Transcriptomic Analysis Reveals the Response Mechanisms of Bell Pepper (Capsicum annuum) to Phosphorus Deficiency.

Phosphorus (P) is an important nutritional element needed by plants. Roots obtain P as inorganic phosphate (Pi), mostly in H2PO-4 form. It is vital for plants to have a sufficient supply of Pi since it participates in important processes like photosynthesis, energy transfer, and protein activation, among others. The physicochemical properties and the organic material usually make Pi bioavailability in soil low, causing crops and undomesticated plants to experience variations in accessibility or even a persistent phosphate limitation. In this study, transcriptome data from pepper roots under low-Pi stress was analyzed in order to identify Pi starvation-responsive genes and their relationship with metabolic pathways and functions. Transcriptome data were obtained from pepper roots with Pi deficiency by RNASeq and analyzed with bioinformatic tools. A total of 97 differentially expressed genes (DEGs) were identified; Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment revealed that metabolic pathways, such as porphyrin and chlorophyll metabolism, were down-regulated, and galactose and fatty acid metabolism were up-regulated. The results indicate that bell pepper follows diverse processes related to low Pi tolerance regulation, such as the remobilization of internal Pi, alternative metabolic pathways to generate energy, and regulators of root development.

Functional annotation and comparative genomics analysis of Balamuthia mandrillaris reveals potential virulence-related genes.

Balamuthia mandrillaris is a pathogenic protozoan that causes a rare but almost always fatal infection of the central nervous system and, in some cases, cutaneous lesions. Currently, the genomic data for this free-living amoeba include the description of several complete mitochondrial genomes. In contrast, two complete genomes with draft quality are available in GenBank, but none of these have a functional annotation. In the present study, the complete genome of B. mandrillaris isolated from a freshwater artificial lagoon was sequenced and assembled, obtaining an assembled genome with better assembly quality parameter values than the currently available genomes. Afterward, the genome mentioned earlier, along with strains V039 and 2046, were subjected to functional annotation. Finally, comparative genomics analysis was performed, and it was found that homologous genes in the core genome potentially involved in the virulence of Acanthamoeba spp. and Trypanosoma cruzi. Moreover, eleven of fifteen genes were identified in the three strains described as potential target genes to develop new treatment approaches for B. mandrillaris infections. These results describe proteins in this protozoan's complete genome and help prioritize which target genes could be used to develop new treatments.

Transcriptomic analysis of bell pepper (Capsicum annuum L.) revealing key mechanisms in response to low temperature stress.

BACKGROUND: Bell pepper (Capsicum annuum L.) is one of the most economically and nutritionally important vegetables worldwide. However, its production can be affected by various abiotic stresses, such as low temperature. This causes various biochemical, morphological and molecular changes affecting membrane lipid composition, photosynthetic pigments, accumulation of free sugars and proline, secondary metabolism, as well as a change in gene expression. However, the mechanism of molecular response to this type of stress has not yet been elucidated. METHODS AND RESULTS: To further investigate the response mechanism to this abiotic stress, we performed an RNA-Seq transcriptomic analysis to obtain the transcriptomic profile of Capsicum annuum exposed to low temperature stress, where libraries were constructed from reads of control and low temperature stress samples, varying on average per treatment from 22,952,190.5-27,305,327 paired reads ranging in size from 30 to 150 bp. The number of differentially expressed genes (DEGs) for each treatment was 388, 417 and 664 at T-17 h, T-22 h and T-41 h, respectively, identifying 58 up-regulated genes and 169 down-regulated genes shared among the three exposure times. Likewise, 23 DEGs encoding TFs were identified at T-17 h, 30 DEGs at T-22 h and 47 DEGs at T-42 h, respectively. GO analysis revealed that DEGs were involved in catalytic activity, response to temperature stimulus, oxidoreductase activity, stress response, phosphate ion transport and response to abscisic acid. KEGG pathway analysis identified that DEGs were related to flavonoid biosynthesis, alkaloid biosynthesis and plant circadian rhythm pathways in the case of up-regulated genes, while in the case of down-regulated genes, they pertained to MAPK signaling and plant hormone signal transduction pathways, present at all the three time points of low temperature exposure. Validation of the transcriptomic method was performed by evaluation of five DEGs by quantitative polymerase chain reaction (q-PCR). CONCLUSIONS: The data obtained in the present study provide new insights into the transcriptome profiles of Capsicum annuum stem in response to low temperature stress. The data generated may be useful for the identification of key candidate genes and molecular mechanisms involved in response to this type of stress.

Cell wall-related genes and lignin accumulation contribute to the root resistance in different maize (Zea mays L.) genotypes to Fusarium verticillioides (Sacc.) Nirenberg infection.

Introduction: The fungal pathogen Fusarium verticillioides (Sacc.) Nirenberg (Fv) causes considerable agricultural and economic losses and is harmful to animal and human health. Fv can infect maize throughout its long agricultural cycle, and root infection drastically affects maize growth and yield. Methods: The root cell wall is the first physical and defensive barrier against soilborne pathogens such as Fv. This study compares two contrasting genotypes of maize (Zea mays L.) roots that are resistant (RES) or susceptible (SUS) to Fv infection by using transcriptomics, fluorescence, scanning electron microscopy analyses, and ddPCR. Results: Seeds were infected with a highly virulent local Fv isolate. Although Fv infected both the RES and SUS genotypes, infection occurred faster in SUS, notably showing a difference of three to four days. In addition, root infections in RES were less severe in comparison to SUS infections. Comparative transcriptomics (rate +Fv/control) were performed seven days after inoculation (DAI). The analysis of differentially expressed genes (DEGs) in each rate revealed 733 and 559 unique transcripts that were significantly (P ≤0.05) up and downregulated in RES (+Fv/C) and SUS (+Fv/C), respectively. KEGG pathway enrichment analysis identified coumarin and furanocoumarin biosynthesis, phenylpropanoid biosynthesis, and plant-pathogen interaction pathways as being highly enriched with specific genes involved in cell wall modifications in the RES genotype, whereas the SUS genotype mainly displayed a repressed plant-pathogen interaction pathway and did not show any enriched cell wall genes. In particular, cell wall-related gene expression showed a higher level in RES than in SUS under Fv infection. Analysis of DEG abundance made it possible to identify transcripts involved in response to abiotic and biotic stresses, biosynthetic and catabolic processes, pectin biosynthesis, phenylpropanoid metabolism, and cell wall biosynthesis and organization. Root histological analysis in RES showed an increase in lignified cells in the sclerenchymatous hypodermis zone during Fv infection. Discussion: These differences in the cell wall and lignification could be related to an enhanced degradation of the root hairs and the epidermis cell wall in SUS, as was visualized by SEM. These findings reveal that components of the root cell wall are important against Fv infection and possibly other soilborne phytopathogens.

Differential Expression of miRNAs Involved in Response to Candidatus Liberibacter asiaticus Infection in Mexican Lime at Early and Late Stages of Huanglongbing Disease.

Huanglongbing (HLB) is one of the most destructive diseases threatening citriculture worldwide. This disease has been associated with α-proteobacteria species, namely Candidatus Liberibacter. Due to the unculturable nature of the causal agent, it has been difficult to mitigate the disease, and nowadays a cure is not available. MicroRNAs (miRNAs) are key regulators of gene expression, playing an essential role in abiotic and biotic stress in plants including antibacterial responses. However, knowledge derived from non-model systems including Candidatus Liberibacter asiaticus (CLas)-citrus pathosystem remains largely unknown. In this study, small RNA profiles from Mexican lime (Citrus aurantifolia) plants infected with CLas at asymptomatic and symptomatic stages were generated by sRNA-Seq, and miRNAs were obtained with ShortStack software. A total of 46 miRNAs, including 29 known miRNAs and 17 novel miRNAs, were identified in Mexican lime. Among them, six miRNAs were deregulated in the asymptomatic stage, highlighting the up regulation of two new miRNAs. Meanwhile, eight miRNAs were differentially expressed in the symptomatic stage of the disease. The target genes of miRNAs were related to protein modification, transcription factors, and enzyme-coding genes. Our results provide new insights into miRNA-mediated regulation in C. aurantifolia in response to CLas infection. This information will be useful to understand molecular mechanisms behind the defense and pathogenesis of HLB.

Transcriptional regulation of cell growth and reprogramming of systemic response in wheat (Triticum turgidum subsp. durum) seedlings by Bacillus paralicheniformis TRQ65.

MAIN CONCLUSIONS: Bacillus paralicheniformis TRQ65 reprograms the gene expression patterns associated with systemic response to potentially facilitate its colonization and stimulate cell growth and plant biomass. Plant growth-promoting rhizobacteria (PGPR) carry out numerous mechanisms that enhance growth in seedlings, such as nutrient solubilization, phytohormone production, biocontrol activity, and regulation of induced systemic resistance (ISR) and acquired systemic resistance (ASR). Bacillus paralicheniformis TRQ65 is a biological and plant growth-promoting bacterium isolated from wheat (Triticum turgidum subsp. durum) rhizosphere. In this study, we performed a transcriptomic analysis of wheat seedlings inoculated with the native rhizobacterium Bacillus paralicheniformis TRQ65 (1 × 107 cells∙g -1 of soil) at early development stages (GS15). A morphometrical assay was carried out to confirm growth promotion and after the cultivation period, TRQ65 was re-isolated to define inoculum persistence. Inoculated seedlings showed a significant (P < 0.05) increase in shoot length (93.48%) and dry weight in both shoot (117.02%) and root (48.33%) tissues; also, the strain persisted in the soil at 1.4 × 107 UFC∙g-1 of soil. A total of 228 differentially expressed genes (DEGs) (FDR < 0.05 and |log2 fold change|≥ 1.3) were observed in response to TRQ65 inoculation, of which 185 were down-regulated and 43 were up-regulated. The transcriptional patterns were characterized by the regulation of multidimensional cell growth (ROS, Ca+2 channel, and NADPH oxidases activity), suppression of defense mechanism (PR proteins, PDFs, ROS, transcription factors), induction of central stimuli receptors (RALF, WAK, MAPK), carbohydrate metabolism (invertase activity) and phytohormone-related transport (ABCG transporter and AAAP). These results suggest that B. paralicheniformis TRQ65 is a promising bioinoculant agent for increasing wheat growth and development by reprogramming ISR and ASR simultaneously, suppressing defense mechanisms and inducing central stimuli response.