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Joint Genome Institute Calls for New Bacterial, Metagenomic, Eukaryotic Resequencing Targets

NEW YORK (GenomeWeb News) – The Joint Genome Institute is asking for scientists to propose new sequencing programs on bacteria and other organisms in order to fulfill the US Department of Energy’s bioenergy and global carbon cycling research goals.
 
JGI wants the latest Community Sequencing Program applicants to pursue targets including bacterial and archaeal isolates, and large-scale eukaryotic or bacterial resequencing research programs that use next-generation sequencing, eukaryotic reference genomes, and environmental microbial genomes.
 
The program will start taking white papers about proposed bacterial and archaeal isolate programs in January 2009, and will review them continuously on a quarterly basis.
 
These organisms should expand the phylogenetic representation among sequenced organisms or should participate in processes directly relevant to DOE missions. These proposals will be ranked and put in a prioritized queue, JGI said.
 
The institute also wants proposals centered on resequencing bacterial isolates for which a reference genome exists. These programs may focus on bacterial community structure, on understanding gene function in bacteria under selective pressure or in mutagenized strains. JGI also will consider collections of highly related strains from nature that show phenotypic differences related to DOE’s missions, such as lignocellulose degradation, fermentation of sugar substrates, or metabolism of environmental toxins.
 
Proposals for metagenomic sequencing and analysis are sought for microbial communities that are relevant to DOE’s interests in alternative energy and carbon cycling, including such targets as rizosphere communities, cellulosic biomass degrading communities, communities capable of degrading environmental toxins, or marine terrestrial communities important in global carbon cycling.
 
These individual projects should be driven by specific project goals rather than environmental surveys, and they could include gene or pathway discovery or complete genome assembly.
 
JGI also will seek proposals for large-scale eukaryotic resequencing efforts that are appropriate for new short-read sequencing technologies. These could include targets such as biomass feedstocks, model organism plants, biomass degrading fungi, and plant pathogens for which a reference genome exists or is currently planned.
 
DOE also wants to obtain target genomes of less than 250 megabases in size that are appropriate for sequencing on new technology platforms. Ideal candidate genomes should be inbred, DOE said, and should have minimal polymorphism and repeat content.
 
If some of this information is not yet available, applicants also may propose pilot-scale sequencing in order to acquire the basic genome information.
 
More information about the sequencing program is available here

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