Validation of candidate reference genes for qRT-PCR studies in symbiotic and non-symbiotic Casuarina glauca Sieb. ex Spreng. under salinity conditions

Selection of a suitable reference gene for gene-expression studies in Trichomonas gallinae under various biotic and abiotic stress conditions

Trichomonas gallinae, a globally distributed protozoan parasite, significantly affects the pigeon-breeding industry. T. gallinae infection mainly causes yellow ulcerative nodules on the upper respiratory tract and crop mucosa of pigeons, impeding normal breathing and feeding and ultimately causing death. Real-time quantitative PCR (qPCR) is a crucial technique for gene-expression analysis in molecular biology. Reference-gene selection for normalization is critical for ensuring this technique's accuracy. However, no systematic screening or validation of T. gallinae reference genes has been reported. This study quantified the transcript levels of ten candidate reference genes in T. gallinae isolates with different genotypes and culture conditions using qPCR. Using the geNorm, NormFinder, and BestKeeper algorithms, we assessed these reference genes' stabilities and ranked them using RankAggreg analysis. The most stable reference gene was tubulin beta chain (TUBB), while the widely used reference genes TUBG and GAPDH demonstrated poor stability. Additionally, we evaluated these candidate reference genes' stabilities using the T. gallinae TgaAtg8 gene. On using TUBB as a reference gene, TgaAtg8's expression profiles in T. gallinae isolates with different genotypes remained relatively consistent under various culture conditions. Conversely, using ACTB as a reference gene distorted the data. These findings provide valuable reference-gene-selection guidance for functional gene research and gene-expression analysis in T. gallinae.

Will Casuarina glauca Stress Resilience Be Maintained in the Face of Climate Change?

Actinorhizal plants have been regarded as promising species in the current climate change context due to their high tolerance to a multitude of abiotic stresses. While combined salt-heat stress effects have been studied in crop species, their impact on the model actinorhizal plant, Casuarina glauca, has not yet been fully addressed. The effect of single salt (400 mM NaCl) and heat (control at 26/22 °C, supra optimal temperatures at 35/22 °C and 45/22 °C day/night) conditions on C. glauca branchlets was characterised at the physiological level, and stress-induced metabolite changes were characterised by mass spectrometry-based metabolomics. C. glauca could withstand single salt and heat conditions. However, the harshest stress condition (400 mM NaCl, 45 °C) revealed photosynthetic impairments due to mesophyll and membrane permeability limitations as well as major stress-specific differential responses in C and N metabolism. The increased activity of enzymatic ROS scavengers was, however, revealed to be sufficient to control the plant oxidative status. Although C. glauca could tolerate single salt and heat stresses, their negative interaction enhanced the effects of salt stress. Results demonstrated that C. glauca responses to combined salt-heat stress could be explained as a sum of the responses from each single applied stress.

Disentangling the role of extracellular polysaccharides in desiccation tolerance in lichen-forming microalgae. First evidence of sulfated polysaccharides and ancient sulfotransferase genes

Trebouxia sp. TR9 and Coccomyxa simplex are desiccation-tolerant microalgae with flexible cell walls, which undergo species-specific remodelling during dehydration-rehydration (D/R) due to their distinct ultrastructure and biochemical composition. Here, we tested the hypothesis that extracellular polysaccharides excreted by each microalga could be quantitatively and/or qualitatively modified by D/R. Extracellular polysaccharides were analysed by size exclusion and anion exchange chromatography, specific stains after gel electrophoresis and gas chromatography/mass spectrometry of trimethylsilyl derivatives (to determine their monosaccharide composition). The structure of a TR9-sulfated polymer was deduced from nuclear magnetic resonance (NMR) analyses. In addition, sugar-sulfotransferase encoding genes were identified in both microalgae, and their expression was measured by RT-qPCR. D/R did not alter the polydispersed profile of extracellular polysaccharides in either microalga but did induce quantitative changes in several peaks. Furthermore, medium-low-sized uronic acid-containing polysaccharides were almost completely substituted by higher molecular mass carbohydrates after D/R. Sulfated polysaccharide(s) were detected, for the first time, in the extracellular polymeric substances of both microalgae, but only increased significantly in TR9 after cyclic D/R, which induced a sugar-sulfotransferase gene and accumulated sulfated ß-D-galactofuranan(s). Biochemical remodelling of extracellular polysaccharides in aeroterrestrial desiccation-tolerant microalgae is species-specific and seems to play a role in the response to changes in environmental water availability.

Tolerance to Cyclic Desiccation in Lichen Microalgae is Related to Habitat Preference and Involves Specific Priming of the Antioxidant System

Oxidative stress is a crucial challenge for lichens exposed to cyclic desiccation and rehydration (D/R). However, strategies to overcome this potential stress are still being unraveled. Therefore, the physiological performance and antioxidant mechanisms of two lichen microalgae, Trebouxia sp. (TR9) and Coccomyxa simplex (Csol), were analyzed. TR9 was isolated from Ramalina farinacea, a Mediterranean fruticose epiphytic lichen adapted to xeric habitats, while Csol is the phycobiont of Solorina saccata, a foliaceous lichen that grows on humid rock crevices. The tolerance to desiccation of both species was tested by subjecting them to different drying conditions and to four consecutive daily cycles of D/R. Our results show that a relative humidity close to that of their habitats was crucial to maintain the photosynthetic rates. Concerning antioxidant enzymes, in general, manganese superoxide dismutases (MnSODs) were induced after desiccation and decreased after rehydration. In TR9, catalase (CAT)-A increased, and its activity was maintained after four cycles of D/R. Ascorbate peroxidase activity was detected only in Csol, while glutathione reductase increased only in TR9. Transcript levels of antioxidant enzymes indicate that most isoforms of MnSOD and FeSOD were induced by desiccation and repressed after rehydration. CAT2 gene expression was also upregulated and maintained at higher levels even after four cycles of D/R in accordance with enzymatic activities. To our knowledge, this is the first study to include the complete set of the main antioxidant enzymes in desiccation-tolerant microalgae. The results highlight the species-specific induction of the antioxidant system during cyclic D/R, suggesting a priming of oxidative defence metabolism.

Reference genes for qRT-PCR normalisation in different tissues, developmental stages, and stress conditions of Hypericum perforatum

Hypericum perforatum L. is a widely known medicinal herb used mostly as a remedy for depression because it contains high levels of naphthodianthrones, phloroglucinols, alkaloids, and some other secondary metabolites. Quantitative real-time PCR (qRT-PCR) is an optimized method for the efficient and reliable quantification of gene expression studies. In general, reference genes are used in qRT-PCR analysis because of their known or suspected housekeeping roles. However, their expression level cannot be assumed to remain stable under all possible experimental conditions. Thus, the identification of high quality reference genes is essential for the interpretation of qRT-PCR data. In this study, we investigated the expression of 14 candidate genes, including nine housekeeping genes (HKGs) (ACT2, ACT3, ACT7, CYP1, EF1-α, GAPDH, TUB-α, TUB-β, and UBC2) and five potential candidate genes (GSA, PKS1, PP2A, RPL13, and SAND). Three programs-GeNorm, NormFinder, and BestKeeper-were applied to evaluate the gene expression stability across four different plant tissues, four developmental stages and a set of abiotic stress and hormonal treatments. Integrating all of the algorithms and evaluations revealed that ACT2 and TUB-β were the most stable combination in different developmental stages samples and all of the experimental samples. ACT2, TUB-β, and EF1-α were identified as the three most applicable reference genes in different tissues and stress-treated samples. The majority of the conventional HKGs performed better than the potential reference genes. The obtained results will aid in improving the credibility of the standardization and quantification of transcription levels in future expression studies on H. perforatum.

Selection and Validation of Reference Genes for Accurate RT-qPCR Data Normalization in Coffea spp. under a Climate Changes Context of Interacting Elevated [CO2] and Temperature

World coffee production has faced increasing challenges associated with ongoing climatic changes. Several studies, which have been almost exclusively based on temperature increase, have predicted extensive reductions (higher than half by 2,050) of actual coffee cropped areas. However, recent studies showed that elevated [CO₂] can strongly mitigate the negative impacts of heat stress at the physiological and biochemical levels in coffee leaves. In addition, it has also been shown that coffee genotypes can successfully cope with temperatures above what has been traditionally accepted. Altogether, this information suggests that the real impact of climate changes on coffee growth and production could be significantly lower than previously estimated. Gene expression studies are an important tool to unravel crop acclimation ability, demanding the use of adequate reference genes. We have examined the transcript stability of 10 candidate reference genes to normalize RT-qPCR expression studies using a set of 24 cDNAs from leaves of three coffee genotypes (CL153, Icatu, and IPR108), grown under 380 or 700 μL CO₂ L^-1, and submitted to increasing temperatures from 25/20°C (day/night) to 42/34°C. Samples were analyzed according to genotype, [CO₂], temperature, multiple stress interaction ([CO₂], temperature) and total stress interaction (genotype, [CO₂], and temperature). The transcript stability of each gene was assessed through a multiple analytical approach combining the Coeficient of Variation method and three algorithms (geNorm, BestKeeper, NormFinder). The transcript stability varied according to the type of stress for most genes, but the consensus ranking obtained with RefFinder, classified MDH as the gene with the highest mRNA stability to a global use, followed by ACT and S15, whereas α-TUB and CYCL showed the least stable mRNA contents. Using the coffee expression profiles of the gene encoding the large-subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RLS), results from the in silico aggregation and experimental validation of the best number of reference genes showed that two reference genes are adequate to normalize RT-qPCR data. Altogether, this work highlights the importance of an adequate selection of reference genes for each single or combined experimental condition and constitutes the basis to accurately study molecular responses of Coffea spp. in a context of climate changes and global warming.

Antioxidative ability and membrane integrity in salt-induced responses of Casuarina glauca Sieber ex Spreng. in symbiosis with N2-fixing Frankia Thr or supplemented with mineral nitrogen

The actinorhizal tree Casuarina glauca tolerates extreme environmental conditions, such as high salinity. This species is also able to establish a root-nodule symbiosis with N2-fixing bacteria of the genus Frankia. Recent studies have shown that C. glauca tolerance to high salt concentrations is innate and linked to photosynthetic adjustments. In this study we have examined the impact of increasing NaCl concentrations (200, 400 and 600mM) on membrane integrity as well as on the control of oxidative stress in branchlets of symbiotic (NOD+) and non-symbiotic (KNO3+) C. glauca. Membrane selectivity was maintained in both plant groups at 200mM NaCl, accompanied by an increase in the activity of antioxidative enzymes (superoxide dismutase, ascorbate peroxidase, glutathione reductase and catalase). Regarding cellular membrane lipid composition, linolenic acid (C18:3) showed a significant decline at 200mM NaCl in both NOD+ and KNO3+ plants. In addition, total fatty acids (TFA) and C18:2 also decreased in NOD+ plants at this salt concentration, resulting in malondialdehyde (MDA) production. Such initial impact at 200mM NaCl is probably due to the fact that NOD+ plants are subjected to a double stress, i.e., salinity and low nitrogen availability. At 400mM NaCl a strong reduction of TFA and C18:3 levels was observed in both plant groups. This was accompanied by a decrease in the unsaturation degree of membrane lipids in NOD+. However, in both NOD+ and KNO3+ lipid modifications were not reflected by membrane leakage at 200 or 400mM, suggesting acclimation mechanisms at the membrane level. The fact that membrane selectivity was impaired only at 600mM NaCl in both groups of plants points to a high tolerance of C. glauca to salt stress independently of the symbiotic relation with Frankia.