Program Book - 27th Fungal Genetics Conference

FULL POSTER SESSION ABSTRACTSknown protein sequences, RNA-Seq data and ab initio predictors. Then, based on comparative genomics with the pathogenic species Ustilago maydis,Ustilago hordei and Sporisorium reilianum, we identified key features that could explain both the avirulent nature of P. flocculosa toward plants and thevirulent features of the pathogenic Ustilaginales.First, the genome structural annotation showed similarities in total gene number, gene density and average gene length. But these similarities hidesmajor differences with regards to average intron per gene and GC content. In fact, P. flocculosa has about 4 times more introns than U. maydis and has avery high GC content of 65.1%. Moreover, P. flocculosa genome shows a lower level of synteny than pathogenic species compared together.Second, comparison of gene content revealed unexpected results. On one hand, the genome of P. flocculosa harbor many traits usually associated withpathogenic species like plant cell-wall degrading enzymes and genes involved in the synthesis of secondary metabolites that are highly conservedcompared to pathogenic species. On the other hand, genes coding for candidate secreted effector proteins (CSEPs) show a much lower level ofconservation, that seem to explain, in part, the differences in lifestyle.Finally, this work led to the identification of certain of the most interesting genetic features in the study of pathogens and biocontrol agents.332. A tale of two poplar pathogens - Moving from sequence to function. B. Dhillon 1 , N. Feau 1 , P. Tanguay 2 , M. Sakalidis 1 , S. Beausiegle 1 , R. Ohm 3 , A.Aerts 3 , I. Grigoriev 3 , G. H. J. Kema 4 , S. B. Goodwin 5 , R. Hamelin 1 . 1) Forest Sciences, University of British Columbia, Vancouver, BC, Canada; 2) CFSLaurentian Forestry Centre, Succ. Sainte-Foy, Québec, Canada; 3) 3DOE Joint Genome Institute, Walnut Creek, California, USA, DOE, USA; 4) Plant ResearchInternational B.V., Wageningen, The Netherlands; 5) USDA-Agricultural Research Service, Purdue University, West Lafayette, Indiana, USA.Two closely related, morphologically indistinct fungal pathogens of poplars, Mycospharella populorum and M. populicola are prevalent in North America.In natural stands, these two fungal species closely follow the distribution of their host, with M. populorum being found on Aiegeiros botanical section andM. populicola on the Tacamahaca section of poplars. Epidemiologically, M. populorum is considered to be more aggressive, as in addition to leaf-spots, ithas the ability to infect woody tissue and cause cankers, an ability that M. populicola lacks. Moreover, introduction of hybrid plantations has added to M.populorum host range. Availability of genomes will allow us a window into understanding the genetic basis for these observed differences in epidemiologyand host-specificity for these two pathogens. Historical observation of host-specificity was confirmed by comparative sequence analysis the estimated thedivergence time between the two poplar pathogens to be ~6.4 Mya, which agrees with the divergence time estimates for the poplar botanical sections(6.8 - 7.8 Mya). Despite the remarkable macro-synteny exhibited between these two recently diverged pathogens, several genes specific to each pathogenwere identified in genomic regions where synteny broke down. In addition to being candidates for the different physiological and epidemiologicalattributes, these species-specific genes could be utilized for diagnostic and monitoring assays. A consistent expansion of several pathogenicity-relatedgene families was observed in M. populorum, suggesting a role for gene-dosage in determining its ability to cause cankers. Preliminary enzyme assaysshowed significant differences in beta-glucosidase and xylanase activities between these two fungi.333. Defining Open Chromatin Regions in Coprinopsis cinerea Oidia by FAIRE. Virginia K. Hench 1,2 , Patricia J. Pukkila 1,2 . 1) Department of Biology,University of North Carolina at Chapel Hill, NC 27599; 2) Office for Undergraduate Research, University of North Carolina at Chapel Hill, NC 27599.Changes in chromatin organization are principal regulatory mechanisms controlling multiple cellular processes including gene expression and meioticcrossover formation. Here we present FAIRE (formaldehye assisted isolation of regulatory elements) data that reveals regions of open chromatin inCoprinopsis cinerea oidia, the asexual spore stage of the C. cinerea life cycle. A standard FAIRE protocol was developed and optimized for oidia and used toenrich for nucleosome-free stretches of chromatin. FAIRE peaks were identified from single-end read whole genome sequence data using ZINBA (Zero-Inflated Negative Binomial Algorithm), which identified 7,276 peaks covering 6.3% of the genome. FAIRE peaks are predominantly intergenic with 78% ofFAIRE domains overlapping noncoding sequence. The peak widths range from 98-1390 bps, with an average width of 310 bps. Nearly half or 47% ofannotated genes (Broad version 3) contain a FAIRE peak in the proximal promoter region (defined as 500 bps immediately upstream of the gene start).Differential transcription has been characterized throughout the synchronous meiotic process in C. cinerea (Burns, C. et al., PLOS Genetics, vol 6, issue 9,2010), but the extent to which nucleosome occupancy might contribute to gene regulation in this multicellular fungus was not known. We found that aminority of meiotic specific (MS; genes expressed in meiosis and not in vegetative tissue) genes had promoter FAIRE peaks (of 819 genes 37% hadpromoter FAIRE peaks). In contrast, 61% of genes significantly changing during meiosis (SCDM; 2,455 genes) had promoter FAIRE peaks. Out of 295 genesthat were MS and SCDM, 38% had promoter FAIRE peaks in oidia. Genes with known meiotic function including spo11, dmc1, and rec8 were amongst theMS/SCDM genes that did not have promoter FAIRE peaks in oidia. In summary, all examined meiotic gene sets included genes associated with and withoutFAIRE peaks in their promoter regions, indicating that complex gene regulation mechanisms contribute to differential, tissue-specific gene expression in C.cinerea. Supported by the U.S. Department of Energy Joint Genome Institute Community Sequencing Program. The work conducted by the U.S. DOE JGI issupported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.334. Ensembl Fungi - genome-scale data portal from fungal species. Uma Maheswari, Heldér Pedro, Mark McDowall, Daniel M. Staines, Paul Kersey.European Bioinformatics Institute (EMBL-EBI), Cambridge, United kingdom.Ensembl Fungi (http://fungi.ensembl.org) is a portal offering access to genome-scale data from fungal species, using the Ensembl genome analysissystem, through a common set of interfaces shared with non-fungal species also represented in the Ensembl system. These include a web-based genomebrowser, Perl and REST-ful APIs, a public MySQL server and a query-orientated data warehouse (BioMart). The current release (January 2013) providesaccess to 36 fungal genomes across 12 different taxonomic orders, including the model species Saccharomyces cerevisiae and Schizosaccharomycespombe, (for which data are imported from the Saccharomyces Genome Database and PomBase respectively) but focuses mainly on plant pathogenspecies: genomic data from these is being integrated with information about infectious phenotypes (derived from PHI-base (http://www.phibase.org) on aper-gene basis, thro ugh a new targeted resource PhytoPath (http://www.phytopathdb.org).Core data provided for all species includes genome sequence, sequence patterns, annotation of protein and non-coding genes and functional annotationimported from direct curation, UniProt and InterPro. Information about gene regulation, sequence variation, evolution and conservation is also integratedin the system. Protein alignments are used to reconstruct evolutionary trees and infer homology relationships, while pairwise alignments between DNAsequences are performed between closely related species. Genomic polymorphisms are presented in the context of the reference genome sequences ofSaccharomyces cerevisiae and the phytopathogens Gibberella zeae, Puccinia graminis and Fusarium oxysporum.Ensembl Fungi will continue to expand with the increase in genomic data , we seek to work with the communities actively generating and using data, andare participants in a growing range of collaborations involved in the annotation and analysis of genomes.202