Transcriptomic profile of tobacco in response to Tomato zonate spot orthotospovirus infection

Transcriptome Dynamics in Triticum aestivum Genotypes Associated with Resistance against the Wheat Dwarf Virus

Wheat dwarf virus (WDV) is one of the most important pathogens of cereal crops worldwide. To understand the molecular mechanism of resistance, here we investigated the comparative transcriptome of wheat genotypes with different levels of resistance (Svitava and Fengyou 3) and susceptibility (Akteur) to WDV. We found a significantly higher number of differentially expressed transcripts (DETs) in the susceptible genotype than in the resistant one (e.g., Svitava). The number of downregulated transcripts was also higher in the susceptible genotype than in the resistant one (Svitava) and the opposite was true for the upregulated transcripts. Further functional analysis of gene ontology (GO) enrichment identified a total of 114 GO terms for the DETs. Of these, 64 biological processes, 28 cellular components and 22 molecular function GO terms were significantly enriched. A few of these genes appear to have a specific expression pattern related to resistance or susceptibility to WDV infection. Validation of the expression pattern by RT-qPCR showed that glycosyltransferase was significantly downregulated in the susceptible genotype compared to the resistant genotypes after WDV infection, while CYCLIN-T1-3, a regulator of CDK kinases (cyclin-dependent kinase), was upregulated. On the other hand, the expression pattern of the transcription factor (TF) MYB (TraesCS4B02G174600.2; myeloblastosis domain of transcription factor) was downregulated by WDV infection in the resistant genotypes compared to the susceptible genotype, while a large number of TFs belonging to 54 TF families were differentially expressed due to WDV infection. In addition, two transcripts (TraesCS7A02G341400.1 and TraesCS3B02G239900.1) were upregulated with uncharacterised proteins involved in transport and regulation of cell growth, respectively. Altogether, our findings showed a clear gene expression profile associated with resistance or susceptibility of wheat to WDV. In future studies, we will explore the regulatory network within the same experiment context. This knowledge will broaden not only the future for the development of virus-resistant wheat genotypes but also the future of genetic improvement of cereals for resilience and WDV-resistance breeding.

Effects of the noncoding subgenomic RNA of red clover necrotic mosaic virus in virus infection

In recent years, a new class of viral noncoding subgenomic RNA (ncsgRNA) has been identified. This RNA is generated as a stable degradation product via an exoribonuclease-resistant RNA (xrRNA) structure, which blocks the progression of 5′→3′ exoribonuclease on viral RNAs in infected cells. Here, we assess the effects of the ncsgRNA of red clover necrotic mosaic virus (RCNMV), called SR1f, in infected plants. We demonstrate the following: (i) the absence of SR1f reduces symptoms and decreases viral RNA accumulation in Nicotiana benthamiana and Arabidopsis thaliana plants; (ii) SR1f has an essential function other than suppression of RNA silencing; and (iii) the cytoplasmic exoribonuclease involved in mRNA turnover, XRN4, is not required for SR1f production or virus infection. A comparative transcriptomic analysis in N. benthamiana infected with wild-type RCNMV or an SR1f-deficient mutant RCNMV revealed that wild-type RCNMV infection, which produces SR1f and much higher levels of virus, has a greater and more significant impact on cellular gene expression than the SR1f-deficient mutant. Upregulated pathways include plant hormone signaling, plant-pathogen interaction, MAPK signaling, and several metabolic pathways, while photosynthesis-related genes were downregulated. We compare this to host genes known to participate in infection by other tombusvirids. Viral reads revealed a 10- to 100-fold ratio of positive to negative strand, and the abundance of reads of both strands mapping to the 3′ region of RCNMV RNA1 support the premature transcription termination mechanism of synthesis for the coding sgRNA. These results provide a framework for future studies of the interactions and functions of noncoding RNAs of plant viruses.

IMPORTANCE Knowledge of how RNA viruses manipulate host and viral gene expression is crucial to our understanding of infection and disease. Unlike viral protein-host interactions, little is known about the control of gene expression by viral RNA. Here, we begin to address this question by investigating the noncoding subgenomic RNA (ncsgRNA) of red clover necrotic mosaic virus (RCNMV), called SR1f. Similar exoribonuclease-resistant RNAs of flaviviruses are well studied, but the roles of plant viral ncsgRNAs, and how they arise, are poorly understood. Surprisingly, we find the likely exonuclease candidate, XRN4, is not required to generate SR1f, and we assess the effects of SR1f on virus accumulation and symptom development. Finally, we compare the effects of infection by wild-type RCNMV versus an SR1f-deficient mutant on host gene expression in Nicotiana benthamiana, which reveals that ncsgRNAs such as SR1f are key players in virus-host interactions to facilitate productive infection.

Effect of the AM Fungus Sieverdingia tortuosa on Common Vetch Responses to an Anthracnose Pathogen

Colletotrichum lentis Damm causes anthracnose in Vicia sativa L, otherwise known as common vetch. It was first reported in China in 2019. This study evaluates the effects of the arbuscular mycorrhizal (AM) fungus Sieverdingia tortuosa (N.C. Schenck & G.S. Sm.) Błaszk., Niezgoda, & B.T. Goto on growth and disease severity in common vetch. Our main finding is that the AM fungus increased root biomass and reduced anthracnose severity of common vetch. Responses correlated with defense, such as chitinase activity, polyphenol oxidase (PPO) activity, the concentrations of jasmonic acid and proline, and the expression of resistance-related genes (e.g., upregulated "signal transduction," "MAPK signaling pathway," "chitinase activity," "response to stress," and the KEGG pathways "phenylpropanoid biosynthesis," "MAPK signaling pathways," and "plant-pathogen interactions"), were also affected These findings provide insight into the mechanism by which this AM fungus regulates the defense response of common vetch to C. lentis.

Arbuscular mycorrhizal fungus alleviates alfalfa leaf spots caused by Phoma medicaginis revealed by RNA-seq analysis

AIMS

One of the major limitations to the production of alfalfa (Medicago sativa) is the fungus Phoma medicaginis, which infects alfalfa and causes leaf spots. This study aims to understand alfalfa's response to P. medicaginis infection, the colonization of arbuscular mycorrhizal fungus (AMF) and the effect of AMF on plant-pathogen interactions.

METHODS AND RESULTS

Transcriptome analysis (RNA-seq) was used to identify differentially expressed genes (DEGs) in alfalfa infected by P. medicaginis and colonized by AMF Rhizophagus intraradices. AMF ameliorated the effects of P. medicaginis infection on alfalfa by reducing leaf spot incidence and disease index by 39·48 and 56·18% respectively. Inoculation with pathogen and AMF induced the activity of defence pathways, including peroxidase (POD), polyphenol oxidase activities and jasmonic acid (JA), salicylic acid concentration. Plants showed differential expression of P. medicaginis resistance-related genes, including genes belonging to pathogenesis-related (PR) proteins, chitinase activity, flavonoid biosynthesis, phenylpropanoid biosynthesis, glutathione metabolism, phenylalanine metabolism and photosynthesis. Inoculation with AMF led to changes in the expression of genes involved in PR proteins, chitinase activity, phenylalanine metabolism and photosynthesis.

CONCLUSION

The physiological and transcriptional changes caused by P. medicaginis infection in non-mycorrhizal and mycorrhizal alfalfa provides crucial information for understanding AMF's association with pathogenic systems.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study showed that AMF alleviated alfalfa leaf spots demonstrating that AMF can serve as a biocontrol strategy for alfalfa disease management.

Differential gene expression and physiological changes during acute or persistent plant virus interactions may contribute to viral symptom differences

Viruses have different strategies for infecting their hosts. Fast and acute infections result in the development of severe symptoms and may cause the death of the plant. By contrast, in a persistent interaction, the virus can survive within its host for a long time, inducing only mild symptoms. In this study, we investigated the gene expression changes induced in CymRSV-, crTMV-, and TCV-infected Nicotiana benthamiana and in PVX- and TMV-U1-infected Solanum lycopersicum plants after the systemic spread of the virus by two different high-throughput methods: microarray hybridization or RNA sequencing. Using these techniques, we were able to clearly differentiate between acute and persistent infections. We validated the gene expression changes of selected genes by Northern blot hybridization or by qRT-PCR. We show that, in contrast to persistent infections, the drastic shut-off of housekeeping genes, downregulation of photosynthesis-related transcripts and induction of stress genes are specific outcomes with acute infections. We also show that these changes are not a consequence of host necrosis or the presence of a viral silencing suppressor. Thermal imaging data and chlorophyll fluorescence measurements correlated very well with the molecular changes. We believe that the molecular and physiological changes detected during acute infections mostly contribute to virus symptom development. The observed characteristic physiological changes associated with economically more dangerous acute infections could serve as a basis for the elaboration of remote monitoring systems suitable for detecting developing virus infections in crops. Moreover, as molecular and physiological changes are characteristics of different types of virus lifestyles, this knowledge can support risk assessments of recently described novel viruses.

Non-Structural Protein NSm of Tomato Spotted Wilt Virus Is an Avirulence Factor Recognized by Resistance Genes of Tobacco and Tomato via Different Elicitor Active Sites

Tomato spotted wilt virus (TSWV) is one of the most destructive viral pathogens of plants. Recently, a single dominant gene conferring complete resistance to TSWV (RTSW) was identified in Nicotina alata and introgressed into cultivated tobacco (N. tabacum). However, whether the TSWV carries an avirulence (Avr) factor directed against RTSW remains obscure. In the present study, we identified the non-structural protein (NSm), the movement protein of TSWV, which is an RTSW-specific Avr factor, by using two different transient expression systems. Using amino acid (aa) substitution mutants, we demonstrated the ability to induce RTSW-mediated hypersensitive response (HR) of NSm is independent of its movement function. Moreover, key substitutions (C118Y and T120N), a 21-aa viral effector epitope, and different truncated versions of NSm, which are responsible for the recognition of the Sw-5b resistance gene of tomato, were tested for their ability to trigger HR to TSWV in tobacco. Together, our results demonstrated that RTSW-mediated resistance is triggered by NSm in the same way as by Sw-5b, however, via different elicitor active sites. Finally, an Avr gene-based diagnostic approach was established and used to determine the presence and effectiveness of resistance genes in tobacco.

De novo transcriptomic assembly and mRNA expression patterns of Botryosphaeria dothidea infection with mycoviruses chrysovirus 1 (BdCV1) and partitivirus 1 (BdPV1)

BACKGROUND

Pear ring rot, caused by Botryosphaeria species, is responsible for substantial economic losses by causing severe recession of pear tree growth in China. Mycovirus-mediated hypovirulence in plant pathogenic fungi is a crucial biological method to control fungal diseases.

METHODS

We conducted a large-scale and comprehensive transcriptome analysis to identify mRNA in B. dothidea in response to mycovirus. De novo sequencing technology from four constructed libraries of LW-C (Botryosphaeria dothidea chrysovirus 1, BdCV1), LW-P (Botryosphaeria dothidea partitivirus 1, BdPV1), LW-CP (LW-1 strain infection with BdCV1 and BdPV1), and Mock (free virus) was used to investigate and compare gene expression changes in B.dothidea strains infected with mycovirus.

RESULTS

In total, 30,058 Unigenes with an average length of 2128 bp were obtained from 4 libraries of B. dothidea strains. These were annotated to specify their classified function. We demonstrate that mRNAs of B. dothidea strains in response to mycovirus are differentially expressed. In total, 5598 genes were up-regulated and 3298 were down-regulated in the LW-CP group, 4468 were up-regulated and 4291 down-regulated in the LW-C group, and 2590 were up-regulated and 2325 down-regulated in the LW-P group. RT-qPCR was used to validate the expression of 9 selected genes. The B. dothidea transcriptome was more affected by BdCV1 infection than BdPV1. We conducted GO enrichment analysis to characterize gene functions regulated by B. dothidea with mycovirus infection. These involved metabolic process, cellular process, catalytic activity, transporter activity, signaling, and other biological pathways. KEGG function analysis demonstrated that the enriched differentially expressed genes are involved in metabolism, transcription, signal transduction, and ABC transport. mRNA is therefore involved in the interaction between fungi and mycovirus. In addition, changes in differential accumulation levels of cp and RdRp of BdCV1 and BdPV1 in B. dothidea strains were evaluated, revealing that the accumulation of BdCV1 and BdPV1 is related to the phenotype and virulence of B. dothidea strain LW-1.

CONCLUSIONS

The identification and analysis of mRNAs from B. dothidea was first reported at the transcriptome level. Our analysis provides further insight into the interaction of B. dothidea strains infection with chrysovirus 1 (BdCV1) and partitivirus 1 (BdPV1) at the transcriptome level.

NS3 Protein from Rice stripe virus affects the expression of endogenous genes in Nicotiana benthamiana

BACKGROUND

Rice stripe virus (RSV) belongs to the genus Tenuivirus. It is transmitted by small brown planthoppers in a persistent and circulative-propagative manner and causes rice stripe disease (RSD). The NS3 protein of RSV, encoded by the viral strand of RNA3, is a viral suppressor of RNA silencing (VSR). NS3 plays a significant role in viral infection, and NS3-transgenic plants manifest resistance to the virus.

METHODS

The stability and availability of NS3 produced by transgenic Nicotiana benthamiana was investigated by northern blot analysis. The accumulation of virus was detected by western blot analysis. Transcriptome sequencing was used to identify differentially expressed genes (DEGs) in NS3-transgenic N. benthamiana.

RESULTS

When the host plants were inoculated with RSV, symptoms and viral accumulation in NS3-transgenic N. benthamiana were reduced compared with the wild type. Transcriptome analysis identified 2533 differentially expressed genes (DEGs) in the NS3-transgenic N. benthamiana, including 597 upregulated genes and 1936 downregulated genes. These DEGs were classified into three Gene Ontology (GO) categories and were associated with 43 GO terms. KEGG pathway analysis revealed that these DEGs were involved in pathways associated with ribosomes (ko03010), photosynthesis (ko00195), photosynthesis-antenna proteins (ko00196), and carbon metabolism (ko01200). More than 70 DEGs were in these four pathways. Twelve DEGs were selected for RT-qPCR verification and subsequent analysis. The results showed that NS3 induced host resistance by affecting host gene expression.

CONCLUSION

NS3, which plays dual roles in the process of infection, may act as a VSR during RSV infection, and enable viral resistance in transgenic host plants. NS3 from RSV affects the expression of genes associated with ribosomes, photosynthesis, and carbon metabolism in N. benthamiana. This study enhances our understanding of the interactions between VSRs and host plants.