A5074833005- Molecular Biology Techniques and Applications
- Plant Disease Resistance and Genetics
- Wheat and Barley Genetics and Pathology
- RNA modifications and cancer
- Legume Nitrogen Fixing Symbiosis
- RNA Research and Splicing
- Plant tissue culture and regeneration
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Plant-Microbe Interactions and Immunity
- Plant Pathogens and Fungal Diseases
- Plant Pathogenic Bacteria Studies
- Plant Taxonomy and Phylogenetics
- Chromosomal and Genetic Variations
- Genome Rearrangement Algorithms
- Plant Molecular Biology Research
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Photosynthetic Processes and Mechanisms
- Plant Gene Expression Analysis
- Sexual Differentiation and Disorders
- Agriculture, Plant Science, Crop Management
- Phytoplasmas and Hemiptera pathogens
- Yeasts and Rust Fungi Studies
- Cancer-related molecular mechanisms research
- Plant Genetic and Mutation Studies
James Hutton Institute
2018-2024
University of Dundee
2021-2024
University of Exeter
2014
A prerequisite to exploiting soil microbes for sustainable crop production is the identification of plant genes shaping microbiota composition in rhizosphere, interface between roots and soil. Here, we use metagenomics information as an external quantitative phenotype map host genetic determinants rhizosphere wild domesticated genotypes barley, fourth most cultivated cereal globally. We identify a small number loci with major effect on communities. One those, designated QRMC-3HS, emerges...
Accurate and comprehensive annotation of transcript sequences is essential for quantification differential gene expression analysis. Single-molecule long-read sequencing technologies provide improved integrity structures including alternative splicing, transcription start polyadenylation sites. However, accuracy significantly affected by errors, mRNA degradation, or incomplete cDNA synthesis.We present a new Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over...
SUMMARY Accurate characterisation of splice junctions (SJs) as well transcription start and end sites in reference transcriptomes allows precise quantification transcripts from RNA‐seq data, enables detailed investigations transcriptional post‐transcriptional regulation. Using novel computational methods a combination PacBio Iso‐seq Illumina short‐read sequences 20 diverse tissues conditions, we generated comprehensive highly resolved barley transcript dataset the European 2‐row spring...
Abstract Barley genomic resources are increasing rapidly, with the publication of a barley pangenome as one latest developments. Two-row spring cultivars intensely studied they source high-quality grain for malting and distilling. Here we provide data from European two-row population containing 209 different genotypes registered UK market between 1830 to 2014. The dataset encompasses RNA-sequencing six tissues across range developmental stages, phenotypic datasets two consecutive years...
Xanthomonas vasicola pathovar vasculorum (Xvv) is the bacterial agent causing gumming disease in sugarcane. Here, we compare complete genome sequences for five isolates of Xvv originating from sugarcane and one maize. This identified two distinct types lipopolysaccharide synthesis gene clusters among isolates: similar to that axonopodis citri (Xac) probably ancestral type, while other those sugarcane-inhabiting species, sacchari. Four six harboured Xac plasmid, pXAC47, showed a Type-IV pilus...
Abstract Barley genomic resources are increasing rapidly, with the publication of a barley pangenome as one latest developments. Two-row spring cultivars intensely studied they source high-quality grain for malting and distilling. Here we provide data from European two-row population containing 209 different genotypes registered UK market between 1830 to 2014. The dataset encompasses RNA-sequencing six tissues across range developmental stages, phenotypic datasets two consecutive years...
It is increasingly apparent that although different genotypes within a species share "core" genes, they also contain variable numbers of "specific" genes and structures are only present in subset individuals. Using common reference genome may thus lead to loss genotype-specific information the assembled Reference Transcript Dataset (RTD) generation erroneous, incomplete or misleading transcriptomics analysis results. In this study, we RTD (sRTD) reference-based (cRTD) from RNA-seq data...
ABSTRACT Accurate characterization of splice junctions as well transcription start and end sites in reference transcriptomes allows precise quantification transcripts from RNA-seq data enable detailed investigations transcriptional post-transcriptional regulation. Using novel computational methods a combination PacBio Iso-seq Illumina short read sequences 20 diverse tissues conditions, we generated comprehensive highly resolved barley transcript dataset (RTD) the European 2-row spring...
Abstract Background Accurate and comprehensive annotation of transcript sequences is essential for quantification differential gene expression analysis. Single molecule long read sequencing technologies provide improved integrity structures including alternative splicing, transcription start polyadenylation sites. However, accuracy significantly affected by errors, mRNA degradation or incomplete cDNA synthesis. Results We present a new Arabidopsis thaliana Reference Transcript Dataset 3...
Abstract A prerequisite to exploiting soil microbes for sustainable crop production is the identification of plant genes shaping microbiota composition in rhizosphere, interface between roots and soil. Here we use metagenomics information as an external quantitative phenotype map host genetic determinants rhizosphere wild domesticated genotypes barley, fourth most cultivated cereal globally. We identify a small number loci with major effect on communities. One those, designated QRMC-3HS ,...
Abstract High quality transcriptome assembly using short reads from RNA-seq data still heavily relies upon reference-based approaches, of which the primary step is to align a single reference genome haploid sequence. However, it increasingly apparent that while different genotypes within species share “core” genes, they also contain variable numbers “specific” genes are only present subset individuals. Using common may thus lead loss genotype-specific information in assembled transcript...