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Dimitrios Floudas,
Manfred Binder, Robert Riley,
Kerrie Barry,
Robert A Blanchette,
Bernard Henrissat,
Angel T Martínez,
Robert Otillar,
Joseph W Spatafora,
Jagjit S Yadav, [......],
Khajamohiddin Syed,
Adrian Tsang,
Ad Wiebenga,
Darcy Young,
Antonio Pisabarro,
Daniel C Eastwood,
Francis Martin,
Dan Cullen,
Igor V Grigoriev,
David S Hibbett
[show abstract]
[hide abstract]
ABSTRACT: Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non-lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.
Science 06/2012; 336(6089):1715-9. · 31.20 Impact Factor
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Dimitrios Floudas,
Manfred Binder, Robert Riley,
Kerrie Barry,
Robert A. Blanchette,
Bernard Henrissat,
Angel T. Martínez,
Robert Otillar,
Joseph W. Spatafora,
Jagjit S. Yadav, [......],
Khajamohiddin Syed,
Adrian Tsang,
Ad Wiebenga,
Darcy Young,
Antonio Pisabarro,
Daniel C. Eastwood,
Francis Martin,
Dan Cullen,
Igor V. Grigoriev,
David S. Hibbett
[show abstract]
[hide abstract]
ABSTRACT: Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the
presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in
the Agaricomycetes, which also contains non–lignin-degrading brown rot and ectomycorrhizal
species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest
that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the
Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel
lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that
the origin of lignin degradation might have coincided with the sharp decrease in the rate of
organic carbon burial around the end of the Carboniferous period.
Science 06/2012; 336(10.1126/science.1221748):1715-1719. · 31.20 Impact Factor
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Mahajabeen Padamsee,
T K Arun Kumar, Robert Riley,
Manfred Binder,
Alex Boyd,
Ana M Calvo,
Kentaro Furukawa,
Cedar Hesse,
Stefan Hohmann,
Tim Y James, [......],
Alla Lapidus,
Erika Lindquist,
Susan Lucas,
Kari Miller,
Sourabha Shantappa,
Igor V Grigoriev,
David S Hibbett,
David J McLaughlin,
Joseph W Spatafora,
M Catherine Aime
[show abstract]
[hide abstract]
ABSTRACT: Wallemia (Wallemiales, Wallemiomycetes) is a genus of xerophilic Fungi of uncertain phylogenetic position within Basidiomycota. Most commonly found as food contaminants, species of Wallemia have also been isolated from hypersaline environments. The ability to tolerate environments with reduced water activity is rare in Basidiomycota. We sequenced the genome of W. sebi in order to understand its adaptations for surviving in osmotically challenging environments, and we performed phylogenomic and ultrastructural analyses to address its systematic placement and reproductive biology. W. sebi has a compact genome (9.8 Mb), with few repeats and the largest fraction of genes with functional domains compared with other Basidiomycota. We applied several approaches to searching for osmotic stress-related proteins. In silico analyses identified 93 putative osmotic stress proteins; homology searches showed the HOG (High Osmolarity Glycerol) pathway to be mostly conserved. Despite the seemingly reduced genome, several gene family expansions and a high number of transporters (549) were found that also provide clues to the ability of W. sebi to colonize harsh environments. Phylogenetic analyses of a 71-protein dataset support the position of Wallemia as the earliest diverging lineage of Agaricomycotina, which is confirmed by septal pore ultrastructure that shows the septal pore apparatus as a variant of the Tremella-type. Mating type gene homologs were identified although we found no evidence of meiosis during conidiogenesis, suggesting there may be aspects of the life cycle of W. sebi that remain cryptic.
Fungal Genetics and Biology 03/2012; 49(3):217-26. · 3.74 Impact Factor
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Igor V Grigoriev,
Henrik Nordberg,
Igor Shabalov,
Andrea Aerts,
Mike Cantor,
David Goodstein,
Alan Kuo,
Simon Minovitsky,
Roman Nikitin,
Robin A Ohm,
Robert Otillar,
Alex Poliakov,
Igor Ratnere, Robert Riley,
Tatyana Smirnova,
Daniel Rokhsar,
Inna Dubchak
[show abstract]
[hide abstract]
ABSTRACT: The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. The JGI Genome Portal (http://genome.jgi.doe.gov) provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. We describe here the general organization of the Genome Portal and the most recent addition, MycoCosm (http://jgi.doe.gov/fungi), a new integrated fungal genomics resource.
Nucleic Acids Research 11/2011; 40(Database issue):D26-32. · 8.03 Impact Factor
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Daniel C Eastwood,
Dimitrios Floudas,
Manfred Binder,
Andrzej Majcherczyk,
Patrick Schneider,
Andrea Aerts,
Fred O Asiegbu,
Scott E Baker,
Kerrie Barry,
Mika Bendiksby, [......],
Jan Stenlid,
Ad Wiebenga,
Xinfeng Xie,
Ursula Kües,
David S Hibbett,
Dirk Hoffmeister,
Nils Högberg,
Francis Martin,
Igor V Grigoriev,
Sarah C Watkinson
[show abstract]
[hide abstract]
ABSTRACT: Brown rot decay removes cellulose and hemicellulose from wood--residual lignin contributing up to 30% of forest soil carbon--and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the "dry rot" fungus Serpula lacrymans, derived from forest ancestors, demonstrated that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, suggesting adaptation to an intercellular interaction with plant tissue. Transcriptome and proteome analysis also identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta. Furthermore, fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota.
Science 08/2011; 333(6043):762-5. · 31.20 Impact Factor
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Christopher E Ellison,
Jason E Stajich,
David J Jacobson,
Donald O Natvig,
Alla Lapidus,
Brian Foster,
Andrea Aerts, Robert Riley,
Erika A Lindquist,
Igor V Grigoriev,
John W Taylor
[show abstract]
[hide abstract]
ABSTRACT: A large region of suppressed recombination surrounds the sex-determining locus of the self-fertile fungus Neurospora tetrasperma. This region encompasses nearly one-fifth of the N. tetrasperma genome and suppression of recombination is necessary for self-fertility. The similarity of the N. tetrasperma mating chromosome to plant and animal sex chromosomes and its recent origin (<5 MYA), combined with a long history of genetic and cytological research, make this fungus an ideal model for studying the evolutionary consequences of suppressed recombination. Here we compare genome sequences from two N. tetrasperma strains of opposite mating type to determine whether structural rearrangements are associated with the nonrecombining region and to examine the effect of suppressed recombination for the evolution of the genes within it. We find a series of three inversions encompassing the majority of the region of suppressed recombination and provide evidence for two different types of rearrangement mechanisms: the recently proposed mechanism of inversion via staggered single-strand breaks as well as ectopic recombination between transposable elements. In addition, we show that the N. tetrasperma mat a mating-type region appears to be accumulating deleterious substitutions at a faster rate than the other mating type (mat A) and thus may be in the early stages of degeneration.
Genetics 07/2011; 189(1):55-69. · 4.01 Impact Factor
