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Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum

Rivero Crespo, Francisco; 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

Authors

Francisco Rivero Crespo F.Rivero-Crespo@hull.ac.uk

Richard Sucgang

Alan Kuo

Xiangjun Tian

William Salerno

Anup Parikh

Christa L Feasley

Eileen Dalin

Hank Tu

Eryong Huang

Kerrie Barry

Erika Lindquist

Harris Shapiro

David Bruce

Jeremy Schmutz

Asaf Salamov

Petra Fey

Pascale Gaudet

Christophe Anjard

M Madan Babu

Siddhartha Basu

Yulia Bushmanova

Hanke van der Wel

Mariko Katoh-Kurasawa

Christopher Dinh

Pedro M Coutinho

Tamao Saito

Marek Elias

Pauline Schaap

Robert R Kay

Bernard Henrissat

Ludwig Eichinger

Francisco Rivero

Nicholas H Putnam

Christopher M West

William F Loomis

Rex L Chisholm

Gad Shaulsky

Joan E Strassmann

David C Queller

Adam Kuspa

Igor V Grigoriev



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.

Journal Article Type Article
Publication Date Dec 31, 2011
Journal GENOME BIOLOGY
Print ISSN 1474-7596
Publisher Springer Verlag
Peer Reviewed Peer Reviewed
Volume 12
Issue 2
Article Number R20
APA6 Citation Rivero Crespo, F. (2011). Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biology, 12(2), https://doi.org/10.1186/gb-2011-12-2-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

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