Reference gene selection for quantitative real-time PCR analysis of Hymenopellis radicata under abiotic stress.

Hymenopellis radicata (H. radicata) is an edible fungus rich in protein and mineral elements, with high edible and medical value. And reference genes suitable for normalization of qRT-PCR data from this species have not been investigated. In this study, therefore, we selected 11 housekeeping genes common in biology. The expression levels of these housekeeping genes were measured in three different tissues and six different abiotic stress treatments in mycelium. They were evaluated for expression stability using online tools. The results showed that gene ACT could be stable expressed in all samples. The expressions of genes TUB and UBQ10 are the most stable under heat stress, ACT and EF are the most stable genes under salt stress, ACT and TUB are the most stable genes under oxidation stress, RPL6 and EF are the most stable genes under pH condition, ACT and RPB2 are the most stable genes under cadmium stress, and RPB2 and UBC are the most stable genes under drought condition. ACT and PP2A are the most stable genes at different tissue sites. This study is of great help to explore the gene expression pattern of H. radicata, and also provides reference for internal reference gene screening under other conditions.

Selection and validation of reference genes for normalization of gene expression in Floccularia luteovirens.

Floccularia luteovirens is one of the rare edible fungi with high nutritional value found on the Qinghai-Tibet Plateau. However, research at the molecular level on this species is currently constrained due to the lack of reliable reference genes for this species. Thirteen potential reference genes (ACT, GAPDH, EF-Tu, SAMDC, UBI, CLN1, ß-TUB, γ-TUB, GTP, H3, UBC, UBC-E2, and GTPBP1) were chosen for the present study, and their expression under various abiotic conditions was investigated. Stability of gene expression was tested using GeNorm, NormFinder, BestKeeper, Delta-Ct, and RefFinder. The results showed that the most suitable reference genes for salt treatment were ACT and EF-Tu. Under drought stress, γ-TUB and UBC-E2 would be suitable for normalization. Under oxidative stress, the reference genes H3 and GAPDH worked well. Under heat stress, the reference genes EF-Tu and γ-TUB were suggested. Under extreme pH stress, UBC-E2 and H3 were appropriate reference genes. Under cadmium stress, the reference genes ACT and UBC-E2 functioned well. In different tissues, H3 and GTPBP1 were appropriate reference genes. The optimal internal reference genes when analyzing all samples were H3 and SAMDC. The expression level of HSP90 was studied to further validate the applicability of the genes identified in this study.

Population genetic structure of Hymenopellis radicata germplasm resources based on genome re-sequencing.

Through whole-genome re-sequencing of 18 Hymenopellis radicata germplasm resources collected from diverse regions in China, we identified significant variations in the form of Single Nucleotide Polymorphisms (SNPs) and Insertions and Deletions (InDels). These variations were comprehensively annotated, shedding light on the mutation types present in the entire genome of the H. radicata germplasm. This analysis revealed the number and position information of each mutation and provided insights into the overall genomic landscape of H. radicata germplasm. Utilizing SNP data, we delved into the population structure of the 18 H. radicata germplasm resources. The results indicated the presence of 2,335,179 Indel sites and 12,050,448 SNP sites. The population structure analysis unveiled two distinct subgroups among the H. radicata germplasm resources. Phenotypic statistics, principal component analysis, and phylogenetic tree results echoed the findings of the population structure analysis. Different strains of H. radicata from various regions in China exhibited notable differences in genetic diversity, mycelial growth rate, yield, and fruiting body characteristics. Significant disparities were observed between the two subgroups, while strains within each subgroup shared common characteristics. This research establishes a solid foundation for integrating H. radicata into diverse breeding programs. The data underscore the potential of H. radicata for genetic improvement and exploitation in breeding initiatives, paving the way for future advancements in this field.

The Research Status and Prospects of Floccularia luteovirens: A Mycorrhizal Fungus with Edible Fruiting Bodies.

Floccularia luteovirens, a rare wild edible and medicinal fungus, is endemic to the Tibetan plateau. However, attempts to artificially domesticate this species have not been successful, resulting in extremely limited utilization of this valuable resource. This paper presents the geographical distribution of F. luteovirens, along with its ecological and biological characteristics. It explores population relations, symbiotic relationships, soil microbial community relations, fruiting body occurrence conditions, nutritional metabolism, and reproductive patterns. The cultivation techniques, as well as the edible and medicinal value of this mushroom, are also reviewed. Through an overall analysis of the physiological characteristics and current research status of F. luteovirens, the paper discusses its development prospects. The aim is to provide a reference for other researchers and promote its artificial domestication, resource development, and utilization.

Combined transcriptomics and metabolomics analysis reveals the molecular mechanism of heat tolerance of Le023M, a mutant in Lentinulaedodes.

Lentinula edodes, one of the most highly regarded edible mushrooms in China, is susceptible to damage from high temperatures. However, a mutant strain derived from L. edodes, known as Le023M, has shown exceptional thermotolerance. Compared to the original strain Le023, Le023M exhibited accelerated mycelial recovery following heat stress. Through RNA-seq analysis, the majority of differentially expressed genes (DEGs) were found to be associated with functions such as "protein refolding", "protein unfolding", "protein folding", and "response to heat", all of which are closely linked to heat shock proteins. Furthermore, qRT-PCR results revealed significant accumulation of heat shock-related genes in Le023M under heat stress. GC-MS analysis indicated elevated levels of trehalose, aspartate, and glutamate in Le023M when subjected to heat stress. The highly expressed genes involved in these metabolic pathways were predominantly found in Le023M. Collectively, these findings highlight the following: (i) the crucial role of heat shock proteins (HSPs) in the thermo-resistant mechanisms of Le023M; (ii) the potential of trehalose accumulation in Le023M to enhance mycelium resistance to heat stress; and (iii) the induction of aspartate and glutamate accumulation in response to heat stress. These results shed light on the molecular mechanisms underlying the thermotolerance of Le023M, providing valuable insights for further understanding and improving heat stress response in L. edodes. The findings also highlight the potential applications of Le023M in the cultivation and production of L. edodes under high-temperature conditions.

Application of omics technology in the research on edible fungi.

Edible fungus is a large fungus distributed all over the world and used as food and medicine. But people's understanding of edible fungi is not as much as that of ordinary crops, so people have started a number of research on edible fungi in recent years. With the development of science and technology, omics technology has gradually walked into people's vision. Omics technology has high sensitivity and wide application range, which is favored by researchers. The application of omics technology to edible fungus research is a major breakthrough, which has transferred edible fungus research from artificial cultivation to basic research. Now omics technology in edible fungi has been flexibly combined with other research methods, involving multiple studies of edible fungus, such as genetic breeding, growth and development, stress resistance, and the use of special components in edible fungus as pharmaceutical additives. It is believed that in the future, the research of edible fungi will also be brought to a deeper level with the help of omics technology. This paper introduces the application progress of modern omics technology to the study on edible fungi and mentions the application prospect of edible fungi research with the constant development of omics technology, thereby providing ideas for the follow-up in-depth research on edible fungi.

Genome-Wide Identification and Analysis of the Heat-Shock Protein Gene in L. edodes and Expression Pattern Analysis under Heat Shock.

Lentinula edodes (L. edodes), one of the most popular edible mushrooms in China, is adversely affected by high temperature. Heat shock proteins (HSPs) play a crucial role in regulating the defense responses against the abiotic stresses in L. edodes. Some HSPs in L. edodes have been described previously, but a genome-wide analysis of these proteins is still lacking. Here, the HSP genes across the entire genome of the L. edodes mushroom were identified. The 34 LeHSP genes were subsequently classified into six subfamilies according to their molecular weights and the phylogenetic analysis. Sequence analysis showed that LeHSP proteins from the same subfamily have conserved domains and one to five similar motifs. Except for Chr 5 and 9, 34 LeHSPs genes were distributed on the other eight chromosomes. Three pairs of paralogs were identified because of sequence alignment and were confirmed as arising from segmental duplication. In LeHSPs' promoters, different numbers of heat shock elements (HSEs) were predicted. The expression profiles of LeHSPs in 18N44 and 18 suggested that the thermo-tolerance of strain 18N44 might be related to high levels of LeHSPs transcript in response to heat stress. The quantitative real-time PCR (qRT-PCR) analysis of the 16 LeHSP genes in strains Le015 and Le027 verified their stress-inducible expression patterns under heat stress. Therefore, these comprehensive findings provide useful in-depth information on the evolution and function of LeHSPs and lay a theoretical foundation in breeding thermotolerant L. edodes varieties.