Erratum to: Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi
Open Access
- 3 January 2014
- journal article
- research article
- Published by Springer Science and Business Media LLC in BMC Genomics
- Vol. 15 (1), 6
- https://doi.org/10.1186/1471-2164-15-6
Abstract
The version of this article published in BMC Genomics 2013, 14: 274, contains 9 unpublished genomes (Botryobasidium botryosum, Gymnopus luxurians, Hypholoma sublateritium, Jaapia argillacea, Hebeloma cylindrosporum, Conidiobolus coronatus, Laccaria amethystina, Paxillus involutus, and P. rubicundulus) downloaded from JGI website. In this correction, we removed these genomes after discussion with editors and data producers whom we should have contacted before downloading these genomes. Removing these data did not alter the principle results and conclusions of our original work. The relevant Figures 1, 2, 3, 4 and 6; and Table 1 have been revised. Additional files 1, 3, 4, and 5 were also revised. We would like to apologize for any confusion or inconvenience this may have caused. Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 94 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also revealed a complex history of lineage-specific expansions and attritions for the PL1 family. Conclusions Our study provides insights into the variety and expansion of fungal CAZyme classes and revealed the relationship of CAZyme size and diversity with their nutritional strategy and host specificity.Keywords
This publication has 55 references indexed in Scilit:
- Cellulases Dig DeepPublished by Elsevier BV ,2012
- Fungal enzyme sets for plant polysaccharide degradationApplied Microbiology and Biotechnology, 2011
- Curation of characterized glycoside hydrolases of Fungal originDatabase: The Journal of Biological Databases and Curation, 2011
- Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassaProceedings of the National Academy of Sciences of the United States of America, 2009
- Crystal Structure of Glycoside Hydrolase Family 55 β-1,3-Glucanase from the Basidiomycete Phanerochaete chrysosporiumPublished by Elsevier BV ,2009
- The Carbohydrate-Active EnZymes database (CAZy): an expert resource for GlycogenomicsNucleic Acids Research, 2008
- Unique aspects of the grass cell wallCurrent Opinion in Plant Biology, 2008
- Aspergillus niger genome-wide analysis reveals a large number of novel alpha-glucan acting enzymes with unexpected expression profilesMolecular Genetics and Genomics, 2008
- ProtTest: selection of best-fit models of protein evolutionBioinformatics, 2005
- Pectin-degrading enzymes and plant-parasite interactionsEuropean Journal of Plant Pathology, 1995