Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii

Background: Solanum commersonii is a wild potato species that exhibits high tolerance to both biotic and abiotic stresses and has been used as a source of genes for introgression into cultivated potato. Among the interesting features of S. commersonii is resistance to the bacterial wilt caused by Ralstonia solanacearum, one of the most devastating bacterial diseases of crops. - Results: In this study, we used deep sequencing of S. commersonii RNA (RNA-seq) to analyze the below-ground plant transcriptional responses to R. solanacearum. While a majority of S. commersonii RNA-seq reads could be aligned to the Solanum tuberosum Group Phureja DM reference genome sequence, we identified 2,978 S. commersonii novel transcripts through assembly of unaligned S. commersonii RNA-seq reads. We also used RNA-seq to study gene expression in pathogen-challenged roots of S. commersonii accessions resistant (F118) and susceptible (F97) to the pathogen. Expression profiles obtained from read mapping to the S. tuberosum reference genome and the S. commersonii novel transcripts revealed a differential response to the pathogen in the two accessions, with 221 (F118) and 644 (F97) differentially expressed genes including S. commersonii novel transcripts in the resistant and susceptible genotypes. Interestingly, 22.6% of the F118 and 12.8% of the F97 differentially expressed genes had been previously identified as responsive to biotic stresses and half of those up-regulated in both accessions had been involved in plant pathogen responses. Finally, we compared two different methods to eliminate ribosomal RNA from the plant RNA samples in order to allow dual mapping of RNAseq reads to the host and pathogen genomes and provide insights on the advantages and limitations of each technique. - Conclusions: Our work catalogues the S. commersonii transcriptome and strengthens the notion that this species encodes specific genes that are differentially expressed to respond to bacterial wilt. In addition, a high proportion of S. commersonii-specific transcripts were altered by R. solanacearum only in F118 accession, while phythormone-related genes were highly induced in F97, suggesting a markedly different response to the pathogen in the two plant accessions studied

Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii

Background: Solanum commersonii is a wild potato species that exhibits high tolerance to both biotic and abiotic stresses and has been used as a source of genes for introgression into cultivated potato. Among the interesting features of S. commersonii is resistance to the bacterial wilt caused by Ralstonia solanacearum, one of the most devastating bacterial diseases of crops. Results: In this study, we used deep sequencing of S. commersonii RNA (RNA-seq) to analyze the below-ground plant transcriptional responses to R. solanacearum. While a majority of S. commersonii RNA-seq reads could be aligned to the Solanum tuberosum Group Phureja DM reference genome sequence, we identified 2,978 S. commersonii novel transcripts through assembly of unaligned S. commersonii RNA-seq reads. We also used RNA-seq to study gene expression in pathogen-challenged roots of S. commersonii accessions resistant (F118) and susceptible (F97) to the pathogen. Expression profiles obtained from read mapping to the S. tuberosum reference genome and the S. commersonii novel transcripts revealed a differential response to the pathogen in the two accessions, with 221 (F118) and 644 (F97) differentially expressed genes including S. commersonii novel transcripts in the resistant and susceptible genotypes. Interestingly, 22.6% of the F118 and 12.8% of the F97 differentially expressed genes had been previously identified as responsive to biotic stresses and half of those up-regulated in both accessions had been involved in plant pathogen responses. Finally, we compared two different methods to eliminate ribosomal RNA from the plant RNA samples in order to allow dual mapping of RNAseq reads to the host and pathogen genomes and provide insights on the advantages and limitations of each technique. Conclusions: Our work catalogues the S. commersonii transcriptome and strengthens the notion that this species encodes specific genes that are differentially expressed to respond to bacterial wilt. In addition, a high proportion of S. commersonii-specific transcripts were altered by R. solanacearum only in F118 accession, while phythormone-related genes were highly induced in F97, suggesting a markedly different response to the pathogen in the two plant accessions studied

Functional Identification of Valerena-1,10-diene Synthase, a Terpene Synthase Catalyzing a Unique Chemical Cascade in the Biosynthesis of Biologically Active Sesquiterpenes in Valeriana officinalis

Valerian is an herbal preparation from the roots of Valeriana officinalis used as an anxiolytic and sedative and in the treatment of insomnia. The biological activities of valerian are attributed to valerenic acid and its putative biosynthetic precursor valerenadiene, sesquiterpenes, found in V. officinalis roots. These sesquiterpenes retain an isobutenyl side chain whose origin has been long recognized as enigmatic because a chemical rationalization for their biosynthesis has not been obvious. Using recently developed metabolomic and transcriptomic resources, we identified seven V. officinalis terpene synthase genes (VoTPSs), two that were functionally characterized as monoterpene synthases and three that preferred farnesyl diphosphate, the substrate for sesquiterpene synthases. The reaction products for two of the sesquiterpene synthases exhibiting root-specific expression were characterized by a combination of GC-MS and NMR in comparison to the terpenes accumulating in planta. VoTPS7 encodes for a synthase that biosynthesizes predominately germacrene C, whereas VoTPS1 catalyzes the conversion of farnesyl diphosphate to valerena-1,10-diene. Using a yeast expression system, specific labeled [13C]acetate, and NMR, we investigated the catalytic mechanism for VoTPS1 and provide evidence for the involvement of a caryophyllenyl carbocation, a cyclobutyl intermediate, in the biosynthesis of valerena-1,10-diene. We suggest a similar mechanism for the biosynthesis of several other biologically related isobutenyl-containing sesquiterpenes

Transcriptome analysis of symptomatic and recovered leaves of geminivirus-infected pepper (<it>Capsicum annuum</it>)

<p>Abstract</p> <p>Background</p> <p>Geminiviruses are a large and important family of plant viruses that infect a wide range of crops throughout the world. The <it>Begomovirus</it> genus contains species that are transmitted by whiteflies and are distributed worldwide causing disease on an array of horticultural crops. Symptom remission, in which newly developed leaves of systemically infected plants exhibit a reduction in symptom severity (recovery), has been observed on pepper (<it>Capsicum annuum</it>) plants infected with <it>Pepper golden mosaic virus</it> (PepGMV). Previous studies have shown that transcriptional and post-transcriptional gene silencing mechanisms are involved in the reduction of viral nucleic acid concentration in recovered tissue. In this study, we employed deep transcriptome sequencing methods to assess transcriptional variation in healthy (mock), symptomatic, and recovered pepper leaves following PepGMV infection.</p> <p>Results</p> <p>Differential expression analyses of the pepper leaf transcriptome from symptomatic and recovered stages revealed a total of 309 differentially expressed genes between healthy (mock) and symptomatic or recovered tissues. Computational prediction of differential expression was validated using quantitative reverse-transcription PCR confirming the robustness of our bioinformatic methods. Within the set of differentially expressed genes associated with the recovery process were genes involved in defense responses including pathogenesis-related proteins, reactive oxygen species, systemic acquired resistance, jasmonic acid biosynthesis, and ethylene signaling. No major differences were found when compared the differentially expressed genes in symptomatic and recovered tissues. On the other hand, a set of genes with novel roles in defense responses was identified including genes involved in histone modification. This latter result suggested that post-transcriptional and transcriptional gene silencing may be one of the major mechanisms involved in the recovery process. Genes orthologous to the <it>C. annuum</it> proteins involved in the pepper-PepGMV recovery response were identified in both <it>Solanum lycopersicum</it> and <it>Solanum tuberosum</it> suggesting conservation of components of the viral recovery response in the Solanaceae.</p> <p>Conclusion</p> <p>These data provide a valuable source of information for improving our understanding of the underlying molecular mechanisms by which pepper leaves become symptomless following infection with geminiviruses. The identification of orthologs for the majority of genes differentially expressed in recovered tissues in two major solanaceous crop species provides the basis for future comparative analyses of the viral recovery process across related taxa.</p

Comparative Transcriptome Analysis of Two Contrasting Maize Inbred Lines Provides Insights on Molecular Mechanisms of Stalk Rot Resistance

Maize stalk rot caused by Fusarium graminearum can lead to severe losses and accumulation of mycotoxins with detrimental effects on livestock health. Because few management strategies are available, the development of resistant varieties is considered the most cost-effective way to control the disease. However, the stalk-tissue-specific mechanisms underlying resistance to F. graminearum remain poorly understood, although it is believed to be strongly influenced by environmental factors. In this study, we performed a temporal transcriptome analysis of two maize inbred lines with contrasting responses to stalk rot using gene expression profiling. We observed differential downregulation of gene expression during the first 2 weeks in a resistant inbred line inoculated with F. graminearum. Time-course gene ontology enrichment analysis suggests that resistance may be caused by a modulation of gene expression associated with redox homeostasis, hormone biosynthesis, cytoskeleton activity, and cell wall remodeling. We validated our gene expression profiling data by measuring the expression of 10 differentially expressed genes using quantitative reverse-transcription PCR. Our analyses also revealed the effect of two environmental conditions with contrasting temperatures and relative humidity on the resistant phenotype and gene expression. This research expands our knowledge of molecular events underlying resistance to stalk rot and the effect of environmental conditions on the disease interaction. Our findings can be exploited for the development of resistant varieties.[Graphic: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license

An Experimental Investigation on the Rock Mechanical Behavior of Synthetic Layered Systems and Load-Cycling of its Individual Constituents

Many authors already made an attempt to understand the effect of load-cycling on material strength and the evolution of elastic parameters. However, until now there was no study on the effect of load-cycling on the evolution of elastic parameters over the complete stress strain curve, i.e. the linear elastic regime, the fracturing regime, and the fractured regime. In addition, none of the authors focussed on the effect of load-cycling on fracture network improvement. Although previous studies already showed that elastic moduli of layered systems may be determined from properties and volume fractions of its individual constituents, there is no study done on the relation between rock mechanical properties, i.e. strains and yield or failure stresses, of (synthetic) layered systems and its constituents. Furthermore, in the literature no description is found on fracture characteristics of a (synthetic) layered system. Hence, an experimental investigation is conducted on the rock mechanical behavior of synthetic layered systems subjected to increased-loading and the effect of load-cycling on its individual constituents’ rock strength, elastic parameter evolution, and fracture network improvement. The increased-loading and load-cycling rock mechanical experiments are unconfined compression tests performed at room temperature. When comparing two of the same rock materials with a maximum deviation of 1% in porosity, load-cycling leads to failure at much lower stress levels when compared to increased-loading. Within the linear elastic regime, load-cycling returns a stabilized Young’s modulus which is always larger than its envelope value, while the Poisson’s ratio of the last load cycle coincides with its envelope value. Load-cycling generates an improved fracture network when compared to increased-loading. Characteristics of the improved fracture network are the increased fracture densities and the more uniform distribution of the fractures over the volume of the material. For vertically stacked synthetic layered systems, the elastic moduli and strains can be well-predicted by the Reuss Average which uses the average rock mechanical properties and volume fractions of the individual constituents. In contrast, for synthetic layered systems the stress level at failure point is independent of the volume fractions of its constituents and is observed to be in the vicinity of its weakest constituent. Despite this, fractures are still observed in the strongest constituents. The fracture propagation through the strongest constituent is ascribed to be due to amplified stress concentrations at the tip of the propagating fracture. However, from 2-layered systems it is observed that fracture propagation through the strongest constituent depends on the thickness of the weakest constituent. At the constituents’ boundary in synthetic layered systems, there is no offset in fracture path when going from one constituent to another nor is there a sudden change in aperture. However, there is a change in fracture inclination in a way such that the fracture inclinations of the individual constituents are respected. In addition, fractures in synthetics include cataclastics over the high porous intervals (±10-25%), while the same fracture is clean over the low porous intervals (±0,5-5%).Civil Engineering and GeosciencesGeoscience & EngineeringPetroleum Engineerin

Wabasso_transcript_assemblies_all_isoforms.fasta

RNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar Wabasso. This file includes all transcript isoforms

Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii

Background: Solanum commersonii is a wild potato species that exhibits high tolerance to both biotic and abiotic stresses and has been used as a source of genes for introgression into cultivated potato. Among the interesting features of S. commersonii is resistance to the bacterial wilt caused by Ralstonia solanacearum, one of the most devastating bacterial diseases of crops. - Results: In this study, we used deep sequencing of S. commersonii RNA (RNA-seq) to analyze the below-ground plant transcriptional responses to R. solanacearum. While a majority of S. commersonii RNA-seq reads could be aligned to the Solanum tuberosum Group Phureja DM reference genome sequence, we identified 2,978 S. commersonii novel transcripts through assembly of unaligned S. commersonii RNA-seq reads. We also used RNA-seq to study gene expression in pathogen-challenged roots of S. commersonii accessions resistant (F118) and susceptible (F97) to the pathogen. Expression profiles obtained from read mapping to the S. tuberosum reference genome and the S. commersonii novel transcripts revealed a differential response to the pathogen in the two accessions, with 221 (F118) and 644 (F97) differentially expressed genes including S. commersonii novel transcripts in the resistant and susceptible genotypes. Interestingly, 22.6% of the F118 and 12.8% of the F97 differentially expressed genes had been previously identified as responsive to biotic stresses and half of those up-regulated in both accessions had been involved in plant pathogen responses. Finally, we compared two different methods to eliminate ribosomal RNA from the plant RNA samples in order to allow dual mapping of RNAseq reads to the host and pathogen genomes and provide insights on the advantages and limitations of each technique. - Conclusions: Our work catalogues the S. commersonii transcriptome and strengthens the notion that this species encodes specific genes that are differentially expressed to respond to bacterial wilt. In addition, a high proportion of S. commersonii-specific transcripts were altered by R. solanacearum only in F118 accession, while phythormone-related genes were highly induced in F97, suggesting a markedly different response to the pathogen in the two plant accessions studied

Data from: Generation of transcript assemblies and identification of single nucleotide polymorphisms from seven lowland and upland cultivars of switchgrass

Switchgrass (Panicum virgatum) is a North American perennial prairie species that has been used as a rangeland and forage crop and has recently been targeted as a potential biofuel feedstock species. Switchgrass, which occurs as tetraploid and octoploid forms, is classified into lowland or upland ecotypes that differ in growth phenotypes and adaptation to distinct habitats. Using RNA-sequencing reads derived from crown, young shoot and leaf tissues, we generated sequence data from seven switchgrass cultivars, three lowland and four upland, to enable comparative analyses between switchgrass cultivars and to identify single nucleotide polymorphisms (SNPs) for use in breeding and genetic analysis. We also generated individual transcript assemblies for each of the cultivars. Transcript data indicate that subgenomes of octoploid switchgrass are not substantially different from subgenomes of tetraploids as expected for an autopolyploid origin of switchgrass octoploids. Using RNA-sequencing reads aligned to the switchgrass Release 0 AP13 reference genome, we identified 1,305,976 high-confidence SNPs. Of these SNPs, 438,464 were unique to lowland cultivars, but only 12,002 were found in all lowlands. Conversely, 723,678 SNPs were unique to upland cultivars with only 34,665 observed in all uplands. Comparison of our high-confidence transcriptome-derived SNPs with SNPs previously identified in a genotyping-by-sequencing study of an association panel revealed limited overlap between the two methods, highlighting the utility of transcriptome-based SNP discovery in augmenting genome diversity polymorphism datasets. The transcript and SNP data described here provide a useful resource for switchgrass gene annotation and marker-based analyses of the switchgrass genome