dictyNews Electronic Edition Volume 38, number 31 December 7, 2012 Please submit abstracts of your papers as soon as they have been accepted for publication by sending them to dicty@northwestern.edu or by using the form at http://dictybase.org/db/cgi-bin/dictyBase/abstract_submit. Back issues of dictyNews, the Dicty Reference database and other useful information is available at dictyBase - http://dictybase.org. Follow dictyBase on twitter: http://twitter.com/dictybase ========= Abstracts ========= A new social gene in Dictyostelium discoideum, chtB Lorenzo A. Santorelli, Adam Kuspa, Gad Shaulsky, David C. Queller & Joan E. Strassmann BMC Evolutionary Biology, in press Background Competitive social interactions are ubiquitous in nature, but their genetic basis is difficult to determine. Much can be learned from single gene knockouts in a eukaryote microbe. The mutants can be competed with the parent to discern the social impact of that specific gene. Dictyostelium discoideum is a social amoeba that exhibits cooperative behavior in the construction of a multicellular fruiting body. It is a good model organism to study the genetic basis of cooperation since it has a sequenced genome and it is amenable to genetic manipulation. When two strains of D. discoideum are mixed, a cheater strain can exploit its social partner by differentiating more spore than its fair share relative to stalk cells. Cheater strains can be generated in the lab or found in the wild and genetic analyses have shown that cheating behavior can be achieved through many pathways. Results We have characterized the knockout mutant chtB, which was isolated from a screen for cheater mutants that were also able to form normal fruiting bodies on their own. When mixed in equal proportions with parental strain cells, chtB mutants contributed almost 60% of the total number of spores. To do so, chtB cells inhibit wild type cells from becoming spores, as indicated by counts and by the wild type cellsÕ reduced expression of the prespore gene, cotB. We found no obvious fitness costs (morphology, doubling time in liquid medium, spore production, and germination efficiency) associated with the cheating ability of the chtB knockout. Conclusions In this study we describe a new gene in D. discoideum, chtB, which when knocked out inhibits the parental strain from producing spores. Moreover, under lab conditions, we did not detect any fitness costs associated with this behavior. Submitted by Lorenzo Santorelli [lorenzo.santorelli@zoo.ox.ac.uk] --------------------------------------------------------------------------- GenColors-based comparative genome databases for small eukaryotic genomes. Felder M, Romualdi A, Petzold A, Platzer M, SŸhnel J, Glšckner G. Nucleic Acids Research database issue Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources. Submitted by Gernot Gloeckner [gernot.gloeckner@uni-koeln.de] --------------------------------------------------------------------------- dictyBase 2013: Integrating Multiple Dictyostelid species Siddhartha Basu, Petra Fey, Yogesh Pandit, Robert Dodson, Warren A. Kibbe, Rex L. Chisholm Nucleic Acids Research database issue 2013 dictyBase (http://dictybase.org) is the model organism database for the social amoeba Dictyostelium discoideum. This contribution provides an update on dictyBase that has been previously presented. During the past three years, dictyBase has taken significant strides toward becoming a genome portal for the whole Amoebozoa clade. In its latest release, dictyBase has scaled up to host multiple Dictyostelids, including Dictyostelium purpureum (Sucgang et al. 2011, Genome biology, 12, R20.), Dictyostelium fasciculatum, and Polysphondylium pallidum (Heidel et al. 2011, Genome research 21(11) 1882-91). The new release includes a new Genome Browser with RNA-Seq expression, interspecies BLAST alignments and a unified BLAST search for cross-species comparisons. Submitted by Petra Fey [pfey@northwestern.edu] ============================================================== [End dictyNews, volume 38, number 31]