L. edodes transcriptome
Transcriptome Analysis of Candidate Genes and Signaling Pathways Associated with Light-induced Brown Film Formation in Lentinula edodes
Background: Light-induced brown film (BF) formation by vegetative mycelium of the edible mushroom, Lentinula edodes, precedes primordia formation and subsequent sporophore morphogenesis, and is a determinant of mushroom yield and quality. Since the underlying molecular mechanisms are unclear, we have used RNA-seq for transcriptome profiling of BF formation in order to gain insight into the role of this process in fruit body development.    Results: Fungal mycelium was grown under three different conditions: 30 d darkness (sample 118), 80 d darkness (313W), and 30 d darkness followed by 50 d in the light (313C). BF formation was recorded with 313C samples only. Using high-throughput Illumina RNA-seq, the transcriptome of poly (A)+ RNA from mycelium grown under the three conditions was analyzed by deep sequencing. Approximately 159.23 million reads were obtained, trimmed, and de novo assembled into 31,511 unigenes with an average length of 1,746 bp and an N50 of 2,480 bp. Based on sequence orientations determined by a BLASTx search against the Nr, SwissProt, COG and KEGG databases, 24,246 (76.94%) unigenes were assigned putative gene descriptions. Comparative analysis of 313C and 118 expression profiles, and 313C and 313W expression profiles, revealed 3958 and 5651 significantly differentially expressed unigenes, respectively. Annotation of these sequences using the COG database revealed that candidate genes for light-induced BF formation encoded proteins linked to light reception (e.g. WC-1, WC-2, phytochrome), light signaling transduction pathways (e.g. two-component phosphorelay system, MAPK) and pigment formation (e.g. polyketide synthase, O-methyltransferase, laccase, P450-monooxygenase, oxidoreductase). Several differentially expressed unigenes were validated and analyzed using quantitative real time PCR (qRT-PCR).    Conclusion: Our data provides the first comparative transcriptomic analysis identifying differential unigenes associated with light-induced BF formation in L. edodes. The transcriptome dataset represents a valuable genomic resource for future studies on the molecular mechanisms underlying sporophore development in this commercially important mushroom.