Correction: Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

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The version of this article published in BMC Genomics 2013, 14: 274, contains 9 unpublished genomes (Botryobasidium botryosum, Gymnopus luxurians, Hypholoma sublateritium, Jaapia argillacea, Hebeloma cylindrosporum, Conidiobolus coronatus, Laccaria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.

Figure 1

Comparative analysis of fungal CAZymes. The numbers of CAZyme modules or domains were represented as horizontal bars. CBM, carbohydrate binding module; CE, carbohydrate esterase; GH, glycoside hydrolases; GT, glycosyltransferase; PL, polysaccharide lyase.

Figure 2

The distribution of each CAZyme family in 94 fungi. Blue bars showed the numbers of fungi that have the members of specific CAZyme family.

Figure 3

Different numbers of CAZymes between Ascomycetes and Basidiomycetes. (A) The number of CAZymes in each class and CBMs were plotted for Ascomycetes and Basidiomycetes. (B) The number of CAZymes in the families which were more abundant in Basidiomycetes than in Ascomycetes (t test, P < 0.01). (C) The number of CAZymes in the families which were more abundant in Ascomycetes than in Basidiomycetes (t test, P < 0.01). See Figure 1 for abbreviations.

Figure 4

Comparison of CAZymes in different plant pathogenic fungi. (A) The number of CAZymes in each class and CBMs were plotted for biotrophic (red), hemibiotrophic (black), and necrotrophic (green) pathogens. (B) The number of CAZymes in the families that showed significant differences among biotrophic, hemibiotrophic, and necrotrophic pathogens. Differentiation was support by the t test at the significant level with P < 0.01. See Figure 1 for abbreviations.

Figure 5

Comparison of CAZymes among fungi pathogenic to monocots and dicots. (A) The number of members in each CAZyme class and CBMs in the predicted proteomes were plotted for fungi that infect dicots (red dots) or monocots (black dots). (B) The number of CAZymes which showed obvious differentiation among fungi that infect dicots or monocots. Dicot pathogens have more pectinases from families GH28 (P < 0.01), GH88 (P < 0.01) and GH105 (P < 0.01) than fungi pathogenic to monocots. Although the significance of the comparison was not supported by the t test (P > 0.05), some dicot pathogens tend to have much more PL1 and PL3 enzymes than monocot pathogens. See Figure 1 for abbreviations.

Figure 6

Comparison of CAZymes between saprophytic fungi and plant pathogenic fungi. (A) The number of members in each CAZyme class and CBM in the predicted proteomes were plotted for plant pathogenic fungi (red dots) and saprophytic fungi (black dots). (B) The number of CAZymes which showed obvious differentiation supported by t test among plant pathogenic fungi and saprophytic fungi.

Figure 7

The maximum likelihood tree of family PL1. The phylogenetic tree was constructed with PhyML3.0 based on a multiple sequence alignment generated with PSI-Coffee [54]. The midpoint rooted base tree was drawn using Interactive Tree Of Life Version 2.1.1 (http://itol.embl.de/). The p-values of approximate likelihood ratios (SH-aLRT) plotted as circle marks on the branches (only p-values >0.5 are indicated) and circle size is proportional to the p-values. Scale bars correspond to 0.2 amino acid substitutions per site. A detailed version of this tree is found in Additional file 8.