The genome of the social amoeba Dictyostelium discoideum

Abstract

The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes encode ~12,500 predicted proteins, a high proportion of which have long repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal rDNA element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal/fungal lineage after the plant/animal split, but Dictyostelium appears to have retained more of the diversity of the ancestral genome than either of these two groups.The amoebozoa are a richly diverse group of organisms whose genomes remain largely unexplored. The soil-dwelling social amoeba Dictyostelium discoideum has been actively studied for the past fifty years and has contributed greatly to our understanding of cellular motility, signalling and interaction 1 . For example, studies in Dictyostelium provided the first descriptions of a eukaryotic cell chemo-attractant and a cell-cell adhesion protein 2, 3 .Dictyostelium amoebae inhabit forest soil consuming bacteria and yeast, which they track by chemotaxis. Starvation, however, prompts the solitary cells to aggregate and to develop as a true multicellular organism, producing a fruiting body comprised of a cellular, cellulosic stalk supporting a bolus of spores. Thus, Dictyostelium has evolved mechanisms that direct the differentiation of a homogeneous population of cells into distinct cell types, regulate the proportions between tissues and orchestrate the construction of an effective structure for the dispersal of spores 4 . Many of the genes necessary for these processes in Dictyostelium were Eichinger et al. Page 2 Nature. Author manuscript; available in PMC 2006 January 27. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript also inherited by metazoa and fashioned through evolution for use within many different modes of development.The amoebozoa are also noteworthy as representing one of the earliest branches from the last common ancestor of all eukaryotes. Each of the surviving branches of the crown group of eukaryotes provides an example of the ways in which the ancestral genome has been sculpted and adapted by lineage-specific gene duplication, divergence and deletion. Comparison between representatives of these branches promises to shed light not only on the nature and content of the ancestral eukaryotic genome, but on the diversity of ways in which its components have been adapted to meet the needs of complex organisms. The genome of Dictyosteliu...

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

“…The size distribution showed distinct peaks at 21 nt of near equal proportion of reads from both wt and drnB - strains (Figure 1(a)). No large difference was observed for 21 nt sequences matching mRNA (sense and antisense) or non-coding RNAs (ncRNAs) such as tRNAs, rRNAs, small nucleolar RNAs (snoRNAs), spliceosomal RNAs (snRNAs), single recognition particle RNAs (SRP RNAs) or Class I RNAs (Figure 1(b)) [22,26,34–36]. The great majority of the 21 nt RNAs from both wt and drnB - strains (68,4% and 67,2%, respectively) derive from the retrotransposon element DIRS-1, which also may function as centromeres in D. discoideum [37,38].…”

“…First, a recent report by Kruse et al indicated that mir-1176 and mir-1177 are dependent on RNA polymerase II (RNA Pol II) transcription [30], suggesting that pri-miRNA transcripts in D. discoideum may be polyadenylated as has been demonstrated in animals and plants [4,5,49]. Secondly, the genome of D. discoideum is very AT-rich (about 78%) [26], where long stretches of As are common within transcripts and therefore most likely allow for selection of RNAs with internal poly(A)-tracts.…”

“…The miRNA pathway in D. discoideum share several features with plants. For example, we show that the majority of the miRNAs derive from lncRNAs, although shorter than in plants presumably due to the compact genome of D. discoideum [26], and that miRNAs generated from introns of protein coding genes are rare. Furthermore, similar to the miRNA processing Dicer-like protein in plants, DrnB is present in the nucleus [73] where it seems to be responsible for both generating pre-miRNA and for maturation of the mir-5p and −3p.…”

“…Genomic sequence [26] and annotations (generated June 3, 2015) were retrieved from www.dictybase.org. Mapping of poly(A)-selected reads was performed with TopHat v. 2.0.8b [77] using default settings.…”

“…D. discoideum has a fascinating life-cycle where growing single cells, upon starvation, are reprogrammed to enter multicellular development where up to 100 000 cells aggregate, differentiate, and finally form a fruiting body consisting of a stalk topped by a ball of spores [24]. Phylogenetically, D. discoideum belongs to the supergroup Amoebozoa, which branched out after plants but before fungi and animals [25,26]. …”