Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum

Sucgang, Richard; Kuo, Alan; Tian, Xiangjun; Salerno, William; Parikh, Anup; Feasley, Christa L; Dalin, Eileen; Tu, Hank; Huang, Eryong; Barry, Kerrie; Lindquist, Erika; Shapiro, Harris; Bruce, David; Schmutz, Jeremy; Salamov, Asaf; Fey, Petra; Gaudet, Pascale; Anjard, Christophe; Madan Babu, M; Basu, Siddhartha; Bushmanova, Yulia; van der Wel, Hanke; Katoh-Kurasawa, Mariko; Dinh, Christopher; Coutinho, Pedro M; Saito, Tamao; Elias, Marek; Schaap, Pauline; Kay, Robert R; Henrissat, Bernard; Eichinger, Ludwig; Rivero, Francisco; Putnam, Nicholas H; West, Christopher M; Loomis, William F; Chisholm, Rex L; Shaulsky, Gad; Strassmann, Joan E; Queller, David C; Kuspa, Adam; Grigoriev, Igor V

Abstract

Background: The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum. Results: We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 x coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. Interesting patterns of gene conservation and divergence are also evident, suggesting function differences; some protein families, such as the histidine kinases, have undergone little functional change, whereas others, such as the polyketide synthases, have undergone extensive diversification. The abundant amino acid homopolymers encoded in both genomes are generally not found in homologous positions within proteins, so they are unlikely to derive from ancestral DNA triplet repeats. Genes involved in the social stage evolved more rapidly than others, consistent with either relaxed selection or accelerated evolution due to social conflict. Conclusions: The findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia.

Citation

Sucgang, R., Kuo, A., Tian, X., Salerno, W., Parikh, A., Feasley, C. L., Dalin, E., Tu, H., Huang, E., Barry, K., Lindquist, E., Shapiro, H., Bruce, D., Schmutz, J., Salamov, A., Fey, P., Gaudet, P., Anjard, C., Madan Babu, M., Basu, S., …Grigoriev, I. V. (2011). Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biology, 12(2), Article R20. https://doi.org/10.1186/gb-2011-12-2-r20

• Journal Article Type: Article
• Acceptance Date: Dec 31, 2011
• Publication Date: Dec 31, 2011
• Publicly Available Date: Aug 30, 2019
• Journal: GENOME BIOLOGY
• Print ISSN: 1474-7596
• Publisher: Springer Verlag
• Peer Reviewed: Peer Reviewed
• Volume: 12
• Issue: 2
• Article Number: R20
• DOI: https://doi.org/10.1186/gb-2011-12-2-r20
• Keywords: differentiation-inducing-factor cellular slime-mold multiple sequence alignment adenylyl-cyclase terminal differentiation polyketide synthase natural-products cheater mutants protein-kinases noncoding rnas
• Public URL: https://hull-repository.worktribe.com/output/400125