title: Transcriptome analysis and its application in identifying genes associated with fruiting body development in basidiomycete Hypsizygus marmoreus.
abstract: To elucidate the mechanisms of fruit body development in H. marmoreus, a total of 43609521 high-quality RNA-seq reads were obtained from four developmental stages, including the mycelial knot (H-M), mycelial pigmentation (H-V), primordium (H-P) and fruiting body (H-F) stages. These reads were assembled to obtain 40568 unigenes with an average length of 1074 bp. A total of 26800 (66.06%) unigenes were annotated and analyzed with the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and Eukaryotic Orthologous Group (KOG) databases. Differentially expressed genes (DEGs) from the four transcriptomes were analyzed. The KEGG enrichment analysis revealed that the mycelium pigmentation stage was associated with the MAPK, cAMP, and blue light signal transduction pathways. In addition, expression of the two-component system members changed with the transition from H-M to H-V, suggesting that light affected the expression of genes related to fruit body initiation in H. marmoreus. During the transition from H-V to H-P, stress signals associated with MAPK, cAMP and ROS signals might be the most important inducers. Our data suggested that nitrogen starvation might be one of the most important factors in promoting fruit body maturation, and nitrogen metabolism and mTOR signaling pathway were associated with this process. In addition, 30 genes of interest were analyzed by quantitative real-time PCR to verify their expression profiles at the four developmental stages. This study advances our understanding of the molecular mechanism of fruiting body development in H. marmoreus by identifying a wealth of new genes that may play important roles in mushroom morphogenesis.
authors.affiliation: College of Life Science, Nanjing Agricultural University, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing, Jiangsu, China; National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People's Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China.
authors.forename: Jinjing
authors.initials: J
authors.lastname: Zhang
authors.affiliation: College of Life Science, Nanjing Agricultural University, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing, Jiangsu, China.
authors.forename: Ang
authors.initials: A
authors.lastname: Ren
authors.affiliation: National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People's Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Chen
authors.affiliation: College of Life Science, Nanjing Agricultural University, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing, Jiangsu, China.
authors.forename: Mingwen
authors.initials: M
authors.lastname: Zhao
authors.affiliation: College of Life Science, Nanjing Agricultural University, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing, Jiangsu, China.
authors.forename: Liang
authors.initials: L
authors.lastname: Shi
authors.affiliation: National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People's Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China.
authors.forename: Mingjie
authors.initials: M
authors.lastname: Chen
authors.affiliation: National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People's Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Wang
authors.affiliation: College of Life Science, Nanjing Agricultural University, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing, Jiangsu, China; National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People's Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Feng
mesh_terms: D000363:Agaricales / Q000235:genetics / Q000254:growth & development*; D001483:Base Sequence; D056931:Cryptochromes / Q000235:genetics / Q000378:metabolism; D000242:Cyclic AMP / Q000235:genetics / Q000378:metabolism; D004271:DNA, Fungal / Q000235:genetics; D048690:Fruiting Bodies, Fungal / Q000235:genetics / Q000254:growth & development*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D020928:Mitogen-Activated Protein Kinases / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D025282:Mycelium / Q000254:growth & development*; D009584:Nitrogen / Q000378:metabolism*; D010858:Pigmentation / Q000235:genetics; D017382:Reactive Oxygen Species / Q000378:metabolism; D017422:Sequence Analysis, DNA; D015398:Signal Transduction / Q000235:genetics*; D058570:TOR Serine-Threonine Kinases / Q000235:genetics / Q000378:metabolism
chemical_list: D056931:Cryptochromes; D004271:DNA, Fungal; D017382:Reactive Oxygen Species; D000242:Cyclic AMP; D058570:TOR Serine-Threonine Kinases; D020928:Mitogen-Activated Protein Kinases; D009584:Nitrogen
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