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Transcriptome analysis and its application in identifying genes associated with fruiting body development in basidiomycete Hypsizygus marmoreus.

Zhang J, Ren A, Chen H, Zhao M, Shi L, Chen M, Wang H, Feng Z - PLoS ONE (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.


Related in: MedlinePlus

KEGG annotation of DGEs.The heat map shows 38 annotated pathways of DGEs in the mycelial knot (H-M), mycelial pigmentation (H-V), primordium (H-P) and fruiting body (H-F) stages of H. marmoreus. Different colors represent different expression levels. Green represents down-regulated expression and red represents up-regulated expression. Each row represents a different pathway. The heat map was constructed based on the log10 values of the RPKM of all unigenes related to a particular pathway in the four developmental stages.
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pone.0123025.g005: KEGG annotation of DGEs.The heat map shows 38 annotated pathways of DGEs in the mycelial knot (H-M), mycelial pigmentation (H-V), primordium (H-P) and fruiting body (H-F) stages of H. marmoreus. Different colors represent different expression levels. Green represents down-regulated expression and red represents up-regulated expression. Each row represents a different pathway. The heat map was constructed based on the log10 values of the RPKM of all unigenes related to a particular pathway in the four developmental stages.

Mentions: To study the function of differential expression genes (DEGs), functional annotation was adopted for these identified genes. The metabolic and regulatory pathways related to the DEGs were analyzed and the heatmap analysis was performed based on the total FPKM values of all the DEGs in each pathway (Fig 5). Among these pathways, most were up-regulated in the H-P and H-F stages. These pathways included “Ribosome”, “Nitrogen metabolism”, “Ca2+ signaling pathway”, “MAPK signaling pathway”, “N−Glycan biosynthesis”, “Ubiquitin mediated proteolysis” and “Amino sugar and nucleotide sugar metabolism”. Only the “Phenylalanine, Tyrosine and tryptophan biosynthesis” pathway was active in H-M, and the “Melanogenesis”, “Glycerolipid metabolism”, “Glutathione metabolism” and “Histidine metabolism” pathways were up-regulated in H-V.


Transcriptome analysis and its application in identifying genes associated with fruiting body development in basidiomycete Hypsizygus marmoreus.

Zhang J, Ren A, Chen H, Zhao M, Shi L, Chen M, Wang H, Feng Z - PLoS ONE (2015)

KEGG annotation of DGEs.The heat map shows 38 annotated pathways of DGEs in the mycelial knot (H-M), mycelial pigmentation (H-V), primordium (H-P) and fruiting body (H-F) stages of H. marmoreus. Different colors represent different expression levels. Green represents down-regulated expression and red represents up-regulated expression. Each row represents a different pathway. The heat map was constructed based on the log10 values of the RPKM of all unigenes related to a particular pathway in the four developmental stages.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383556&req=5

pone.0123025.g005: KEGG annotation of DGEs.The heat map shows 38 annotated pathways of DGEs in the mycelial knot (H-M), mycelial pigmentation (H-V), primordium (H-P) and fruiting body (H-F) stages of H. marmoreus. Different colors represent different expression levels. Green represents down-regulated expression and red represents up-regulated expression. Each row represents a different pathway. The heat map was constructed based on the log10 values of the RPKM of all unigenes related to a particular pathway in the four developmental stages.
Mentions: To study the function of differential expression genes (DEGs), functional annotation was adopted for these identified genes. The metabolic and regulatory pathways related to the DEGs were analyzed and the heatmap analysis was performed based on the total FPKM values of all the DEGs in each pathway (Fig 5). Among these pathways, most were up-regulated in the H-P and H-F stages. These pathways included “Ribosome”, “Nitrogen metabolism”, “Ca2+ signaling pathway”, “MAPK signaling pathway”, “N−Glycan biosynthesis”, “Ubiquitin mediated proteolysis” and “Amino sugar and nucleotide sugar metabolism”. Only the “Phenylalanine, Tyrosine and tryptophan biosynthesis” pathway was active in H-M, and the “Melanogenesis”, “Glycerolipid metabolism”, “Glutathione metabolism” and “Histidine metabolism” pathways were up-regulated in H-V.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.


Related in: MedlinePlus