Biology subjects

Harper, A. L.

Publications and source records attributed to Harper, A. L..

3 recordsLinked to original sources

bioRxiv2025

DNA methylation mediates transcriptional stability and transposon-driven trans-regulation under drought in wheat

Bread wheat (Triticum aestivum) is a major component of half the global populations diet, but increasingly frequent droughts threaten its productivity and food security. While massive transcriptional reprogramming under drought in wheat seedlings is well characterised, DNA methylations contribution remains poorly understood. Using paired whole-genome bisulphite sequencing (WGBS) and RNA-seq before and after drought stress in wheat landraces, we probed the nuanced role of DNA methylation in the drought response, uncovering antagonistic trends between cytosine contexts and novel mechanisms, with the ROS1a family potentially playing a key demethylation role under drought. Examination of gene methylation profiles revealed that gene body methylation was strongly positively correlated with gene expression but negatively with stress responsiveness, simultaneously identifying that gene body differentially methylated regions (DMRs) targeted stress-associated genes. Many DMR-associated genes maintained consistent transcription under stress, suggesting a stabilising role for DNA methylation. Most DMRs localised to intergenic regions and transposable elements (TEs), with the ancient LTR retrotransposon RLX_famc9 emerging as a critical target of differential methylation under drought. We propose a model in which the RLX_famc9 family, enriched in differential methylation and exhibiting substantial sequence similarity to drought-responsive genes, is involved in the trans-regulation of stress-associated genes under control conditions through the generation of regulatory siRNA precursors, a mechanism suppressed by drought-inducible hypermethylation. Our findings suggest an intricate regulatory role of DNA methylation under drought, with genic DNA methylation promoting high, stable expression, ROS1a glycosylases coordinating targeted demethylation, and methylation-controlled TEs modulating the expression of downstream genes in trans.

plant biology↗

bioRxiv2025

Assembly and annotation of Solanum dulcamara and Solanum nigrum plant genomes, two nightshades with different susceptibilities to Ralstonia solanacearum

To understand why close wild plant relatives of crops, such as Solanum dulcamara, are resistant to Ralstonia solanacearum we need genetic resources to perform comparative studies and identify key genes and pathways. We de-novo assembled and annotated the genome of resistant S. dulcamara and susceptible Solanum nigrum plants using a hybrid approach including Oxford Nanopore Technologies and Illumina sequencing. Comparative genomic analysis was then performed to find differences between the genome of S. dulcamara and other susceptible Solanaceous species including potato, tomato, aubergine, and S. nigrum and one susceptible and one resistant S. americanum accession. We identified genes associated with auxin-transport only in S. dulcamara and a collection of pattern recognition receptors (PRRs) was identified in orthogroups only found in plant species with resistant/tolerant phenotype, suggesting novel plant receptors in these accessions that may improve recognition of pathogen-associated molecular patterns (PAMPs) associated with R. solanacearum. We also identified differences in methylation frequency across the gene bodies in both species, which may be associated with epigenetic regulation of resistance. Future work should assess the functional role of these PRRs during bacterial wilt development to determine if they could offer potential novel targets for breeding improved wilt resistance.

plant biology↗

bioRxiv2024

Fraxinus excelsior updated long-read genome reveals the importance of MADS-box genes in tolerance mechanisms against ash dieback

Ash dieback caused by the fungus Hymenoscyphus fraxineus has devastated the European ash tree population since it arrived in Europe in 1992. Great effort has been put into breeding programmes to increase the genetic diversity of ash trees and find heritable genetic markers associated with resistance, or tolerance mechanisms, to ash dieback. To facilitate identification of molecular markers, we used Oxford Nanopore Technologies combined with Illumina sequencing to obtain an accurate and contiguous ash genome. We used this genome to reanalyse transcriptome data from a Danish ash panel of 182 tree accessions. Using associative transcriptomics, we identified 175 gene expression markers (GEMs), including 11 genes annotated as dormancy MADS-box transcription factors which are associated with ash bud dormancy, flowering and senescence. We hypothesize that tolerant trees both break dormancy earlier in the year by increasing the expression of flowering-related SOC1 MADS-box and reducing the expression of SVP-like MADS-box, whilst also accelerating senescence by increasing the expression of JOINTLESS MADS-box genes. DNA methylation differences in the promoters of MADS-box genes between one tolerant and one susceptible tree indicate potential epigenetic regulation of these traits. Article SummaryAsh dieback has devastated European ash tree populations. To aid in breeding programmes focused on finding solutions against this pathogen, we have assembled a new ash genome. This new genome helped us to identify genes related to tree biological life cycles, expressed differently in tolerant and susceptible trees. For the first time, we have also discovered that susceptible and tolerant trees showed different DNA methylation frequencies in those genes, suggesting epigenetic regulation. DNA methylation can turn on/off gene expression without changing the DNA sequence. These genes, and their regulatory elements, are ideal targets during breeding programmes combating this pathogen.

plant biology↗