Validation of Reliable Reference Genes for RT-qPCR Studies of Target Gene Expression in Colletotrichum camelliae During Spore Germination and Mycelial Growth and Interaction With Host Plants

Selection of stable reference genes for qPCR expression of Colletotrichum lindemuthianum, the bean anthracnose pathogen

Phaseolus vulgaris L., commonly known as the common bean, is a highly nutritious crop often called the "poor man's meat". However, it is susceptible to various diseases throughout the cropping season, with anthracnose caused by Colletotrichum lindemuthianum being a significant threat that leads to substantial losses. There is still a lack of understanding about the molecular basis of C. lindemuthianum pathogenicity. The first step in understanding this is to identify pathogenicity genes that express more during infection of common beans. A reverse transcription quantitative real-time PCR (qPCR) method can be used for virulence gene expression. However, this approach requires selecting appropriate reference genes to normalize relative gene expression data. Currently, there is no reference gene available for C. lindemuthianum. In this study, we selected eight candidate reference genes from the available genome of C. lindemuthianum to bridge the gap. These genes were ACT (Actin), β-tub (β-tubulin), EF (Elongation Factor), Cyt C (Cytochrome C), His H3 (Histone H3), CHS1 (Chitin synthetase), GAPDH (Glyceraldehyde-3-phosphate dehydrogenase) and abfA (Alpha-l-Arabinofuranosidase A). The primers for these candidate reference genes were able to amplify cDNA only from the pathogen, demonstrating their specificity. The qPCR efficiency of the primers ranged from 80% to 103%. We analyzed the stability of gene expression in C. lindemuthianum by exposing the mycelium to nine different stress conditions. We employed algorithms, such as GeNorm, NormFinder, BestKeeper, and RefFinder tools, to identify the most stable gene. The analysis using these tools revealed that EF, GAPDH, and β-tub most stable genes, while ACT and CHS1 showed relatively low expression stability. A large number of potential effector genes have been identified through bioinformatics analysis in C. lindemuthianum. The stable genes for qPCR (EF and GAPDH) discovered in this study will aid the scientific community in determining the relative expression of C. lindemuthianum effector genes.

Assessment of Candidate Reference Genes for Gene Expression Studies Using RT-qPCR in Colletotrichum fructicola from Litchi

Litchi (Litchi chinensis Sonn.) is a tropical fruit originating from southern China that is currently cultivated in subtropical and tropical regions worldwide. Litchi anthracnose, caused by Colletotrichum fructicola, a dominant species of Colletotrichum spp., is an important disease of litchi that damages the fruits in fields and in post-harvest storage. Real-time quantitative PCR (RT-qPCR) is a common technique with which to detect the expression of and function of target genes quickly and precisely, and stable reference genes are crucial. However, there is no comprehensive information on suitable reference genes of C. fructicola present. Here, we designed eight candidate genes (GAPDH, α-tubulin, 18S, β-tubulin, EF1a, TATA, RPS5, and EF3) using RefFinder software (programs: geNorm, ΔCt, BestKeeper, and NormFinder) to investigate their reliability in the detection of C. fructicola under five different treatments (fungal development stage, temperature, UV, culture medium, and fungicide). The results showed the optimal reference genes under different conditions: EF1a and α-tubulin for developmental stage; α-tubulin and β-tubulin for temperature; α-tubulin and RPS5 for UV treatment; RPS5 and α-tubulin for culture medium; α-tubulin, GAPDH, and TATA for fungicide treatments. The corresponding expression patterns of HSP70 (Heat shock protein 70) were significantly different when the most and the least stable reference genes were selected when treated under different conditions. Our study provides the first detailed list of optimal reference genes for the analysis of gene expression in C. fructicola via RT-qPCR, which should be useful for future functional studies of target genes in C. fructicola.

Tea plant (Camellia sinensis) lipid metabolism pathway modulated by tea field microbe (Colletotrichum camelliae) to promote disease

Tea is one of the most popular healthy and non-alcoholic beverages worldwide. Tea anthracnose is a disease in tea mature leaves and ultimately affects yield and quality. Colletotrichum camelliae is a dominant fungal pathogen in the tea field that infects tea plants in China. The pathogenic factors of fungus and the susceptible factors in the tea plant are not known. In this work, we performed molecular and genetic studies to observe a cerato-platanin protein CcCp1 from C. camelliae, which played a key role in fungal pathogenicity. △CcCp1 mutants lost fungal virulence and reduced the ability to produce conidia. Transcriptome and metabolome were then performed and analysed in tea-susceptible and tea-resistant cultivars, Longjing 43 and Zhongcha 108, upon C. camelliae wild-type CCA and △CcCp1 infection, respectively. The differentially expressed genes and the differentially accumulated metabolites in tea plants were clearly overrepresented such as linolenic acid and linoleic acid metabolism, glycerophospholipid metabolism, phenylalanine biosynthesis and metabolism, biosynthesis of flavonoid, flavone and flavonol etc. In particular, the accumulation of jasmonic acid was significantly increased in the susceptible cultivar Longjing 43 upon CCA infection, in the fungal CcCp1 protein dependent manner, suggesting the compound involved in regulating fungal infection. In addition, other metabolites in the glycerophospholipid and phenylalanine pathway were observed in the resistant cultivar Zhongcha 108 upon fungal treatment, suggesting their potential role in defense response. Taken together, this work indicated C. camelliae CcCp1 affected the tea plant lipid metabolism pathway to promote disease while the lost function of CcCp1 mutants altered the fungal virulence and plant response.

Pectate Lyase Genes Abundantly Expressed During the Infection Regulate Morphological Development of Colletotrichum camelliae and CcPEL16 Is Required for Full Virulence to Tea Plants

Colletotrichum camelliae is the dominant species causing foliar diseases of tea plants (Camellia sinensis) in China. Transcriptome data and reverse transcription-quantitative PCR (qRT-PCR) analysis have demonstrated that the pectate lyase genes in C. camelliae (CcPELs) were significantly upregulated during infectious development on tea plants (cv. Longjing43). To further evaluate the biological functions of CcPELs, we established a polyethylene glycol (PEG)-mediated protoplast transformation system of C. camelliae and generated targeted deletion mutants of seven CcPELs. Phenotypic assays showed that the genes contribute to mycelial growth, conidiation, and appressorium development. The polypeptides encoded by each CcPEL gene contained a predicted N-terminal signal peptide, and a yeast invertase secretion assay suggested that each CcPEL protein could be secreted. Cell death-suppressive activity assays confirmed that all seven CcPELs did not suppress Bax-induced cell death in tobacco leaf cells. However, deletion of CcPEL16 significantly reduced necrotic lesions on tea leaves. Taken together, these results indicated that CcPELs play essential roles in regulating morphological development, and CcPEL16 is required for full virulence in C. camelliae. IMPORTANCE In this study, we first established a PEG-mediated protoplast transformation system of C. camelliae and used it to investigate the biological functions of seven pectate lyase genes (CcPELs) which were abundantly expressed during infection. The results provided insights into the contributions of pectate lyase to mycelial growth, conidial production, appressorium formation, and the pathogenicity of C. camelliae. We also confirmed the secretory function of CcPEL proteins and their role in suppressing Bax-induced cell death. Overall, this study provides an effective method for generating gene-deletion transformants in C. camelliae and broadens our understanding of pectate lyase in regulating morphological development and pathogenicity.

Identifying stable reference genes in polyethene glycol precipitated urinary extracellular vesicles for RT-qPCR-based gene expression studies in renal graft dysfunction patients

BACKGROUND

Urinary extracellular vesicles (UEVs) hold RNA in their cargo and are potential sources of biomarkers for gene expression studies. The most used technique for gene-expression studies is quantitative polymerase chain reaction (qPCR). It is critical to use stable reference genes (RGs) as internal controls for normalising gene expression data, which aren't currently available for UEVs.

METHODS

UEVs were precipitated from urine of graft dysfunction patients and healthy controls by Polyethylene glycol, Mn6000 (PEG6K). Vesicular characterisation confirmed the presence of UEVs. Gene expression levels of five commonly used RGs, i.e., Beta-2-Microglobulin (B2M), ribosomal-protein-L13a (RPL13A), Peptidylprolyl-Isomerase-A (PPIA), hydroxymethylbilane synthase (HMBS), and glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) were quantified, and their stability was established through the RefFinder. The stability of identified RGs was validated by quantification of Perforin and granzyme B, signature molecules of renal graft dysfunction.

RESULTS

Urine precipitated with 12% 6 K PEG yielded round and double-membraned UEVs of size ranging from 30 to 100 nm, as confirmed through transmission electron microscopy. Nanoparticle tracking analysis (59 ± 22 nm) and Dynamic-light-scattering (78 ± 56.5 nm) confirmed their size profile. Semi-quantitative Exocheck antibody array demonstrated the presence of EV protein markers in UEV. Using the comparative ΔCт method and RefFinder analysis, B2M (1.6) and RPL13A (1.8) genes emerged as the most stable reference genes. Validation of target gene expression in renal graft dysfunction patients confirmed the efficiency of B2M and RPL13A through significant upregulation compared to other RGs.

CONCLUSIONS

Our study identified and validated B2M and RPL13A as optimal RGs for mRNA quantification studies in the UEVs of patients with renal graft dysfunction.

Selection of potential reference genes for RT-qPCR in the plant pathogenic fungus Colletotrichum fructicola

Colletotrichum is widespread, and these pathogenic fungi can cause various plant diseases. Studies have shown that Colletotrichum fructicola cause oil-tea (Camellia oleifera) anthracnose and is widely distributed as a dominant fungus in all Ca. oleifera-producing regions. Real-time quantitative PCR(RT-qPCR) is considered the most reliable technique for simultaneously measuring relative gene expression levels in different tissues. Target genes are typically quantified using RT-qPCR to explore gene function, and reliable RT-qPCR results require data normalization using stable reference genes. No studies have reported a suitable reference gene in C. fructicola. This study has eight candidate reference genes (CfCk, CfRpp, CfUce, CfRrp, CfAdrh, CfDd, CfAct, and CfTub) which were selected from C. fructicola-Ca. oleifera transcriptome data and evaluated and sequenced using geNorm, NormFinder, and BestKeeper algorithms. The results showed that CfRrp had better stability in C. fructicola, both during the growth of pure pathogenic fungi and during the invasion of different oil-tea leaves. After normalization with CfRrp, the differentially expressed target genes were similar to the transcriptome. Our work provides suitable reference genes for future studies to quantify target gene expression levels in C. fructicola.

A Spatial-Temporal Analysis of Cellular Biopolymers on Leaf Blight-Infected Tea Plants Using Confocal Raman Microspectroscopy

The objective of the present study was to characterize the temporal and spatial variation of biopolymers in cells infected by the tea leaf blight using confocal Raman microspectroscopy. We investigated the biopolymers on serial sections of the infection part, and four sections corresponding to different stages of infection were obtained for analysis. Raman spectra extracted from four selected regions (circumscribing the vascular bundle) were analyzed in detail to enable a semi-quantitative comparison of biopolymers on a micron-scale. As the infection progressed, lignin and other phenolic compounds decreased in the vascular bundle, while they increased in both the walls of the bundle sheath cells as well as their intracellular components. The amount of cellulose and other polysaccharides increased in all parts as the infection developed. The variations in the content of lignin and cellulose in different tissues of an individual plant may be part of the reason for the plant's disease resistance. Through wavelet-based data mining, two-dimensional chemical images of lignin, cellulose and all biopolymers were quantified by integrating the characteristic spectral bands ranging from 1,589 to 1,607 cm^-1, 1,087 to 1,100 cm^-1, and 2,980 to 2,995 cm^-1, respectively. The chemical images were consistent with the results of the semi-quantitative analysis, which indicated that the distribution of lignin in vascular bundle became irregular in sections with severe infection, and a substantial quantity of lignin was detected in the cell wall and inside the bundle sheath cell. In serious infected sections, cellulose was accumulated in vascular bundles and distributed within bundle sheath cells. In addition, the distribution of all biopolymers showed that there was a tylose substance produced within the vascular bundles to prevent the further development of pathogens. Therefore, confocal Raman microspectroscopy can be used as a powerful approach for investigating the temporal and spatial variation of biopolymers within cells. Through this method, we can gain knowledge about a plant's defense mechanisms against fungal pathogens.

Transcriptome-Based Selection and Validation of Reference Genes for Gene Expression Analysis of Alicyclobacillus acidoterrestris Under Acid Stress

Alicyclobacillus acidoterrestris is a major concern in fruit juice industry due to its spoilage potential of acidic fruit juice. Quantifying the expression levels of functional genes by real-time quantitative polymerase chain reaction (RT-qPCR) is necessary to elucidate the response mechanisms of A. acidoterrestris to acid stress. However, appropriate reference genes (RGs) for data normalization are required to obtain reliable RT-qPCR results. In this study, eight novel candidate RGs were screened based on transcriptome datasets of A. acidoterrestris under acid stress. The expression stability of eight new RGs and commonly used RG 16s rRNA was assessed using geNorm, NormFinder, and BestKeeper algorithms. Moreover, the comprehensive analysis using the RefFinder program and the validation using target gene ctsR showed that dnaG and dnaN were the optimal multiple RGs for normalization at pH 4.0; ytvI, dnaG, and 16s rRNA at pH 3.5; icd and dnaG at pH 3.0; and ytvI, dnaG, and spoVE at pH 2.5. This study revealed for the first time that A. acidoterrestris had different suitable RGs under different acid conditions, with implications for further deciphering the acid response mechanisms of this spoilage-causing bacterium.

Selection and validation of reference genes for measuring gene expression in Toona ciliata under different experimental conditions by quantitative real-time PCR analysis

BACKGROUND

Before studying gene expression of different organisms, it is important to determine the best reference gene. At present, the most accurate method of detecting gene expression is quantitative real-time PCR (RT-qPCR). With this method, reference genes that are stable in different biological systems and under different conditions can be obtained. Toona ciliata Roem (T. ciliata). is a valuable and fast-growing timber specie. In this study, 20 reference genes were identified using RT-qPCR, as a primary prerequisite for future gene expression analysis. Four different methods, geNorm, NormFinder, BestKeeper, and RankAggreg were used to evaluate the expression stability of the 20 candidate reference genes in various tissues under different conditions.

RESULTS

The experimental results showed that TUB-α was the most stably expressed reference gene across all samples and UBC17 was the most stable in leaves and young stems under Hypsipyla robusta (H. robusta) and methyl jasmonate (MeJA) treatments. In addition, PP2C59 and UBC5B were the best-performing genes in leaves under H. robusta treatment, while HIS1 and ACT7 were the best reference genes in young stems. The two best reference genes were 60S-18 and TUB-α after treatment at 4 °C. The expression of HIS6 and MUB1 was the most stable under PEG6000 treatment. The accuracy of the selected reference genes was verified using the transcription factor MYB3 (TcMYB3) gene.

CONCLUSIONS

This is the first report to verify the best reference genes for normalizing gene expression in T. ciliata under different conditions, which will facilitate future elucidation of gene regulations in this species.

Screening and Validation of Reference Genes for RT-qPCR Under Different Honey Bee Viral Infections and dsRNA Treatment

Honey bee viruses are one of the most important pathogens that have contributed to the decrease in honey bee colony health. To analyze the infection dynamics of honey bee viruses, quantification of viral gene expression by RT-qPCR is necessary. However, suitable reference genes have not been reported from viral and RNAi studies of honey bee. Here, we evaluated the expression of 11 common reference genes (ache2, rps18, β-actin, tbp, tif, rpl32, gadph, ubc, α-tubulin, rpl14, and rpsa) from Apis mellifera (Am) and Apis cerana (Ac) under Israeli acute paralysis virus (IAPV), chronic bee paralysis virus (CBPV), and Chinese sacbrood virus (CSBV) infection as well as dsRNA-PGRP-SA treatment, and we confirmed their validation by evaluating the levels of the defensin 1 and prophenoloxidase (ppo) genes during viral infection. Our results showed that the expression of selected genes varied under different viral infections. ache2, rps18, β-actin, tbp, and tif can be used to normalize expression levels in Apis mellifera under IAPV infection, while the combination of actin and tif is suitable for CBPV-infected experiments. The combination of rpl14, tif, rpsa, ubc, and ache2 as well as more reference genes is suitable for CSBV treatment in Apis cerana. Rpl14, tif, rps18, ubc, and α-tubulin were the most stable reference genes under dsRNA treatment in Apis mellifera. Furthermore, the geNorm and NormFinder algorithms showed that tif was the best suitable reference gene for these four treatments. This study screened and validated suitable reference genes for the quantification of viral levels in honey bee, as well as for RNAi experiments.

Lifestyle Characteristics and Gene Expression Analysis of Colletotrichum camelliae Isolated from Tea Plant [Camellia sinensis (L.) O. Kuntze] Based on Transcriptome

Colletotrichum camelliae is one of the most serious pathogens causing anthracnose in tea plants, but the interactive relationship between C. camelliae and tea plants has not been fully elucidated. This study investigated the gene expression changes in five different growth stages of C. camelliae based on transcriptome analysis to explain the lifestyle characteristics during the infection. On the basis of gene ontology (GO) enrichment analyses of differentially expressed genes (DEGs) in comparisons of germ tube (GT)/conidium (Con), appressoria (App)/Con, and cellophane infectious hyphae (CIH)/Con groups, the cellular process in the biological process category and intracellular, intracellular part, cell, and cell part in the cellular component category were significantly enriched. Hydrolase activity, catalytic activity, and molecular_function in the molecular function category were particularly enriched in the infection leaves (IL)/Con group. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the DEGs were enriched in the genetic information processing pathway (ribosome) at the GT stage and the metabolism pathway (metabolic pathways and biosynthesis of secondary metabolism) in the rest of the stages. Interestingly, the genes associated with melanin biosynthesis and carbohydrate-active enzymes (CAZys), which are vital for penetration and cell wall degradation, were significantly upregulated at the App, CIH and IL stages. Subcellular localization results further showed that the selected non-annotated secreted proteins based on transcriptome data were majorly located in the cytoplasm and nucleus, predicted as new candidate effectors. The results of this study may establish a foundation and provide innovative ideas for subsequent research on C. camelliae.