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Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum

Richard Sucgang1, Alan Kuo2, Xiangjun Tian3, William Salerno1, Anup Parikh4, Christa L Feasley5, Eileen Dalin2, Hank Tu2, Eryong Huang4, Kerrie Barry2, Erika Lindquist2, Harris Shapiro2, David Bruce2, Jeremy Schmutz2, Asaf Salamov2, Petra Fey6, Pascale Gaudet6, Christophe Anjard7, M Madan Babu8, Siddhartha Basu6, Yulia Bushmanova6, Hanke van der Wel5, Mariko Katoh-Kurasawa4, Christopher Dinh1, Pedro M Coutinho9, Tamao Saito10, Marek Elias11, Pauline Schaap12, Robert R Kay8, Bernard Henrissat9, Ludwig Eichinger13, Francisco Rivero14, Nicholas H Putnam3, Christopher M West5, William F Loomis7, Rex L Chisholm6, Gad Shaulsky34, Joan E Strassmann3, David C Queller3, Adam Kuspa134* and Igor V Grigoriev2

  • * Corresponding author: Adam Kuspa akuspa@bcm.edu

  • † Equal contributors

Author affiliations

1 Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA

2 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 9458, USA

3 Department of Ecology and Evolutionary Biology, Rice University, 6100 Main Street, Houston, TX 77005, USA

4 Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA

5 Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, 110 N. Lindsay, Oklahoma City, OK 73104, USA

6 dictyBase, Center for Genetic Medicine, Northwestern University, 750 N. Lake Shore Drive, Chicago, IL 60611, USA

7 Section of Cell and Developmental Biology, Division of Biology, University of California, 9500 Gilman Dr, San Diego, La Jolla, CA 92093, USA

8 Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge CB2 2QH, UK

9 Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universities of Aix-Marseille I & II, 13288 Marseille, France

10 Department of Materials and Life Sciences, Sophia University 7-1 Kioi-Cho, Chiyoda-Ku, Tokyo 102-8554, Japan

11 Departments of Botany and Parasitology, Faculty of Science, Charles University in Prague, Albertov 6, Prague 128 43, Czech Republic

12 College of Life Sciences, University of Dundee, Dow Street, Dundee, DD15EH, UK

13 Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany

14 Centre for Biomedical Research, The Hull York Medical School and Department of Biological Sciences, University of Hull, Hull, HU6 7RX, UK

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Citation and License

Genome Biology 2011, 12:R20  doi:10.1186/gb-2011-12-2-r20

Published: 28 February 2011

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 × 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.