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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: The KEGG enrichment analysis revealed that the mycelium pigmentation stage was associated with the MAPK, cAMP, and blue light signal transduction pathways.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.

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

Gene Ontology classification of the H. marmoreus transcriptome.Histogram of the GO annotation was generated by the Blast2GO software (http://www.blast2go.com/b2ghome). The unigenes were grouped into three main GO categories: cellular component, molecular function and biological process. The right Y-axis indicates the number of unigenes in a category. The left Y-axis indicates the percentage of a specific category. One unigene could be assigned with more than one GO term.
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pone.0123025.g004: Gene Ontology classification of the H. marmoreus transcriptome.Histogram of the GO annotation was generated by the Blast2GO software (http://www.blast2go.com/b2ghome). The unigenes were grouped into three main GO categories: cellular component, molecular function and biological process. The right Y-axis indicates the number of unigenes in a category. The left Y-axis indicates the percentage of a specific category. One unigene could be assigned with more than one GO term.

Mentions: We used Gene Ontology (GO) assignments to classify the functions of the annotated unigenes to other fungi, and these unigenes also strongly matched the L. bicolor genome. Of the annotated unigenes, 11282 were categorized into 53 functional groups (Fig 4), with 25 involved in biological process, 15 involved in cellular component and 13 involved in molecular function. Most of the corresponding genes were involved in “Cellular and metabolic processes” in the categories of biological process. In the cellular component categories, most of the corresponding genes were involved in “Cell”, “Cell part” and “Membrane”. In the molecular function categories, most of the corresponding genes were involved in “Binding” and “Catalytic activity”. Forty-five unigenes were assigned to the ‘Developmental process’ and ‘Growth’ categories, and the expression patterns of these unigenes are shown in S4 Fig. In addition, 15565 unigenes are annotated in the Kyoto Encyclopedia of Genes and Genomes (KEGG) and mapped to 305 reference canonical KEGG pathways.


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)

Gene Ontology classification of the H. marmoreus transcriptome.Histogram of the GO annotation was generated by the Blast2GO software (http://www.blast2go.com/b2ghome). The unigenes were grouped into three main GO categories: cellular component, molecular function and biological process. The right Y-axis indicates the number of unigenes in a category. The left Y-axis indicates the percentage of a specific category. One unigene could be assigned with more than one GO term.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0123025.g004: Gene Ontology classification of the H. marmoreus transcriptome.Histogram of the GO annotation was generated by the Blast2GO software (http://www.blast2go.com/b2ghome). The unigenes were grouped into three main GO categories: cellular component, molecular function and biological process. The right Y-axis indicates the number of unigenes in a category. The left Y-axis indicates the percentage of a specific category. One unigene could be assigned with more than one GO term.
Mentions: We used Gene Ontology (GO) assignments to classify the functions of the annotated unigenes to other fungi, and these unigenes also strongly matched the L. bicolor genome. Of the annotated unigenes, 11282 were categorized into 53 functional groups (Fig 4), with 25 involved in biological process, 15 involved in cellular component and 13 involved in molecular function. Most of the corresponding genes were involved in “Cellular and metabolic processes” in the categories of biological process. In the cellular component categories, most of the corresponding genes were involved in “Cell”, “Cell part” and “Membrane”. In the molecular function categories, most of the corresponding genes were involved in “Binding” and “Catalytic activity”. Forty-five unigenes were assigned to the ‘Developmental process’ and ‘Growth’ categories, and the expression patterns of these unigenes are shown in S4 Fig. In addition, 15565 unigenes are annotated in the Kyoto Encyclopedia of Genes and Genomes (KEGG) and mapped to 305 reference canonical KEGG pathways.

Bottom Line: The KEGG enrichment analysis revealed that the mycelium pigmentation stage was associated with the MAPK, cAMP, and blue light signal transduction pathways.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.

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