The genome of the social amoeba Dictyostelium discoideum

By L. Eichinger, Justin A. Pachebat, G. Glöckner, M. Rajandream, Richard Sucgang, Matthew Berriman, J. Song, R. Olsen, K. Szafranski, Q. Xu and 87 more. Nature, 2005

1,352 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0717652654674d5350a84771350e1e0ced2487af

How researchers see this paper

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In Genetics

1. John S. Mattick
2. R. Singer
3. Ryan J. Taft
4. Detlev Arendt
5. Michael Pheasant
6. P. Keeling
7. Andreas Gnirke
8. Julian Gough

In Molecular Biology

1. Patricia P. Chan
2. Todd M. Lowe
3. John S. Mattick
4. P. Keeling
5. Ryan J. Taft
6. Michael Pheasant
7. Allysia J. Mak
8. Brian Y. Lin

Citations in the corpus

• tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes (2019, methodology): “The collected sequences (65 eukaryotic (45-56), 61 bacterial (57), and 13 archaeal (42,58-61)) were aligned to the original tRNA covariance models from tRNAscan-SE 1.”
• Horizontal gene transfer in eukaryotic evolution (2008, background): “The Dictyostelium discoideum genome, for example, was reported to have 18 potential cases of bacterial genes, many of them related to life in the soil (for example, dipeptidases for degrading bacterial cell walls, a siderophore for the transport of ferric iron, and soil toxin-resistance genes”
• The evolution of cell types in animals: emerging principles from molecular studies (2008, background): “The ciliary line of photoreceptor evolution seems to even date back to early metazoans, as indicated by the presence of c-opsin-related photopigment in the ciliary photoreceptors of jellyfish eye”
• SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny (2008, background): “Tandem repeats of trinu-cleotides are abundant in dictyostelids (11).”
• Transcriptional pulsing of a developmental gene. (2006, methodology): “We used the AX3 strain, as the chromosomal region containing the discoidin I genes is duplicated [14].”
• Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006, neutral): “In fact, the AT pull is so strong in coding regions that amino-acid composition of proteins is shifted toward those coded by codons with high AT content, as seen in other species with extreme AT bias (e.g., [64]).”
• Circular RNA Is Expressed across the Eukaryotic Tree of Life (2014, neutral): “gz ([38]) respectively.”
• The relationship between non-protein-coding DNA and eukaryotic complexity. (2007, result): “Conversely, there is some indication that there has been an increase in proteincoding gene number in genomes where initial predictions, conditioned by corresponding expectations, were low.((55,65))”
• Sequence and structural analysis of BTB domain proteins (2005, background): “We identified an intermediate number, 41, in the social amoeba Dictyostelium discoideum [39] (Figure 5).”
• Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries (2011, background): “Cloning bias hindered efforts to sequence the AT-rich genomes of Dictyostelium [12] and Plasmodium [13] and excluded the GC-rich first exons of about 10% of protein-coding genes in the dog (K Lindblad-Toh, personal communication) from an otherwise high-quality reference genome assembly [14].”