Limits...
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

Differentially expressed genes (DEGs) between the four developmental stages in H. marmoreus.Each column represents an experimental sample (e.g., H-M, H-V, H-P and H-F), and each row represent a gene. Expression differences are shown in different colors. Red indicates high expression and green indicates low expression.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4383556&req=5

pone.0123025.g006: Differentially expressed genes (DEGs) between the four developmental stages in H. marmoreus.Each column represents an experimental sample (e.g., H-M, H-V, H-P and H-F), and each row represent a gene. Expression differences are shown in different colors. Red indicates high expression and green indicates low expression.

Mentions: Co-expression analysis, which is based on the premise that a set of genes involved in a biological process is co-expressed under given conditions, has been successfully used to identify novel genes in several studies [38]. To verify the correlation between the expression of differentially expressed genes (DEGs) and developmental stages, heatmap analysis was performed based on the FPKM values of 31 DEGs involved in metabolism, gene regulation, signal transduction and cell organization (Fig 6). The functional annotation for these unigenes are listed in S4 Table. As shown in Fig 6, genes involved in carbon metabolism, such as the unigenes manganese peroxidase (comp412_c0_seq1) and laccase (comp3447_c0_seq1), had higher expression in H-M. The gene encoding tyrosinase (comp1847_c0_seq3) exhibited the highest expression level in H-V. In H-P, different unigenes, such as Precursor priA (comp1204_c0_seq1), adenylate kinase (comp1662_c0_seq1), RhoA GTPase effector (comp2834_c0_seq3) and serine threonine protein kinase (comp3444_c0_seq1) were up-regulated. In H-F, the genes encoding Ca-transporting ATPase (comp2607_c0_seq7), Ras GTPase-activating protein (comp2797_c0_seq1) and AMP binding protein (comp5124_c0_seq5) were up-regulated.


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)

Differentially expressed genes (DEGs) between the four developmental stages in H. marmoreus.Each column represents an experimental sample (e.g., H-M, H-V, H-P and H-F), and each row represent a gene. Expression differences are shown in different colors. Red indicates high expression and green indicates low expression.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0123025.g006: Differentially expressed genes (DEGs) between the four developmental stages in H. marmoreus.Each column represents an experimental sample (e.g., H-M, H-V, H-P and H-F), and each row represent a gene. Expression differences are shown in different colors. Red indicates high expression and green indicates low expression.
Mentions: Co-expression analysis, which is based on the premise that a set of genes involved in a biological process is co-expressed under given conditions, has been successfully used to identify novel genes in several studies [38]. To verify the correlation between the expression of differentially expressed genes (DEGs) and developmental stages, heatmap analysis was performed based on the FPKM values of 31 DEGs involved in metabolism, gene regulation, signal transduction and cell organization (Fig 6). The functional annotation for these unigenes are listed in S4 Table. As shown in Fig 6, genes involved in carbon metabolism, such as the unigenes manganese peroxidase (comp412_c0_seq1) and laccase (comp3447_c0_seq1), had higher expression in H-M. The gene encoding tyrosinase (comp1847_c0_seq3) exhibited the highest expression level in H-V. In H-P, different unigenes, such as Precursor priA (comp1204_c0_seq1), adenylate kinase (comp1662_c0_seq1), RhoA GTPase effector (comp2834_c0_seq3) and serine threonine protein kinase (comp3444_c0_seq1) were up-regulated. In H-F, the genes encoding Ca-transporting ATPase (comp2607_c0_seq7), Ras GTPase-activating protein (comp2797_c0_seq1) and AMP binding protein (comp5124_c0_seq5) were up-regulated.

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