Toby E. Newman
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View article: Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen
Recombination and transposition drive genomic structural variation potentially impacting life history traits in a host-generalist fungal plant pathogen Open
Background An understanding of plant pathogen evolution is important for sustainable management of crop diseases. Plant pathogen populations must maintain adequate heritable phenotypic variability to survive. Polymorphisms ≥ 50 bp, known a…
View article: Gut microbiome metagenomic sequences of honey bees ( <i>Apis mellifera</i> ) exposed to crops
Gut microbiome metagenomic sequences of honey bees ( <i>Apis mellifera</i> ) exposed to crops Open
The gut microbiome of the European honey bee ( Apis mellifera ) is vital to its health, yet large-scale studies are scarce. We present metagenomic sequencing data from 180 samples collected near and far from eight crops across Canada over …
View article: Cryptic recombination and transposition drive structural variation to shape genomic plasticity and life history traits in a host generalist fungal plant pathogen
Cryptic recombination and transposition drive structural variation to shape genomic plasticity and life history traits in a host generalist fungal plant pathogen Open
Background An understanding of plant pathogen evolution is important for sustainable management of crop diseases. Plant pathogen populations must maintain adequate heritable phenotypic variability to survive. Polymorphisms >= 50 bp, known …
View article: The complex relationship between disease resistance and yield in crops
The complex relationship between disease resistance and yield in crops Open
Summary In plants, growth and defence are controlled by many molecular pathways that are antagonistic to one another. This results in a ‘growth‐defence trade‐off’, where plants temporarily reduce growth in response to pests or diseases. Du…
View article: Genetic dissection of domestication traits in interspecific chickpea populations
Genetic dissection of domestication traits in interspecific chickpea populations Open
Chickpea ( Cicer arietinum ) is a pulse crop that provides an integral source of nutrition for human consumption. The close wild relatives Cicer reticulatum and Cicer echinospermum harbor untapped genetic diversity that can be exploited by…
View article: Genome-wide identification of Sclerotinia sclerotiorum small RNAs and their endogenous targets
Genome-wide identification of Sclerotinia sclerotiorum small RNAs and their endogenous targets Open
Background Several phytopathogens produce small non-coding RNAs of approximately 18–30 nucleotides (nt) which post-transcriptionally regulate gene expression. Commonly called small RNAs (sRNAs), these small molecules were also reported to …
View article: The broad host range pathogen <i>Sclerotinia sclerotiorum</i> produces multiple effector proteins that induce host cell death intracellularly
The broad host range pathogen <i>Sclerotinia sclerotiorum</i> produces multiple effector proteins that induce host cell death intracellularly Open
Sclerotinia sclerotiorum is a broad host range necrotrophic fungal pathogen, which causes disease on many economically important crop species. S. sclerotiorum has been shown to secrete small effector proteins to kill host cells and acquire…
View article: The evolutionary and molecular features of the broad‐host‐range plant pathogen <i>Sclerotinia sclerotiorum</i>
The evolutionary and molecular features of the broad‐host‐range plant pathogen <i>Sclerotinia sclerotiorum</i> Open
Sclerotinia sclerotiorum is a pathogenic fungus that infects hundreds of plant species, including many of the world's most important crops. Key features of S. sclerotiorum include its extraordinary host range, preference for dicotyledonous…
View article: Identification of Sclerotinia stem rot resistance quantitative trait loci in a chickpea (Cicer arietinum) recombinant inbred line population
Identification of Sclerotinia stem rot resistance quantitative trait loci in a chickpea (Cicer arietinum) recombinant inbred line population Open
Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum, is one of the most economically devastating diseases in chickpea (Cicer arietinum L.). No complete resistance is available in chickpea to this disease, and the inheritance of …
View article: Modeling first order additive × additive epistasis improves accuracy of genomic prediction for sclerotinia stem rot resistance in canola
Modeling first order additive × additive epistasis improves accuracy of genomic prediction for sclerotinia stem rot resistance in canola Open
The fungus Sclerotinia sclerotiorum infects hundreds of plant species including many crops. Resistance to this pathogen in canola ( Brassica napus L. subsp. napus ) is controlled by numerous quantitative trait loci (QTL). For such polygeni…
View article: Analysis of Differentially Expressed Sclerotinia Sclerotiorum Genes During the Interaction With Moderately Resistant and Highly Susceptible Chickpea Lines
Analysis of Differentially Expressed Sclerotinia Sclerotiorum Genes During the Interaction With Moderately Resistant and Highly Susceptible Chickpea Lines Open
Background : Sclerotinia sclerotiorum , the cause of Sclerotinia stem rot (SSR), is a host generalist necrotrophic fungus that can cause major yield losses in chickpea ( Cicer arietinum ) production. This study used RNA sequencing to condu…
View article: Additional file 12 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen
Additional file 12 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen Open
Additional file 12: Supplementary Table 9. Primers used in this study.
View article: Additional file 7 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen
Additional file 7 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen Open
Additional file 7: Supplementary Table 4. Genes targeted by conserved miRNAs only in the infected sample.
View article: Additional file 10 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen
Additional file 10 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen Open
Additional file 10: Supplementary Table 7. GO term enrichment analysis of 5918 transcripts possibly regulated by pha-siRNAs based on psRNA target analysis.
View article: Additional file 4 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen
Additional file 4 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen Open
Additional file 4: Supplementary Table 1. All small RNA biogenesis loci identified using the program Sho:rtStack.
View article: Additional file 5 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen
Additional file 5 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen Open
Additional file 5: Supplementary Table 2. Cleaved products of the 73 miRNA families. All targets identified using degradome sequencing in infected and mock samples are included.
View article: Additional file 9 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen
Additional file 9 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen Open
Additional file 9: Supplementary Table 6. Known and novel miRNAs identified in this study.
View article: Additional file 4 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen
Additional file 4 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen Open
Additional file 4: Supplementary Table 1. All small RNA biogenesis loci identified using the program Sho:rtStack.
View article: Additional file 7 of Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines
Additional file 7 of Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines Open
Additional file 7: Table S7. Description of temporal S. sclerotiorum in planta upregulated genes involved in cell wall degradation during chickpea infection relative to in vitro control (P. Adj. <0.05; LogFC ≥ 2).
View article: Additional file 11 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen
Additional file 11 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen Open
Additional file 11: Supplementary Table 8. GO term enrichment analysis of psRNA target-predicted targets of 1601 targets of miR1885-triggered ta-siRNAs.
View article: Additional file 11 of Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines
Additional file 11 of Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines Open
Additional file 11: Table S11. Predicted S. sclerotiorum putative effector candidate’s upregulated at some timepoint MR and S lines infection relative to in vitro control (P. Adj. <0.05; LogFC ≥ 2).
View article: Additional file 11 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen
Additional file 11 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen Open
Additional file 11: Supplementary Table 8. GO term enrichment analysis of psRNA target-predicted targets of 1601 targets of miR1885-triggered ta-siRNAs.
View article: Additional file 1 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen
Additional file 1 of fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen Open
Additional file 1: Supplementary File 1. Output of the software PHAS Tank showing candidate PHAS loci.
View article: Additional file 5 of Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines
Additional file 5 of Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines Open
Additional file 5: Table S5. Enrichment analysis of S. sclerotiorum upregulated genes during interaction with moderately resistant (MR) and susceptible (S) chickpea lines at 6, 12, 24, and 72 hours post inoculation relative to in vitro con…
View article: Additional file 2 of Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines
Additional file 2 of Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines Open
Additional file 2: Table S2. List of differentially expressed S. sclerotiorum genes during the interaction with moderately resistant (MR) and susceptible (S) chickpea lines at 6, 12, 24, 48 and 72 hours post inoculation ( P. Adj. <0.05; Lo…
View article: Additional file 9 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen
Additional file 9 of Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen Open
Additional file 9: Supplementary Table 6. Known and novel miRNAs identified in this study.