Selection and Validation of Reference Genes for qRT-PCR in Lentinula edodes under Different Experimental Conditions

Interrelationship among substrate utilization, metabolic productions, and housekeeping-related gene expression levels in Mortierella alpine CBS 754.68

The impacts of Magnesium oxide nanoparticles (MgONPs) on the expression of 10 potential housekeeping genes of Mortierella alpine were assayed. Actin emerged as the good candidate when Mortierella alpine entered the death phase subsequent to the growth phase while Dihydropteridine reductase and 28 s were identified as suitable candidates when Mortierella alpine remained in the growth phase.

Transcriptome Reveals the Key Genes Related to the Metabolism of Volatile Sulfur-Containing Compounds in Lentinula edodes Mycelium

Lentinula edodes (L. edodes) is a globally popular edible mushroom because of its characteristic sulfur-containing flavor compounds. However, the formation of the volatile sulfur-containing compounds in the mycelium of L. edodes has not been studied. We found that there were also sulfur-containing aroma compounds in the mycelium of L. edodes, and the content and composition varied at different stages of mycelial growth and development. The γ-glutamyl-transpeptidase (GGT) and cysteine sulfoxide lyase (C-S lyase) related to the generation of sulfur compounds showed the highest activities in the 15-day sample. Candidate genes for the metabolism of volatile sulfur compounds in mycelium were screened using transcriptome analysis, including encoding the GGT enzyme, C-S lyase, fatty acid oxidase, HSP20, and P450 genes. The expression patterns of Leggt3 and Leccsl3 genes were consistent with the measured activities of GGT and C-S lyase during the cultivation of mycelium and molecular dynamics simulations showed that they could stably bind to the substrate. Our findings provide insights into the formation of sulfur-containing flavor compounds in L. edodes. The mycelium of L. edodes is suggested for use as material for the production of sulfur-containing flavor compounds.

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, β-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.

Genome-Wide Screening and Stability Verification of the Robust Internal Control Genes for RT-qPCR in Filamentous Fungi

In real-time quantitative PCR (RT-qPCR), internal control genes (ICGs) are crucial for normalization. This study screened 6 novel ICGs: Pre-mRNA-splicing factor cwc15 (Cwf15); ER associated DnaJ chaperone (DnaJ); E3 ubiquitin-protein ligase NEDD4 (HUL4); ATP-binding cassette, subfamily B (MDR/TAP), member 1 (VAMP); Exosome complex exonuclease DIS3/RRP44 (RNB); V-type H⁺-transporting ATPase sub-unit A (V-ATP) from the 22-transcriptome data of 8 filamentous fungi. The six novel ICGs are all involved in the basic biological process of cells and share the different transcription levels from high to low. In order to further verify the stability of ICGs candidates, the six novel ICGs as well as three traditional housekeeping genes: β-actin (ACTB); β-tubulin (β-TUB); glyceraldehyde-3-phosphate dehydrogenase gene (GAPDH) and the previously screened reference genes: SPRY-domain-containing protein (SPRYp); Ras-2 protein (Ras); Vacuolar protein sorting protein 26 (Vps26) were evaluated by geNorm and NormFinder statistical algorithms. RT-qPCR of 12 ICGs were performed at different developmental stages in Flammulina filiformis and under different treatment conditions in Neurospora crassa. The consistent results of the two algorithms suggested that the novel genes, RNB, V-ATP, and VAMP, showed the highest stability in F. filiformis and N. crassa. RNB, V-ATP, and VAMP have high expression stability and universal applicability and therefore have great potential as ICGs for standardized calculation in filamentous fungi. The results also provide a novel guidance for the screening stable reference genes in RT-qPCR and a wide application in gene expression analysis of filamentous fungi.

Selection and validation of reliable reference genes for Tolypocladium guangdongense gene expression analysis under differentially developmental stages and temperature stresses

Tolypocladium guangdongense, formerly known as Cordyceps guangdongensis, is a widely cultivated fungus of the Cordyceps s.l. species that has been investigated over the last 12 years. It has the potential to be used in a number of applications in the health and pharmaceutical industries for it has shown its high nutritional and medicinal values according to previous animal studies. qRT-PCR (quantitative reverse transcription polymerase chain reaction) is extensively used to analyze the expression pattern and molecular mechanisms of functional genes under differentially experimental conditions. The expression stability of reference genes used for normalization determines the reliability of qRT-PCR results, indicating the importance of selection and validation of reference genes before gene expression analysis. In the present study, three statistical algorithms, geNorm, NormFinder and BestKeeper, were used for analyzing the expression stability of nineteen candidate reference genes (CRGs) in T. guangdongense. Investigation were carried out under differentially experimental conditions, which included differentially developmential stages (mycelia, primordia, young and mature fruiting bodies), different carbon sources, cold and heat stresses. The results showed that histone H4 and tubulin beta chain 2 (β-tub2) were the most and least stable genes, respectively, across all the experimental samples. Moreover, analysis of individual data sets exhibited different stability and expression profiles of reference genes. The vacuolar protein sorting gene VPS was the most stable gene expressed under the differentially developmental stages and temperature stresses, whereas H4 was the most stably expressed gene under different carbon sources. Therefore, it can be proposed that VPS and H4 are the preferred reference genes for normalization of gene expression under different experimental conditions. The results of our present study will enable more accurate evaluation of gene expression in T. guangdongense using the optimal reference gene for qRT-PCR analysis.