Journal
GENOME BIOLOGY
Volume 12, Issue 2, Pages -Publisher
BMC
DOI: 10.1186/gb-2011-12-2-r20
Keywords
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Funding
- US Department of Energy's Office of Science, Biological and Environmental Research
- University of California
- Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]
- Lawrence Livermore National Laboratory [DE-AC52-07NA27344]
- Los Alamos National Laboratory [DE-AC02-06NA25396]
- National Institute of Health [HD39691, GM64426, HG0022, GM84383]
- National Science Foundation [EF-0626963, DEB-0918931]
- Keck Center for Interdisciplinary Bioscience Training of the Gulf Coast Consortia (NIH) [1 T90 DA022885, 1 R90 DA023418]
- EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH & HUMAN DEVELOPMENT [P01HD039691] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM087371, R01GM064426, R01GM084383] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE ON DRUG ABUSE [T90DA022885, R90DA023418] Funding Source: NIH RePORTER
- Direct For Biological Sciences [0816690] Funding Source: National Science Foundation
- Division Of Environmental Biology [1204352] Funding Source: National Science Foundation
- Biotechnology and Biological Sciences Research Council [BB/D013453/1, BB/E016308/1] Funding Source: researchfish
- Medical Research Council [MC_U105185859, MC_U105115237] Funding Source: researchfish
- BBSRC [BB/E016308/1, BB/D013453/1] Funding Source: UKRI
- MRC [MC_U105115237, MC_U105185859] Funding Source: UKRI
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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.
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