Genome Survey and Transcriptome Analysis on Mycelia and Primordia of Agaricus blazei

Abstract

Agaricus blazei, a type of edible straw-rotting mushroom with somewhat sweet taste and fragrance of almonds, has attracted considerable scientific and practical attention. High-throughput Illumina PE150 and PacBio RSII platform were employed to generate a genomic sequence. De novo assembly generated 36 contigs with 38,686,133 bp in size, containing 10,119 putative predicted genes. Additionally, we also studied transcriptional regulation of the mycelia and the primordia for exploration of genes involved in fruiting body formation. Expression profiling analysis revealed that 2,164 genes were upregulated in mycelia and 1,557 in primordia. Functional enrichment showed that differentially expressed genes associated with response to stress, ribosome biogenesis, arginine biosynthesis, and steroid biosynthesis pathway were more active in fruiting body. The genome and transcriptome analysis of A. blazei provide valuable sequence resources and contribute to our understanding of genes related to the biosynthesis pathway of polysaccharide and benzaldehyde, as well as the fruiting body formation.

Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes

“…Transcriptomic data provided clear evidence for expression peaks of genes related to mitotic or meiotic cell division, as well as associated processes in DNA replication, repair, chromosome dynamics/movement etc., during fruiting body development. The enrichment of meiotic/mitotic genes during fruiting body development and sporulation was noted in C. cinerea (Burns et al 2010;Muraguchi et al 2015;Krizsán et al 2019), Pisolithus microcarpus (Pereira et al 2017), Tricholoma matsutake (Tang et al 2020) and L. edodes (Song et al 2018b), Agaricus blazei (Lu et al 2020) as well as in a six-species comparison published by Krizsan et al (Krizsán et al 2019), among others. Similar signal for meiotic gene upregulation has been detected in Ascomycota fruiting bodies as well (Rodenburg et al 2018).…”

Whole-Genome and Transcriptome Sequencing of Phlebopus portentosus Reveals Its Associated Ectomycorrhizal Niche and Conserved Pathways Involved in Fruiting Body Development

“…Furthermore, peroxisome, ribosome, oxidative phosphorylation, citrate cycle and MAPK signaling pathways were enriched in the stage of F in P. portentosus. Ribosome pathways were increased significantly during the fruiting body growth stage in Ophiocordyceps sinensis ( Zhang et al, 2021 ), F. velutipes ( Liu et al, 2014 ), Auricularia polytricha ( Zhou et al, 2014 ), and Agaricus blazei ( Lu et al, 2020 ) to provide proteins for fruiting body formation or carry out some other functions, e.g., DNA repair, development, and cell division. In fungi, the activity of peroxisomes was required for sexual development ( Peraza-Reyes and Berteaux-Lecellier, 2013 ).…”

Selection and Evaluation of Potential Reference Genes for Quantitative Real-Time PCR in Agaricus blazei Based on Transcriptome Sequencing Data

“…Spawn of strain JA was cultured on straw-manure compost [26]. For RNA extraction, samples of mycelia (MY) and fruit bodies at different developmental stages (primordia (PR), harvested stage (HA), and pileus opening stage (OP)) were collected according to the method described by Lu et al [25,26]. Fruit bodies at button stage (BU) and tissue samples (stipe and pileus from fruit bodies at button stage, harvested stage, and pileus opening stage) were also harvested, respectively, and frozen in liquid nitrogen immediately.…”

“…Traditional Internal Control Genes. Transcriptome data across four different developmental stages (Table 1) [25,26] were calculated by an FPKM formula. To assess expression stability, we calculated the following indices of FPKM values [21], including standard deviation (SD), mean expression value (MV), and coefficient of variation value (CV, dividing SD by MV) for each gene in accordance with the method by de Jonge et al [27].…”

“…However, the stability of this gene has not been estimated in this fungus. Recently, genome and transcriptome of A. blazei were investigated to identify genes involved with fruit body development and biosynthesis pathway of polysaccharide and benzaldehyde [25,26]. The transcriptome datasets could be used as a potential source for selection of appropriate candidate reference genes in A. blazei.…”