciculatum lack the GABA synthesis gene (gadA), suggesting different regulation of AcbA release compared to D. discoideum.
- The cytokinin synthesis gene (iptA) was acquired via horizontal gene transfer in the common ancestor of group 4 dictyostelids after divergence from groups 1 and 2.
Conclusions:
- Comparative genomics elucidates the evolutionary history and relationships within the Dictyostelida.
- Significant differences in key signaling pathways, such as GABA and cytokinin synthesis, exist among dictyostelid species, impacting their development and intercellular communication.
- The findings provide a foundation for further research into the functional genomics and evolutionary adaptations of these model organisms.
Related Concept Videos
02:16Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
01:15Diversity of Protists I
Excavata is a diverse group of protists that includes both chemoorganotrophic and phototrophic species, with some thriving in anaerobic environments. Among the key groups within Excavata are diplomonads and parabasalids, which are flagellated protists that lack mitochondria and chloroplasts. These microorganisms typically inhabit anoxic environments, such as the intestines of animals, where they exist either symbiotically or as parasites, relying on fermentation for energy production. Some...
01:29Modern Molecular Taxonomy
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
01:08Evolution of Microbial Genome
Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.
01:27Diversity of Protists IV
Amoebozoa represent a diverse group of terrestrial and aquatic protists that utilize lobe-shaped pseudopodia for locomotion and feeding. This characteristic differentiates them from the Rhizaria, which possess threadlike pseudopodia. The primary classifications within Amoebozoa include gymnamoebas, entamoebas, and the plasmodial and cellular slime molds. Phylogenetic evidence indicates that Amoebozoa diverged from a lineage that ultimately gave rise to fungi and animals.Gymnamoebas and...