Generation and analysis of expressed sequence tags from a cDNA library of the fruiting body of Ganoderma lucidum

Hongmei Luo,Jin Lan,Xiwen Li,Chao Sun,Ying Li,Shilin Chen,Jingyuan Song

doi:10.1186/1749-8546-5-9

Abstract

BackgroundLittle genomic or trancriptomic information on Ganoderma lucidum (Lingzhi) is known. This study aims to discover the transcripts involved in secondary metabolite biosynthesis and developmental regulation of G. lucidum using an expressed sequence tag (EST) library.MethodsA cDNA library was constructed from the G. lucidum fruiting body. Its high-quality ESTs were assembled into unique sequences with contigs and singletons. The unique sequences were annotated according to sequence similarities to genes or proteins available in public databases. The detection of simple sequence repeats (SSRs) was preformed by online analysis.ResultsA total of 1,023 clones were randomly selected from the G. lucidum library and sequenced, yielding 879 high-quality ESTs. These ESTs showed similarities to a diverse range of genes. The sequences encoding squalene epoxidase (SE) and farnesyl-diphosphate synthase (FPS) were identified in this EST collection. Several candidate genes, such as hydrophobin, MOB2, profilin and PHO84 were detected for the first time in G. lucidum. Thirteen (13) potential SSR-motif microsatellite loci were also identified.ConclusionThe present study demonstrates a successful application of EST analysis in the discovery of transcripts involved in the secondary metabolite biosynthesis and the developmental regulation of G. lucidum.

Highlights

Little genomic or trancriptomic information on Ganoderma lucidum (Lingzhi) is known
Genes involved in the triterpenoids biosynthesis pathways in G. lucidum including squalene synthase (SQS), farnesyl-Diphosphate Synthase (GlFPS) and HMG-CoA
RNA extraction and complementary DNA (cDNA) library construction The fruiting body of G. lucidum was obtained from the co-author Jin Lan, who has long been engaged in Ganoderma research in the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China

Summary

Introduction

Little genomic or trancriptomic information on Ganoderma lucidum (Lingzhi) is known. This study aims to discover the transcripts involved in secondary metabolite biosynthesis and developmental regulation of G. lucidum using an expressed sequence tag (EST) library. Lingzhi in Chinese, which belongs to the Polyporaceae family, has been used in China as medicine for centuries to promote health and longevity [1,2]. G. lucidum is an anti-tumour agent that acts via immune modulation or stimulating cytokine production [5,6,7]. The bioactive constituents of G. lucidum include more than 120 different triterpenes and polysaccharides, proteins and other compounds [2,8]. Genes involved in the triterpenoids biosynthesis pathways in G. lucidum including squalene synthase (SQS), farnesyl-Diphosphate Synthase (GlFPS) and HMG-CoA

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