## 3 Results
### Transcriptome Analysis of Caoyuanheimo-1 (Agaricus sp.) during Growth and Development  
A total of 50,303 transcripts and 8208 unigenes were obtained through transcriptome assembly (Table S2). The N50 of the transcripts and unigenes were 4761 bp and 4404 bp, respectively. Among them, the number of transcripts and unigenes with a length greater than 2000 bp were 28,320 and 3586, accounting for 56.30% and 43.69%, respectively (Figure S2). A total of 66.78 Gb of clean data was obtained, with an average of 7.42 Gb of clean data per sample, and the average percentage of Q30 was 92.39% (Table S3). A total of 6843 unigenes were annotated in all databases, including COG (2533), GO (3831), KEGG (4768), KOG (3293), Pfam (3967), Swissprot (4053), and NR (6807). In all databases, the proportion of annotated genes with a length greater than 1000 bp was over 74.23% (Figure 3a). For the species distribution of the top BLAST hits in the NR database, 6564 (96.43%) annotated unigenes matched the sequence of _Agaricus bisporus_ (Figure 3b). Differentially expressed genes (DEGs) from three different developmental periods were analyzed for the principal component analysis (PCA); the results showed that the primordium period (HY) was separated from the fruiting period (HZ and HC), viewed on the horizontal axis, and the two periods for the fruiting body converged (Figure S3). By analyzing the HY vs. HC group data, the results showed a total of 505 DEGs, of which 234 were upregulated and 271 were downregulated in the rip fruiting body period (HC) (Figure 3c). Further analysis revealed that the pathways mainly enriched by the 234 upregulated genes included protein processing in endoplasmic reticulum; phenylalanine, tyrosine, and tryptophan biosynthesis; ribosome and N-glycan biosynthesis; MAPK signaling pathway--yeast; beta-alanine metabolism; various types of N-glycan biosynthesis; tyrosine metabolism; terpenoid backbone biosynthesis; and tryptophan metabolism. The main pathways enriched by the 271 downregulated genes in  
Figure 3: A differential gene analysis between the different development stages: HY represents the primordium period of Caoyuanheimo\(-1\); HZ represents the young fruiting period of Caoyuanheimo\(-1\); and HC represents the rip fruiting period of Caoyuanheimo\(-1\). (**a**) Functional annotation numbers of the unigenes in the COG, GO, KEGG, KOG, Pfam, Swissprot, and NR databases. (**b**) An annotated species distribution in the NR database. (**c**) A statistical analysis of the number of upregulated and downregulated DEGs in the HY vs. HC, HY vs. HZ, and HZ vs. HC groups, respectively. (**d**) A Venn diagram showing the shared and unique genes among the HY vs. HZ, HY vs. HC, and HZ vs. HC groups. The numbers represent the number of genes that were unique or shared. (**e**) The heatmap is linked by a dendrogram representing clustering of the transcriptomic data. The color code is as follows: red indicates upregulated transcripts; blue indicates downregulated transcripts; and white indicates unchanged transcripts. The color scale of the heatmap ranges from blue (\(-2.0\)) to red (\(2.0\)) in the natural logarithmic scale. cluded ABC transporters; the biosynthesis of unsaturated fatty acids, glycosphingolipid biosynthesis--globo and isoglobo series; D-arginine and D-ornithine metabolism; caffeine metabolism; glycerolipid metabolism; ascorbate and aldarate metabolism; sphingolipid metabolism; peroxisome; glutathione metabolism; galactose metabolism; alpha-linolenic acid metabolism; fatty acid degradation; arginine and proline metabolism; endocytosis; mitophagy--yeast; methane metabolism; valine, leucine, and isoleucine degradation; and ubiquinone and other terpenoid-quinone biosynthesis (Figure S4). In the HZ vs. HC groups, there was a total of 181 DEGs, of which 117 were upregulated and 64 were downregulated (Figure 3c).