dictyNews
Electronic Edition
Volume 38, number 31
December 7, 2012

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Abstracts
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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 cells’ 
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 [[log in to unmask]]
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GenColors-based comparative genome databases for small 
eukaryotic genomes.

Felder M, Romualdi A, Petzold A, Platzer M, Sühnel J, Glöckner 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 [[log in to unmask]]
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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 [[log in to unmask]]
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[End dictyNews, volume 38, number 31]