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Introduction

Ganoderm lucidum (ChiZhi) is one of the most well-known medical macrofungi. Several whole genome-sequencing projects have been simultaneously completed recently to understand its genetic makeup. A database is needed urgently so that users can mine the wealth of genomic, genetic, and chemical information generated from these projects.

To provide a central repository for storing, querying, browsing, and retrieving of genomic, genetic, and chemical information on G. lucidum, we constructed the G. lucidum Database (GaLuDB). This database’s contents include genome assembly, 16,113 gene models and their corresponding gene function annotations, and transcriptomic data from three different developmental stages, namely, mycelia, primordial, and fruiting bodies. It also presents 24 predicted gene clusters and 156 chemical compounds identified in G. lucidum. This information can be used to further define biosynthesis pathways leading to the production of various chemical compounds in G. lucidum. In addition to providing a portal for querying and retrieving these data, it also provides three categories of utilities, namely, Gbrowse, Tools, and Wiki pages. Gbrowse allows users to navigate the genome to view the structure, the annotation, and the expression levels of particular genes. Tools can be divided into four sub-categories, namely, (1) database searching based on sequence similarity; (2) retrieval of annotations and sequences of a list of genes and IDs of genes around a particular gene of interest; (3) curation of gene models; and (4) identification of gene clusters enriched with genes belonging to particular functional groups and the mapping of genes to chromosomes. Finally, a wiki has been set up for members of the G. lucidum research community to share and exchange information.

In summary, the recent completion of whole genome-sequencing projects makes G. lucidum a potential model system for studying the biosynthesis of secondary metabolites and their regulation. GaLuDB would be a valuable resource for the mining of genomic, genetic and chemical information for G. lucidum and would lay the foundation for the realization of G. lucidum’s pharmaceutical and industrial potentials.

For questions and comments, please send email to cliu@implad.ac.cn or yjzhu@implad.ac.cn.

Last Updated: Nov 2nd, 2014

Center for Bioinformatics
Institute of Medicinal Plant Development
PeKing Union Medical College
Chinese Academy of Medical Sciences
Address: No. 151, Malianwa North Road, Haidian District, Beijing 100193, P.R.China
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