VAAM-Jahrestagung 2011 Karlsruhe, 3.–6. April 2011

questions may help to solve ongoing debate on plant-fungal co-evolutionand on the functional role of AMF in natural systems.ISV18The genomic standards consortium: Bringing standardsto LifeF.O. GlöcknerMicrobial Genomics and Bioinformatics, Max Planck Institute for MarineMicrobiology, Bremen, GermanyThe application of high-throughput sequencing technologies has transformedthe way microbiologists approach questions in their field. The shift ofsequencing capacity is now resulting in a dramatic increase in the amount ofdata available to a wider community, forming a rich stream of information.These data hold the promise of unparalleled insights into fundamentalquestions across a range of fields including evolution, ecology, environmentbiology, health and medicine. To fully exploit the promise of these data weneed both scientific innovation and community agreement on how toprovide appropriate stewardship of these resources for the benefit of all. Onekey insight into the function of a gene or organism is the environment whereit occurs. Collection of contextual (meta) data, which delineates the sourceof a sequence in terms of the space, time, habitat, and characteristics of theenvironment, is thus essential in interpreting the unknown genes andspecies, as well as gaining new insights into the known fraction. At present,the valuable contextual data halo is often missing for sequences deposited inthe International Nucleotide Sequence Database Collaboration (INSDC). In2005, members of the community came together to form the GenomicStandards Consortium (GSC), an open-membership working body with thestated mission of working towards better descriptions of our genomes,metagenomes, and related data (www.gensc.org). Supported by the expertiseof the members involved in many of the aforementioned mega-sequencingprojects, the GSC has formalized the contextual data requirements forgenomes and metagenomes as the Minimum Information about aGenome/Metagenome Sequence checklist (MIGS/MIMS) [1]. Furthermore,the extension of MIGS/MIMS to cover the description of phylogenetic andfunctional marker genes is in progress as the Minimum Information about anEnvironmental Sequence (MIENS) checklist(www.gensc.org/gc_wiki/index.php/MIENS) [2]. This family of minimuminformation checklists (MIxS) provides researchers with a condensed set ofcontextual data requirements, which range from description of theenvironment to sequencing procedures. Active participation to furtherdevelop the MIxS standards is highly appreciated. Requests for new featuresand reporting of bugs can be easily done via http://mixs.gensc.org.[1] Field, D. et al (2008): The minimum information about a genome sequence (MIGS) specification.Nat. Biotechnol. 26:541-547.[2] Yilmaz, P. et al, for the Genomic Standards Consortium (under revision) The „MinimumInformation about an ENvironmental Sequence” (MIENS) specification. Nat. Biotechnol.ISV19Standards in genomic sciences: A standards compliantopen-access journal for the ‘omics communityG. Garrity* 1 , N. Kyrpides 2 , D. Field 3 , P. Sterk 3,4 , H.-P. Klenk 51 Microbiology & Molecular Genetics, Michigan State University, EastLansing, USA2 DOE Joint Genome Institute, Walnut Creek, USA3 Center for Ecology & Hydrology, Molecular Evolution and BioinformaticsGroup, Oxfordshire, United Kingdom4 The Sanger Institute, Wellcome Trust Genome Campus, Hinkston Down,United Kingdom5 German Collection of Microorganisms and Cell Cultures (DSMZ),Braunschweig, GermanyStandards in Genomics Sciences (SIGS; www.standardsingenomics.org) isan Open Access eJournal that was created to promote the datastandardization efforts of the Genomic Standards Consortium (GSC) and toprovide a venue for publication of highly structured, MIGS compliantreports of genome and metagenome sequences, standard operatingprocedures, meeting reports, white papers and other articles that promote arein keeping with the objectives of the GSC. Whereas peer-reviewedcompanion publications of genomes were once commonplace in a number ofjournals, many general and discipline specific publications routinely declinesuch papers today. This leads to a loss of contextual information that isneeded for analyzing and interpreting genome sequence data.The GSC was founded in 2005 by an international community of likemindedscientists to work towards improving the descriptions of ourgrowing collection of genomes and metagenomes. Without metadatastandards, exchanging and integrating genomic data into analytical modelsand public knowledge bases increases while the overall value of eachadditional sequence diminishes. This is problematic because the ease andcost of producing sequence data have dropped sharply while the cost ofannotation and documentation have increased.At the time of writing, SIGS had already published over 100 articles,including more than 80 short genome reports that had been viewed by morethan 25,000 readers in 130 countries. SIGS is listed in CrossRef, TheDirectory of Open Access Journals (DOAJ) and PubMed Central and has,within a period of less than two years, become one of top five journalspublishing papers on new genome sequences.ISV20Reversing the paradigm -- The genome sequence ofCandidatus Sulfuricurvum sp. derived from a complexshort-read metagenome with more than 300 OTUsenables detailed studies of the novel epsilonproteobacterium.F. MeyerMathematics and Computer Science Division, Institute for Genomics andSystems Biology Argonne National Laboratory, Argonne, USACharacterizing genomes of unculturable microbes (most species on earth)requires new approaches for genome assembly from environmental samples,e.g. communities involved in bioremediation at the Old Rifle uraniumcontaminatedsite. Here we show we can reconstruct the complete genome(Candidatus Sulfuricurvum sp) via short-read metagenomics and novelapproaches for assembly based on simple statistical principles. Whileprevious examples of complete genome sequences from metagenomes stemfrom samples of very limited complexity (>10 OTUs), this sequence wasobtained from a complex mix of over 300 OTUs. Traditional approaches failbecause uneven numbers of sequence reads from common and rare species,and pan-genome variation, confuses traditional genome assemblers; specieswithout close relatives sequenced cannot co-assemble: without ourapproach, additional sequence data hurts rather than helps assembly. Inaddition, the metabolic reconstruction of this genome permitted cultivationof this dominant organism from an ecosystem relevant to bioremediation.This novel approach will allow the assembly of genomes and cultivation ofkey species from diverse environments/enrichment cultures, thus providingnew pangenomic insights into processes ranging from biofuel generation toidentification of emerging pathogens.ISV21Translocation of Oomycete effectors into host cellsP. van West*, S. Wawra, S. Grouffaud, C. R. Bruce, N. R. Horner, J. Bain,A. Matena, C. MM Gachon, I. de Bruijn, K. L. Minor, J. A. Boddey, S. C.Whisson, P. Bayer, P. R.J. Birch, A. J. Porter, C. J. SecombesAberdeen Oomycete Laboratory, College of Life Sciences and Medicine,Institute of Medical Sciences, University of Aberdeen, Foresterhill,Aberdeen, ScotlandThe fungus-like oomycetes contain several species that are devastatingpathogens of plants and animals. During infection several oomycetestranslocate effector proteins into host cells where they interfere with hostdefence responses. Several oomycete effectors have a conserved Arg-Xaa-Leu-Arg (RxLR)-motif that is thought to be important for their delivery. Wedemonstrate that, whereas the RxLR-leader sequence of SpHtp1 from thefish pathogen Saprolegnia parasitica shows fish cell-specific translocation,the RXLR-leader of AVR3a from the potato-late-blight pathogenPhytophthora infestans promotes efficient binding of the C-terminal effectordomain to several cell types. Our results demonstrate that the RxLR-leadersof SpHtp1 and AVR3a are dimerisation sites, able to form heteromers. Wefurther demonstrate that cell surface binding of both RxLR-proteins ismediated by an interaction with modified cell surface molecules. Theseresults reveal a novel effector translocation route based on effectordimerisation and receptor modification, which could be highly relevant for awide range of host-microbe interactions.spektrum | Tagungsband 2011