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

被引：48
作者：
Choi, Jaeyoung [1 ,2 ]
Kim, Ki-Tae [1 ,2 ]
Jeon, Jongbum [1 ,2 ]
Lee, Yong-Hwan [1 ,2 ,3 ,4 ,5 ,6 ]
机构：
[1] Seoul Natl Univ, Fungal Bioinformat Lab, Seoul 151921, South Korea
[2] Seoul Natl Univ, Dept Agr Biotechnol, Seoul 151921, South Korea
[3] Seoul Natl Univ, Ctr Fungal Pathogenesis, Seoul 151921, South Korea
[4] Seoul Natl Univ, Ctr Fungal Genet Resource, Seoul 151921, South Korea
[5] Seoul Natl Univ, Plant Genom & Breeding Inst, Seoul 151921, South Korea
[6] Seoul Natl Univ, Res Inst Agr & Life Sci, Seoul 151921, South Korea
来源：
BMC GENOMICS | 2013年 / 14卷
基金：
新加坡国家研究基金会;
关键词：
MAGNAPORTHE-GRISEA; GENE; ENDOPOLYGALACTURONASE; IDENTIFICATION; POLYGALACTURONASE; PATHOGENICITY; VIRULENCE; SECRETOME; ORYZAE;
D O I：
10.1186/1471-2164-14-S5-S7
中图分类号：
Q81 [生物工程学（生物技术）]; Q93 [微生物学];
学科分类号：
071005 ; 0836 ; 090102 ; 100705 ;
摘要：
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/). 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/).
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