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This article is part of the supplement: Twelfth International Conference on Bioinformatics (InCoB2013): Computational Biology

Open Access Research

Fungal plant cell wall-degrading enzyme database: a platform for comparative and evolutionary genomics in fungi and Oomycetes

Jaeyoung Choi12, Ki-Tae Kim12, Jongbum Jeon12 and Yong-Hwan Lee123456*

Author Affiliations

1 Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea

2 Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea

3 Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Korea

4 Center for Fungal Genetic Resource, Seoul National University, Seoul 151-921, Korea

5 Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea

6 Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea

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BMC Genomics 2013, 14(Suppl 5):S7  doi:10.1186/1471-2164-14-S5-S7

Published: 16 October 2013

Abstract

Background

Plant 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/ webcite).

Results

In 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.

Conclusions

The 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/ webcite).