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真菌植物细胞壁降解酶数据库：真菌和卵菌比较与进化基因组学的平台。

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

作者信息

Choi Jaeyoung, Kim Ki-Tae, Jeon Jongbum, Lee Yong-Hwan

出版信息

BMC Genomics. 2013;14 Suppl 5(Suppl 5):S7. doi: 10.1186/1471-2164-14-S5-S7. Epub 2013 Oct 16.

DOI:10.1186/1471-2164-14-S5-S7
PMID:24564786
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3852112/
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/).

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/).

摘要

背景

植物细胞壁降解酶（PCWDEs）在真菌的整个生命过程中发挥着重要作用，包括获取营养和分解植物细胞壁。此外，许多植物细胞壁降解酶也被生物燃料和纸浆工业所利用。为了开发一个专注于真菌植物细胞壁降解酶的比较基因组学平台，并为进化研究提供资源，构建了真菌植物细胞壁降解酶数据库（FPDB，网址：http://pcwde.riceblast.snu.ac.kr/）。

结果

为了存档真菌植物细胞壁降解酶，构建了22个序列图谱，并在328个真菌、卵菌、植物和动物的基因组上进行搜索。共预测出6682个编码植物细胞壁降解酶的推定基因，这些基因根据其生活方式、宿主范围和分类学表现出不同的分布。已知参与真菌致病性的基因，包括多聚半乳糖醛酸酶（PG）和果胶裂解酶，在植物病原体中富集。此外，作物病原体比腐生真菌拥有更多的植物细胞壁降解酶，这意味着本研究中分析的植物细胞壁降解酶对于侵入植物宿主比木材腐朽过程更为必需。对34个选定基因组中的多聚半乳糖醛酸酶进行的进化分析表明，基因复制和丢失事件主要由分类学差异驱动，部分由物种水平的事件导致，特别是在植物病原体中。

结论

FPDB将提供一个真菌专用的基因组学平台，一个用于植物细胞壁降解酶基因家族进化研究的资源，并通过实施“收藏夹”提供扩展分析选项，“收藏夹”是比较真菌基因组学平台（CFGP 2.0；网址：http://cfgp.snu.ac.kr/）中内置的数据交换和分析中心。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cce2/3852112/b5ee9989dea6/1471-2164-14-S5-S7-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cce2/3852112/b92771f1f3f6/1471-2164-14-S5-S7-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cce2/3852112/33b45ba530c3/1471-2164-14-S5-S7-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cce2/3852112/93a3cf2376c9/1471-2164-14-S5-S7-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cce2/3852112/b5ee9989dea6/1471-2164-14-S5-S7-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cce2/3852112/b92771f1f3f6/1471-2164-14-S5-S7-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cce2/3852112/33b45ba530c3/1471-2164-14-S5-S7-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cce2/3852112/93a3cf2376c9/1471-2164-14-S5-S7-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cce2/3852112/b5ee9989dea6/1471-2164-14-S5-S7-4.jpg

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