Table 1.
Mapping results of C. militaris transcriptome.
Figure 1.
Pipelines of transcriptome and proteome analysis of C. militaris.
(A) Mycelium and mature fruiting body images of C. militaris; scale bars, 1 cm. (B) Analysis Pipelines of transcriptome and proteome of C. militaris.
Figure 2.
Distribution statistics of genes’ coverage.
The pie charts showed the distributions of genes’ coverage of mycelium (A) and fruiting body (B) respectively. Gene coverage is the percentage of a gene covered by reads. The value equals to ratio of the number of bases in a gene covered by unique mapping reads to number of total bases in that gene.
Figure 3.
Alternative splicing (AS) and novel transcripts prediction.
(A) Numbers of alternative splicing events and involved genes in different developmental stages of C. militaris. The x-axis represents types of alternative splicing events. (B) Prediction of novel transcripts in mycelium and fruiting body.
Figure 4.
Comprehensive analysis of differentially expressed genes (DEGs) between mycelium and fruiting body of C. militaris.
(A) Estimation of significantly up-regulated and down-regulated genes between different developmental stages. (B) The heat map of DEGs. log (base 10) value of RPKM data was used to draft the map. As is shown in the above brand, −4 value indicates the absence of particular genes in its corresponding transcriptome. The green color represents relatively lower expression and red color represents higher. (C) Verification of the gene expression by semi-quantitative RT-PCR. M: mycelium; F: fruiting body. The actin gene CCM_03787 was used as a reference. The detailed information of 17 selected genes was listed in Table 2. * The experimental result is not in accordance with the transcriptome data. (D) GO terms enrichment analysis. Ten terms that show smallest p value in three main categories (biological process, cellular component, molecular function) were chosen. * p≤0.05, it indicates the significant enriched GO terms in DEGs. (E) KEGG pathway enrichment analysis. Ten pathways that show smallest Q value were selected. * Q ≤0.05, it represents the significant enriched pathways in DEGs. X-axes of (D) and (E) represent the fold changes of GO terms (D) and KEGG pathways (E) of DEGs in comparison with the genome. (F) GO terms of DEGs. Crossbands in black represent up-regulated genes in mycelium compared with fruiting body, and crossbands in red represent up-regulated genes in fruiting body compared with mycelium. * represents nucleobase, nucleoside, nucleotide and nucleic acid metabolism. 1365 up-regulated genes in mycelium and 339 in fruiting body got GO annotation.
Table 2.
The expression information in different stages of selected genes for semi-quantitative RT-PCR.
Figure 5.
Differentially expressed genes associated with putative cordycepin metabolic pathway at different developmental stages.
(A) Putative cordycepin metabolic pathway derived from purine metabolic pathway. Red boxes represent some genes in the steps are up-regulated in mycelium, while green boxes represent that in fruiting body. Black boxes mean the common expression level of genes in the steps between mycelium and fruiting body. The detailed information of genes involved in the pathway was listed in Table 3. (B) Validation of the gene expression in cordycepin metabolic pathway by quantitative RT-PCR. Actin gene CCM_03787 was the reference. The expression levels of randomly selected genes in fruiting body were set as control samples and those in mycelium were normalized to the control. The values are the results of three technical repetitions (mean ± SD).
Table 3.
Differential expression of genes putatively involved in cordycepin metabolism pathway.
Figure 6.
One-dimensional SDS-PAGE separation of C. militaris mycelium and fruiting body proteins.
The grids indicate how the gel bands (M_1–5, F_1–5) were cut for mass spectrometry. The right of the figure indicates the molecular weight of the markers (kDa).
Figure 7.
Overview of the protein identified from different samples and their functional annotation summary.
M: mycelium; F: fruiting body. The top venn diagram showing the specific and common proteins in mycelium and fruiting body detected by LC-MS/MS. The bottom venn diagrams showing the number of proteins from different samples annotated by GO, COG, and KEGG database respectively.
Figure 8.
Functional annotation analysis of proteins from C. militaris mycelium and fruiting body.
(A) Distributions of GO terms of proteins in different samples. The percentage of proteins contained in a particular GO term is shown. * represents nucleobase, nucleoside, nucleotide and nucleic acid metabolism. (B) The heat map of proteins at different stages annotated by COG. The percentage of proteins in each COG category was used to draft the map. (C) Top 39 different KEGG pathway distributions of proteins between mycelium and fruiting body. The y-axis indicates the percentage of proteins involved in a particular KEGG pathway. M_up represents the percentage of proteins in a COG category (B) or KEGG pathway (C) from mycelium is higher than that in fruiting body, F_up is reverse.
Table 4.
Comparison of the amount of noteworthy proteins in different stages of C. militaris.