Project information

Ganoderma lucidum, also called Lingchi, Lingzhi, and Reishi by people in East Asia, have been worshipped as a magic medicinal mushroom for thousands of years. Its therapeutic potential has been gradually recognized as numerous pieces of biochemical evidence both in vivo and in vitro have accumulated in recent years. So far, ~400 bioactive compounds have been discovered in G. lucidum, including various triterpenoids, polysaccharides, peptides, etc. These compounds have been shown to possess potent pharmacological effects like immunomodulation in mice and cytotoxicity against tumor cells.

Aside from its medicinal values, G. lucidum is appealing to biologists due to its unique features that could be of ecological and economical values. G. lucidum is a wood-rotting mushroom, potentially playing a role in nutrient cycling. G. lucidum is one of the few fungal species that can be induced to form fruiting bodies from mycelia in vitro. G. lucidum is a multi-cellular fungal species that has different mating types and shows a complex life cycle.

To facilitate a systematic investigation of the biological pathways in G. lucidum, the consortium of G. lucidum has sequenced the genome of a G. lucidum strain BCRC 37177, and generated the first version of assembled contigs. This expressed sequence tag (EST) project is a companion project of the G. lucidum genome project, aiming to provide experimental evidence to the gene build. To date, ~48,000 ESTs have been analyzed. In particular, ~480 genes that could not be predicted by ab initio gene finders, ~260 genes with alternative splice forms, and ~100 pairs of anti-sense transcripts were found.

This web site is dedicated to presenting the results and providing browse and search interfaces to assist users to look for interesting features of in the G. lucidum transcriptome.

Materials

>> Strain

Two strains of G. lucidum have so far been used in this EST project (2010/11/01):

The mycelia of BCRC 36123 were cultured at 30 degree Celsius for 5, 14, 18, 30 days, respectively. As a comparison, the mycelia of the monokaryotic strain, BCRC 37180, was cultured under a similar condition for 18 days. The number of ESTs collected for mycelia cultured for different days were listed as follows:

EST library1# filtered EST
5D_36123 (dikaryon)1,001
14D_36123 (dikaryon)6,848
18D_36123 (dikaryon)21,547
18D_37180 (monokaryon)11,059
30D_36123 (dikaryon)6,830
Total47,285

Table 1. GL cDNA libraries and ESTs

1: D refers to days of culture, and the number suffixed to each library name refers to a BCRC strain.

>> Library information

See here.

Sequencing

Complementary DNA (cDNA) libraries of G. lucidum were prepared by using the library construction kit offered by Stratagen (USA). These libraries were sequenced using the Dye terminator chemistry and capillary electrophoresis analysis (Applied Biosystems 3730xl DNA analyzer and GE Healthcare MegaBAC 1000).

Data processing and annotation

>> Data processing

53,323 chromatograms were initially generated from the DNA analyzer. These chromatograms were base-called into raw expressed sequence tags (ESTs) using Phred. Then a three-step filtering process was applied:

After discarding processed ESTs shorter than 50 bases in length, we have collected 47,285 ESTs (corresponding libraries listed in Table 1).

>> EST-based transcript and gene build

To acquire non-redundant transcript and gene information from these ESTs, we took the following steps:

This Ensembl pipeline implemented a cluster-and-merge algorithm as described in (1), taking advantage of consensus splicing junction patterns to cluster ESTs that may be derived a mRNA splice form and merge them into a non-redundant EST-based transcript. Each set of overlapped EST-based transcripts was further grouped into an EST-based gene if they are mapped to the same strand of a genomic locus. See also Section 13.12 on the Ensembl webcvs repository.

>> Annotation

Statistics

>> EST processing and genome mapping

>> EST-based transcripts and genes

>> EST-based and predicted genes

  • 109 predicted genes that were supported by >50 ESTs [See here]
  • 44 predicted genes that were supported by more age-specific ESTs [See here]
  • Reference

    1. Eyras, E., Caccamo, M., Curwen, V. and Clamp, M. (2004) ESTGenes: alternative splicing from ESTs in Ensembl. Genome Res, 14, 976-987.