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Maize bisulfite coupled sequence capture (SeqCap-Epi-v2) probe design. Contained in the dataset are descriptions of the "target” regions, which are the bait regions corresponding to the sequence capture probes. Also contained are the... more
Maize bisulfite coupled sequence capture (SeqCap-Epi-v2) probe design. Contained in the dataset are descriptions of the "target” regions, which are the bait regions corresponding to the sequence capture probes. Also contained are the coordinates of the target region in the B73 v4 maize genome build (Jiao et al. 2017); the strand orientation of the target; the original “target” probe capture region for the maize v2 genome build. This submission also describes the “specific” regions of interest within the captured “target” bait regions; the coordinates of the specific region in the B73 v4 maize genome build (Jiao et al. 2017); and the original “specific” region of interest for the maize v2 genome build.
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In plants, the molecular function(s) of the nucleus-localized 5′-3′ EXORIBONUCLEASES (XRNs) are unclear; however, their activity is reported to have a significant effect on gene expression and SAL1-mediated retrograde signaling. Using... more
In plants, the molecular function(s) of the nucleus-localized 5′-3′ EXORIBONUCLEASES (XRNs) are unclear; however, their activity is reported to have a significant effect on gene expression and SAL1-mediated retrograde signaling. Using parallel analysis of RNA ends, we documented a dramatic increase in uncapped RNA substrates of the XRNs in both sal1 and xrn2xrn3 mutants. We found that a major consequence of reducing SAL1 or XRN activity was RNA Polymerase II 3′ read-through. This occurred at 72% of expressed genes, demonstrating a major genome-wide role for the XRN-torpedo model of transcription termination in Arabidopsis (Arabidopsis thaliana). Read-through is speculated to have a negative effect on transcript abundance; however, we did not observe this. Rather, we identified a strong association between read-through and increased transcript abundance of tandemly orientated downstream genes, strongly correlated with the proximity (less than 1,000 bp) and expression of the upstream gene. We observed read-through in the proximity of 903 genes up-regulated in the sal1-8 retrograde signaling mutant; thus, this phenomenon may account directly for up to 23% of genes up-regulated in sal1-8. Using APX2 and AT5G43770 as exemplars, we genetically uncoupled read-through loci from downstream genes to validate the principle of read-through-mediated mRNA regulation, providing one mechanism by which an ostensibly posttranscriptional exoribonuclease that targets uncapped RNAs could modulate gene expression.
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Research Interests: Genetics, Biology, Epigenetics, Genome Wide Association Studies (GWAS), Medicine, and 13 moreFeatures, Biological Sciences, Environmental Sciences, Patterns, Mutation, Rice, Methylation, DNA methylation, Drought tolerance, Single Nucleotide Polymorphism, Genetic variation, Complex, and demethylation
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SUMMARYThe DOMAINS REARRANGED METHYLTRANSFERASEs (DRMs) are crucial for RNA‐directed DNA methylation (RdDM) in plant species. Setaria viridis is a model monocot species with a relatively compact genome that has limited transposable... more
SUMMARYThe DOMAINS REARRANGED METHYLTRANSFERASEs (DRMs) are crucial for RNA‐directed DNA methylation (RdDM) in plant species. Setaria viridis is a model monocot species with a relatively compact genome that has limited transposable element (TE) content. CRISPR‐based genome editing approaches were used to create loss‐of‐function alleles for the two putative functional DRM genes in S. viridis to probe the role of RdDM. Double mutant (drm1ab) plants exhibit some morphological abnormalities but are fully viable. Whole‐genome methylation profiling provided evidence for the widespread loss of methylation in CHH sequence contexts, particularly in regions with high CHH methylation in wild‐type plants. Evidence was also found for the locus‐specific loss of CG and CHG methylation, even in some regions that lack CHH methylation. Transcriptome profiling identified genes with altered expression in the drm1ab mutants. However, the majority of genes with high levels of CHH methylation directly surrounding the transcription start site or in nearby promoter regions in wild‐type plants do not have altered expression in the drm1ab mutant, even when this methylation is lost, suggesting limited regulation of gene expression by RdDM. Detailed analysis of the expression of TEs identified several transposons that are transcriptionally activated in drm1ab mutants. These transposons are likely to require active RdDM for the maintenance of transcriptional repression.
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Research Interests: Genetics, Nonlinear dynamics, Plant Biology, Biology, Cell Biology, and 15 moreOxidative Stress, Medicine, Plant Science, Gene expression, Gene Silencing, Global Analysis, Chlorophyll Fluorescence, DNA methylation, Light, Gene, Arabidopsis, Parallel Analysis, Plant cell, Biochemistry and cell biology, and Gene expression profiling
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Research Interests: Genetics, Biology, Medicine, Multidisciplinary, DNA methylation, and 3 moreGenome, Gene, and Chromatin
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Research Interests: Genetics, Biology, Medicine, DNA methylation, Structural Variation, and 3 moreGenome, Chromatin, and Epigenome
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Key to the success of plants is their ability to co-ordinate timely responses to stressful environments using intricate intracellular signaling mechanisms. Most, if not all stress signaling cascades register in the nucleus and trigger... more
Key to the success of plants is their ability to co-ordinate timely responses to stressful environments using intricate intracellular signaling mechanisms. Most, if not all stress signaling cascades register in the nucleus and trigger transcriptional changes that are fundamental for acclimation to stress. Over the last decade it has also become apparent that chloroplasts operate as sensors of prevailing environmental conditions, perceiving abiotic stress and orchestrating the remodelling of the nuclear transcriptome. Nevertheless, these retrograde signals may also have roles beyond bilateral chloroplast-to-nucleus communication when considered in the context of the broader complexity of a cell. Accordingly, identifying the signaling mechanisms and understanding how intracellular signals are translated into expression changes is essential. Throughout a plant's life history, stress also alters subsequent plant responses. As a result, the prospect of epigenetic memory is an evocative subject with exciting research and agronomic possibilities. Yet the more common strategy employed by plants is likely to be recovery and resetting, underpinned by post transcriptional processes and RNA metabolism. This thesis demonstrates the existence of the 'SAL1-PAP-XRN' retrograde signaling pathway in Arabidopsis thaliana (Arabidopsis), providing mechanistic insight into the functions of retrograde signaling during stress. Key to this model is the discovery that the signal is transmitted and interpreted via the nucleotide 3'-phosphoadenosine 5'-phosphate (PAP) and the 5'-3' exoribonucleases (XRNs) respectively. Evidence that key changes in gene expression are mediated by regulation of RNA Polymerase II read-through and activation of downstream genes is also presented, contributing to our understanding of the transmission and specificity of the PAP signal. Beyond a linear retrograde signaling pathway, it is also demonstrated that PAP-signaling is entwined with other components in the complex networks of the eukaryotic cell. In partic [...]
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Research Interests: Genetics, Biology, Epigenetics, Epigenomics, Mutagenesis, and 4 moreCRISPR, CAS, Chromatin, and Genome Editing
Research Interests: Genetics, Plant Biology, Biology, Medicine, Mutagenesis, and 4 moreCRISPR, CAS, Genome, and Genome Editing
DNA methylation is a chromatin modification that has generally been associated with gene silencing or heterochromatin. Plants have mechanisms to allow for the stable inheritance of DNA methylation through mitosis or meiosis. This creates... more
DNA methylation is a chromatin modification that has generally been associated with gene silencing or heterochromatin. Plants have mechanisms to allow for the stable inheritance of DNA methylation through mitosis or meiosis. This creates the potential for DNA methylation to provide epigenetic inheritance for traits in maize and other crops. Epigenetics refers to heritable transmission of information that is not solely attributable to DNA sequence. Several examples of epigenetic inheritance were first described in maize including paramutation, imprinting, and transposable element inactivation. There is evidence that DNA methylation is associated with each of these epigenetic phenomena. In addition, natural variation for epigenetic states may contribute substantially to variation among maize inbreds and could be an important source of variation for crop improvement. Advances in our understanding of the molecular mechanisms controlling DNA methylation in Arabidopsis have provided clues to the genes and pathways likely to be important in maize. Recent technological developments have provided the opportunity to characterize the genome-wide distribution of DNA methylation in the maize genome. This has provided insights into the patterns of DNA methylation in plant species with large, complex genomes and has led to the identification of potential cryptic genomic information that is silenced by DNA methylation. We will summarize current understanding of the mechanisms that regulate methylation and factors that influence variation and stability of the maize methylome.
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Incursions of the Queensland fruit fly Bactrocera tryoni (Qfly) into areas without permanent Qfly populations present serious threats to the Australian and New Zealand horticultural industries. Identifying the origins of recent incursions... more
Incursions of the Queensland fruit fly Bactrocera tryoni (Qfly) into areas without permanent Qfly populations present serious threats to the Australian and New Zealand horticultural industries. Identifying the origins of recent incursions will help reduce future threats by enabling the targeting of problematic incursion routes for more stringent quarantine protocols. Here we present an analytical framework based on supervised and unsupervised machine learning to identify the origins and recent population history of incursion individuals. Our framework is based on a recently developed reference dataset of genome-wide markers for 35 Qfly populations from across the ranges of Qfly and the related taxon Bactrocera aquilonis (NTfly). We apply our framework to recent incursions into New Zealand, Tasmania and South Australia. Two distinct Qfly sources were identified for incursions into New Zealand (total 18 individuals), one from the east coast of Australia and one from New Caledonia. All eight recent incursion collections analysed (total 85 individuals) from South Australia and Tasmania most likely originated from just one of six clusters of populations in our reference database, Qfly from the east coast of Australia. None were found to originate from clusters containing NTfly or Qfly/NTfly hybrids in the Northern Territory or north Western Australia. Several, but not all, of the collections showed signals of small founding population size and two Tasmanian collections each included individuals apparently derived from three different sources within the east coast of Australia. In total, several more incursion events were detected than previously known, although some were founded by relatively few individuals.
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Fusarium wilt of banana is a devastating disease that has decimated banana production worldwide. Host resistance to Fusarium oxysporum f. sp. cubense (Foc), the causal agent of this disease, is genetically dissected in this study using... more
Fusarium wilt of banana is a devastating disease that has decimated banana production worldwide. Host resistance to Fusarium oxysporum f. sp. cubense (Foc), the causal agent of this disease, is genetically dissected in this study using two Musa acuminata ssp. malaccensis segregating populations segregating for Foc Tropical (TR4) and Subtropical (STR4) race 4 resistance. Marker loci and trait association using 11 SNP-based PCR markers allowed the candidate region to be delimited to a 12.9 cM genetic interval corresponding to a 959 kb region on Chromosome 3 of ‘DH-Pahang’ reference assembly v4. Within this region, there is a cluster of pattern recognition receptors, namely leucine rich repeat ectodomain containing receptor-like protein kinases, cysteine-rich cell wall associated protein kinases, and leaf rust 10 disease-resistance locus receptor-like proteins positioned in an interspersed arrangement. Their transcript levels were rapidly upregulated in the resistant but not in suscept...
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The stability of mRNA is an important determinant of its abundance and, consequently, protein production. There has been extensive research on the pathways governing mRNA stability and translation, however, it is unclear the extent to... more
The stability of mRNA is an important determinant of its abundance and, consequently, protein production. There has been extensive research on the pathways governing mRNA stability and translation, however, it is unclear the extent to which these processes are modulated by environmental conditions. We previously modelled rapid recovery gene down-regulation (RRGD) following light stress in Arabidopsis thaliana (Arabidopsis) using mathematical calculations to account for transcription in order to predict half-lives and led to the hypothesis of recovery-specific transcript destabilisation. Here, we test this hypothesis by quantifying changes in transcription, mRNA stability, and translation in leaves of mature Arabidopsis undergoing light stress and recovery and investigate processes regulating transcript abundance and fate. Compared to juvenile plants from prior work, here we find that stability is altered for a range of transcripts that encode proteins involved in post-transcriptiona...
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Additional file 1. Supplementary Methods. Supplementary Reference. Supplementary Table S1. Supplementary Table S2.
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Additional file 2: Table S1. Summary of data generated in this study. Table S2. DMRs with significant SNPs. Table S3. Associations between DMR and gene expression in kernel and leaf. Table S4. Associations between DMRs and metabolic traits.
Additional file 1: Figure S1. DMR validation. Comparison between DNA methylation of the capture based assay and the whole genome bisulfite sequencing assay (WGBS) in DMRs between B73 and Mo17. Figure S2. Distribution of DMR size and... more
Additional file 1: Figure S1. DMR validation. Comparison between DNA methylation of the capture based assay and the whole genome bisulfite sequencing assay (WGBS) in DMRs between B73 and Mo17. Figure S2. Distribution of DMR size and genomic features. Figure S3. DNA methylation can reflect genetic distances. Figure S4. DNA methylation levels in DMRs are different among maize subgroups. Figure S5. Summary of DMRs associated with SNPs and structure variants (SVs). Figure S6. The associations between gene expression and DNA methylation. Figure S7. DMRs affect gene expression as a cause. Figure S8. Mendelian randomization analysis. Figure S9. The association between DMR and metabolic trait chr di-C.