Loading...
  • whole genome
  • Recognizing the power of comparative approaches clarified by recent yeast whole genome comparisons , this new selection has an emphasis on 10 major clusters of related species. (broadinstitute.org)
  • However as whole-genome sequences became available for fungi, it became possible to predict the repeat content of a whole genome and calculate RIP mutation across a large number of sequences from multiple repeat families. (edu.au)
  • After decoding the whole genome of an avirulent isolate of M. oryzae , we predicted 11440 protein coding genes and then identified four candidate effector proteins which are exclusively expressed in the infectious structure, appresoria. (frontiersin.org)
  • Comparisons against whole genome Sc. (edu.au)
  • Within the sub-phylum Saccharomycotina, the CVTree clearly resolves two clades: (1) species that translate CTG as serine instead of leucine (the CTG clade) and (2) species that have undergone whole-genome duplication (the WGD clade). (biomedcentral.com)
  • Whole-genome shotgun sequencing (7× coverage) was performed on M. globosa type strain CBS 7966 [ supporting information (SI) Table 2 ]. (pnas.org)
  • genomics
  • Value of the organism as a tool for studies of fungal diversity and comparative genomics. (broadinstitute.org)
  • Scientists will, therefore, need to embrace genomics, as well as develop and nurture the human capacity to sequence genomes and utilise the 'tsunami' of data that emerge from genome sequencing. (scielo.org.za)
  • The ultimate goals of the project are to produce a well-resolved phylogeny of the basal branches of the fungal kingdom, to identify key evolutionary events associated with diversification and reproduction, and to use genomics to predict ecological roles of uncultured lineages. (fungalgenomes.org)
  • A Genome-Wide Functional Genomics Approach Identifies Susceptibility Pathways to Fungal Bloodstream Infection in Humans. (nih.gov)
  • Joint Genome In
  • This work will involve collaborations with the ZyGOLife research network ( zygolife.org ) and the Joint Genome Institute (JGI). (fungalgenomes.org)
  • The project was funded by the Joint Genome Institute (JGI) at the Department of Energy (DOE) in the US. (lu.se)
  • New Software Tools Streamline DNA Sequence Design-and-Build Process Researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI) have developed a suite of build-optimization software tools (BOOST) to streamline the design-build transition in synthetic biology engineering workflows. (doe.gov)
  • taxa
  • Repeat-induced point mutation (RIP) occurs in some fungal taxa, preferentially mutating C:G nucleotide pairs that reside within repetitive DNA and converting them to T:A. Within the taxon Pezizomycotina, RIP is biased towards mutation of CpA dinucleotides. (edu.au)
  • In most fungal taxa, AT-rich regions are a signature of repeat-induced point mutation (RIP), which targets repetitive DNA and decreases GC-content though the conversion of cytosine to thymine bases. (edu.au)
  • virus genomes
  • Hidden Giants in Forest Soils In Nature Communications, giant virus genomes have been discovered for the first time in a forest soil ecosystem by JGI and University of Massachusetts-Amherst researchers. (doe.gov)
  • A detailed analysis of the KilA-N and Bro-N domains and the associated domains points to extensive domain shuffling and lineage-specific gene family expansion within DNA virus genomes. (biomedcentral.com)
  • several genomes
  • Over the last five years, several genomes of basidiomycetes have been published, including Cryptococcus neoformans , Ustilago maydis , Phanerochaete chrysosporium , Malassezia globosa , and Postia placenta . (inra.fr)
  • It has been a busy Fall term and there were several genomes that were completed but slipped through our announcements. (fungalgenomes.org)
  • virulence
  • We also located genome structural variations, including aneuploidies and large fragment CNVs, in regions that are functionally related to virulence. (nih.gov)
  • Ascomycete
  • Of course, increased genome and taxon sampling may alter the model presented, but clearly the rise of phytopathogenesis has involved multiple phenotype acquisitions and a complex evolutionary history, suggesting that even within relatively closely related ascomycete groups, pathogenic and saprotrophic organisms are likely to have many key differences. (plantcell.org)
  • Sequencing
  • In November 2000, Dr. Gerry Fink invited a small group of fungal geneticists and biologists to discuss ways to accelerate the slow pace of fungal genome sequencing. (broadinstitute.org)
  • Participants included academic and industrial fungal scientists as well as those with experience in genome sequencing and analysis. (broadinstitute.org)
  • In February 2002, the first White paper developed by the Fungal Genome Initiative organization was submitted to the National Human Genome Research Institute to be reviewed to determine priority for genome sequencing. (broadinstitute.org)
  • Please visit our Status page to check on the sequencing progress regarding on-going fungal sequencing projects at the Broad Institute. (broadinstitute.org)
  • A major component of the work will be to develop or improve methods for sequencing genomes and transcriptomes using single or few cells or genome assembly using metagenomic approaches. (fungalgenomes.org)
  • In all, 82 fungal genomes covering 5 phyla were obtained from the relevant genome sequencing centers. (biomedcentral.com)
  • comparative
  • Comparative analysis of fungal and oomycete CYPomes revealed cases of both extreme expansion and contraction. (biomedcentral.com)
  • Further, we report a comparative survey of the genome and secretory proteome of Malassezia restricta , a close relative implicated in similar skin disorders. (pnas.org)
  • gene prediction
  • As these methods do not require sets of homologous proteins, improving gene prediction from these resources is of benefit to fungal researchers. (edu.au)
  • Conclusions: We demonstrate the success of a novel method of incorporating RNA-seq data into GHMM fungal gene prediction. (edu.au)
  • mycology
  • I am also digesting the science from the talks and social interactions with a variety of people enthusiastic about mycology, genomes, and evolution (which could be a conference unto itsself). (fungalgenomes.org)
  • geneticists
  • We'll try and blog a bit about the interesting talks and data. I'm curious how many fungal geneticists are in fact reading blogs like these and if this medium will work for idea dissemination. (fungalgenomes.org)
  • Proteins
  • Cytochrome P450 proteins (CYPs) play diverse and pivotal roles in fungal metabolism and adaptation to specific ecological niches. (biomedcentral.com)
  • Computational analysis of viral DNA-binding regulatory proteins and identification of their previously undetected homologs encoded by cellular genomes might lead to a better understanding of their function and evolution in both viral and cellular systems. (biomedcentral.com)
  • pipelines
  • The software tool RIPCAL was developed for this purpose and since its release has become widely used in fungal genome analysis pipelines. (edu.au)
  • Laccaria
  • In contrast, the number of published genomes from basidiomycetous mushrooms was scarce and limited to the ectomycorrhizal Laccaria bicolor . (inra.fr)
  • phytopathogens
  • Fungal phytopathogens interact with their hosts largely via the secretion of effectors, which manipulate and elicit plant defences. (edu.au)
  • Pathways
  • Although these represent a wide array of mechanisms, it is likely that the full range of anti-fungal resistance pathways is even greater, for several reasons. (biomedcentral.com)
  • Methods
  • These alignment-based methods (to be called the standard methods hereafter) need independent verification in order to put the fungal Tree of Life (TOL) on a secure footing. (biomedcentral.com)
  • The ever-increasing number of sequenced fungal genomes and the recent success of our newly proposed alignment-free composition vector tree (CVTree, see Methods) approach have made the verification feasible. (biomedcentral.com)