Abstract
BackgroundPlant cell wall-degrading enzymes (PCWDEs) play significant roles throughout the fungal life including acquisition of nutrients and decomposition of plant cell walls. In addition, many of PCWDEs are also utilized by biofuel and pulp industries. In order to develop a comparative genomics platform focused in fungal PCWDEs and provide a resource for evolutionary studies, Fungal PCWDE Database (FPDB) is constructed (http://pcwde.riceblast.snu.ac.kr/).ResultsIn order to archive fungal PCWDEs, 22 sequence profiles were constructed and searched on 328 genomes of fungi, Oomycetes, plants and animals. A total of 6,682 putative genes encoding PCWDEs were predicted, showing differential distribution by their life styles, host ranges and taxonomy. Genes known to be involved in fungal pathogenicity, including polygalacturonase (PG) and pectin lyase, were enriched in plant pathogens. Furthermore, crop pathogens had more PCWDEs than those of rot fungi, implying that the PCWDEs analysed in this study are more needed for invading plant hosts than wood-decaying processes. Evolutionary analysis of PGs in 34 selected genomes revealed that gene duplication and loss events were mainly driven by taxonomic divergence and partly contributed by those events in species-level, especially in plant pathogens.ConclusionsThe FPDB would provide a fungi-specialized genomics platform, a resource for evolutionary studies of PCWDE gene families and extended analysis option by implementing Favorite, which is a data exchange and analysis hub built in Comparative Fungal Genomics Platform (CFGP 2.0; http://cfgp.snu.ac.kr/).
Highlights
Plant cell wall-degrading enzymes (PCWDEs) play significant roles throughout the fungal life including acquisition of nutrients and decomposition of plant cell walls
The sensitivity and specificity reached to 95.31% and 98.55%, respectively. These results indicate that our pipeline accurately captures fungal signatures of PCWDEs, and has a good discrimination power against the protein sequences from closely related enzymes to the PCWDEs
The Fungal PCWDE Database (FPDB) is developed to take the advantages of a number of fully sequenced fungal genomes and to provide fungicentric platform for studying PCWDEs
Summary
Plant cell wall-degrading enzymes (PCWDEs) play significant roles throughout the fungal life including acquisition of nutrients and decomposition of plant cell walls. In order to develop a comparative genomics platform focused in fungal PCWDEs and provide a resource for evolutionary studies, Fungal PCWDE Database (FPDB) is constructed (http://pcwde.riceblast.snu.ac.kr/). Besides the phytopathological impact mentioned above, PCWDEs have attained a lot of attention for their potential applications in pulp and biofuel industries, to find and develop the most economic and efficient combinations of enzymes to yield fermentable saccharides from plant biomass [4]. Carbohydrate-Active Enzymes (CAZY) database archives a wide spectrum of glycosyl hydrolases [8], it is not focused on fungi and not all of them are PCWDEs. In order to understand fungal PCWDEs in kingdom level, we developed a new web-based platform, Fungal PCWDE Database (FPDB; http://pcwde.riceblast.snu.ac.kr/), to identify and classify genes encoding PCWDEs from fungal genomes (Figure 1)
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