Biology subjects

Simpson, C. G.

Publications and source records attributed to Simpson, C. G..

6 recordsLinked to original sources

bioRxiv2026

EoRNA2: Autonomous Data Discovery and Processing for Databasing of Gene Expression Data

We describe a major new release of the EoRNA database, a gene expression database for barley based on public data, first published in 20211. EoRNA v.2 (https://ics.hutton.ac.uk/eorna2/index.html) features an order of magnitude more samples and is based on a new automated workflow of sample discovery and processing which has enabled a dramatic scale-up the original database. EoRNA v.2 also features a major rebuild of the web user interface with rich new functionality. All infrastructure-related code and database schemas and web components are now species agnostic and publicly available for reuse with other taxa. A dedicated new reference transcript dataset has been created for EoRNA v.2 which is largely based on the recently published barley pan-transcriptome and represents the most comprehensive dataset of its kind to date.

bioinformatics↗

bioRxiv2025

Transcriptional response to Phytophthora root rot in raspberry identifies RiABP19, a Germin-like protein (GLP) gene with a putative role in resistance

Most phytophthora root rot (PRR) outbreaks in symptomatic commercially cultivated raspberry varieties are associated with the prevalence of Phytophthora rubi. Reduced availability of chemical actives and the persistent presence of Phytophthora oospores in the soil contribute to its devastating impact on raspberry-growing regions. In this study, we examined the variation in root morphology in two contrasting raspberry cultivars, Latham (PRR resistant) and Glen Moy (PRR susceptible). We performed RNA-sequencing on Latham roots challenged with P. rubi, to study the transcriptomic response and uncover mechanisms underpinning resistance. We established a new raspberry reference transcript dataset that allowed quantification of raspberry root gene expression. Transcripts significantly upregulated in Latham challenged with P. rubi, included many with characterised roles in resistance, such as Pathogenesis-related proteins and a Germin-like protein, designated RiABP19. The homologous Glen Moy RiABP19 gene showed no differential transcriptional response to PRR infection, indicating a resistance cultivar-specific induction signature following PRR challenge. Three-dimensional structural modelling predicts that RiABP19 contains conserved active sites implicated in auxin-binding and superoxide dismutase activity and can form a homo-hexamer like true germins. Co-immunoprecipitation assays confirmed that RiABP19 can form both homo- and heterodimers in planta. Virus-induced gene silencing of RiABP19 orthologs of in the model plant Nicotiana benthamiana strongly impacts immune signalling, enhancing Phytophthora infestans colonization and attenuating resistance and cell death triggered by the tomato Cf4/Avr4 interaction. These findings suggest that RiABP19 functions as a positive regulator of immunity and may represent a target for future crop improvement in raspberries.

plant biology↗

bioRxiv2024

Silencing of a raspberry homologue of VRN1 is associated with disruption of dormancy induction and misregulation of subsets of dormancy-associated genes.

Winter dormancy is a key process in the phenology of temperate perennials. The changing climate is severely impacting its course leading to economic losses in agriculture. A better understanding of the underlying mechanisms, as well as the genetic basis of the different responses, are necessary for the development of climate-resilient cultivars. This study aims to provide an insight into winter dormancy in red raspberry (Rubus idaeus L). We report the transcriptomic profiles during dormancy in two raspberry cultivars with contrasting responses. The cultivar Glen Ample showed a typical perennial phenology, whereas Glen Dee registered consistent dormancy dysregulation, exhibiting active growth and flowering out of season. RNA-seq combined with weighted gene co-expression network analysis (WGCNA) highlighted gene clusters in both genotypes that exhibited time-dependent expression profiles, Functional analysis of Glen Ample gene clusters highlighted the significance of the cell and structural development prior to dormancy entry as well the role of genetic and epigenetic processes such as RNAi and DNA methylation in regulating gene expression. On the contrary, dormancy release in Glen Ample was associated with upregulation of transcripts associated with the resumption of metabolism, nucleic acid biogenesis and processing signal response pathways. Many of the processes occurring in Glen Ample were dysregulated in Glen Dee and twenty-eight transcripts exhibiting time-dependent expression in Ample that also had an Arabidopsis homologue were not found in all samples from Glen Dee. These included a gene with homology to Arabidopsis VRN1 (RiVRN1.1) that exhibited a sharp decline in expression following dormancy induction in Glen Ample. Characterisation of the gene region in the Glen Dee genome revealed two large insertions upstream of the ATG start codon. We propose that non-expression of a specific VRN1 homologue in Glen Dee causes dormancy misregulation as a result of inappropriate expression of a subset of genes that are directly or indirectly regulated by RiVRN1.1. HIGHLIGHTThe raspberry cultivar Glen Dee exhibits aberrant winter dormancy status associated with insertions in the upstream promoter region of a VRN1 (RiVRN1.1) homologue that silence expression, allowing the identification of dormancy-associated genetic modules that are regulated by RiVRN1.1.

plant biology↗

bioRxiv2020

EoRNA, a barley gene and transcript abundance database.

A high-quality, barley gene reference transcript dataset (BaRTv1.0), was used to quantify gene and transcript abundances from 22 RNA-seq experiments, covering 843 separate samples. Using the abundance data we developed a Barley Expression Database (EoRNA* - Expression of RNA) to underpin a visualisation tool that displays comparative gene and transcript abundance data on demand as transcripts per million (TPM) across all samples and all the genes. EoRNA provides gene and transcript models for all of the transcripts contained in BaRTV1.0, and these can be conveniently identified through either BaRT or HORVU gene names, or by direct BLAST of query sequences. Browsing the quantification data reveals cultivar, tissue and condition specific gene expression and shows changes in the proportions of individual transcripts that have arisen via alternative splicing. TPM values can be easily extracted to allow users to determine the statistical significance of observed transcript abundance variation among samples or perform meta analyses on multiple RNA-seq experiments. * Eorna is the Scottish Gaelic word for Barley

genomics↗

bioRxiv2020

Nonsense mediated RNA decay factor UPF1 is critical for post-transcriptional and translational gene regulation in Arabidopsis

Nonsense mediated RNA decay (NMD) is an evolutionary conserved RNA control mechanism that has also been implicated in the broader regulation of gene expression. Nevertheless, a role for NMD in genome regulation has not been fully assessed, partially because NMD inactivation is lethal in many organisms. Here, we performed in depth comparative analysis of Arabidopsis mutants lacking key proteins involved in different steps of NMD. We observed that UPF3, UPF1, and SMG7 have different impacts on NMD and the Arabidopsis transcriptome, with UPF1 having the biggest effect. Transcriptome assembly using stringent pipeline in UPF1-null plants revealed genome wide changes in alternative splicing, including switches in mRNA variants, suggesting a role for UPF1 in splicing. We further found that UPF1 inactivation leads to translational repression, manifested by a global shift in mRNAs from polysomes to monosomes and a downregulation of genes involved in translation and ribosome biogenesis. Despite this global change, NMD targets and low-expressed mRNAs with short half-lives were enriched in polysomes, indicating that UPF1 specifically suppresses the translation of aberrant RNAs. Particularly striking was an increase in the translation of TIR domain-containing, nucleotide-binding, leucine-rich repeat (TNL) immune receptors. The regulation of TNLs via UPF1/NMD-mediated mRNA stability and translational de-repression offers a dynamic mechanism for the rapid activation of TNLs in response to pathogen attack.

molecular biology↗

bioRxiv2019

BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq

BackgroundTime consuming computational assembly and quantification of gene expression and splicing analysis from RNA-seq data vary considerably. Recent fast non-alignment tools such as Kallisto and Salmon overcome these problems, but these tools require a high quality, comprehensive reference transcripts dataset (RTD), which are rarely available in plants.\n\nResultsA high-quality, non-redundant barley gene RTD and database (Barley Reference Transcripts - BaRTv1.0) has been generated. BaRTv1.0, was constructed from a range of tissues, cultivars and abiotic treatments and transcripts assembled and aligned to the barley cv. Morex reference genome (Mascher et al., 2017). Full-length cDNAs from the barley variety Haruna nijo (Matsumoto et al., 2011) determined transcript coverage, and high-resolution RT-PCR validated alternatively spliced (AS) transcripts of 86 genes in five different organs and tissue. These methods were used as benchmarks to select an optimal barley RTD. BaRTv1.0-Quantification of Alternatively Spliced Isoforms (QUASI) was also made to overcome inaccurate quantification due to variation in 5 and 3 UTR ends of transcripts. BaRTv1.0-QUASI was used for accurate transcript quantification of RNA-seq data of five barley organs/tissues. This analysis identified 20,972 significant differentially expressed genes, 2,791 differentially alternatively spliced genes and 2,768 transcripts with differential transcript usage.\n\nConclusionA high confidence barley reference transcript dataset consisting of 60,444 genes with 177,240 transcripts has been generated. Compared to current barley transcripts, BaRTv1.0 transcripts are generally longer, have less fragmentation and improved gene models that are well supported by splice junction reads. Precise transcript quantification using BaRTv1.0 allows routine analysis of gene expression and AS.

genomics↗