Biology subjects

Whiting, M.

Publications and source records attributed to Whiting, M..

3 recordsLinked to original sources

bioRxiv2025

PHO2 suppresses arbuscular mycorrhizal symbiosis in high phosphate conditions

Arbuscular mycorrhizal (AM) symbiosis is an ancient relationship formed between most plants and Glomeromycotina fungi, typically in response to phosphate (Pi) limitation in soils. By hosting these fungi in their roots, plants extend their access to essential mineral nutrients and water beyond the rhizosphere, while providing the fungus with carbon in return. This mutualistic symbiosis presents a promising tool for enhancing sustainability in agriculture, as it not only supports plant nutrition but also immunity and wider soil health. However, achieving high crop yields currently relies on supplementing plants with excess Pi, which suppresses AM symbiosis. We found that this suppression is mediated by a key negative regulator of the Pi starvation response (PSR) in rice (Oryza sativa), Phosphate overaccumulator 2 (PHO2). PHO2 encodes an E2 ubiquitin-conjugating enzyme which targets various proteins involved in the PSR in Pi-sufficient conditions for protein degradation. Here we report that pho2 mutants of rice and Nicotiana benthamiana retained high AM fungal colonisation even in high Pi conditions. Our transcriptomic analysis of uninoculated rice roots revealed that pho2 mutants are less sensitive to Pi treatment and retain susceptibility to AM symbiosis by maintaining expression of a core set of AM-related genes gating the early stage AM fungal entry, such as genes involved in strigolactone biosynthesis, LysM-containing plant receptors for fungal molecules, and components of the common symbiosis signalling pathway (CSSP). Furthermore, isotope tracing using 33P and phosphate transporter (PHT1) gene expression patterns collectively suggest enhanced direct and symbiotic Pi overaccumulation in pho2 mutant leaves. Together, our data reveal a new role for PHO2, as a negative regulator of AM colonisation and symbiotic Pi accumulation in shoots.

plant biology↗

bioRxiv2020

Characterization of ethylene-inducible pedicel-fruit abscission zone formation in non-climacteric sweet cherry (Prunus avium L.)

Harvesting of sweet cherry (Prunus avium L.) fruit is a labor-intensive process. Mechanical harvesting of sweet cherry fruit is feasible; however, it is dependent on the formation of an abscission zone at the fruit-pedicel junction. The natural propensity for pedicel-fruit abscission zone (PFAZ) formation varies by cultivar, and the general molecular basis for PFAZ formation is not well characterized. In this study, ethylene-inducible change in pedicel fruit retention force (PFRF) was recorded in a developmental time course with a concomitant analysis of the PFAZ transcriptome from three sweet cherry cultivars. In Skeena, mean PFRF for both control and treatment fruit dropped below the 0.40kg-force (3.92N) threshold for mechanical harvesting and indicating the formation of a discrete PFAZ. In Bing, mean PFRF for both control and treatment groups decreased over time. However, a mean PFRF conducive to mechanical harvesting was achieved only in the ethylene-treated fruit. While in Chelan the mean PFRF of the control and treatment groups did not meet the threshold required for efficient mechanical harvesting. Transcriptome analysis of the PFAZ followed by the functional annotation, differential expression analysis, and gene ontology (GO) enrichment analyses of the data facilitated the identification of phytohormone-responsive and abscission-related transcripts as well as processes that exhibited differential expression and enrichment in a cultivar-dependent manner over the developmental time-course. Additionally, read alignment-based variant calling revealed several short variants in differentially expressed genes, associated with enriched gene ontologies and associated metabolic processes, lending potential insight into the genetic basis for different abscission responses between the cultivars. These results provide genetic targets for induction or inhibition of PFAZ formation, depending on the desire to harvest the fruit with or without the stem attached. Understanding the genetic mechanisms underlying the development of the PFAZ will inform future cultivar development while laying a foundation for mechanized sweet cherry harvest.

plant biology↗

bioRxiv2019

Codon Pairs are Phylogenetically Conserved: Codon pairing as a new class of phylogenetic characters

Identical codon pairing and co-tRNA codon pairing increase translational efficiency within genes when two codons that encode the same amino acid are located within a ribosomal window. By examining both identical and co-tRNA codon pairing across 23 423 species, we determined that both pairing techniques are phylogenetically informative across all domains of life using either an alignment-free or parsimony framework. We also determined that conserved codon pairing typically has a smaller window size than the length of a ribosome. We also analyzed frequencies of codon pairing for each codon to determine which codons are most likely to pair. The alignment-free method does not require orthologous gene annotations and recovers species relationships that are comparable to other alignment-free techniques. Parsimony generally recovers phylogenies that are more congruent with the established phylogenies than the alignment-free method. However, four of the ten taxonomic groups do not have sufficient ortholog annotations and are therefore recoverable using only the alignment-free methods. Since the recovered phylogenies using only codon pairing largely match established phylogenies and are comparable to other algorithms, we propose that codon pairing biases are phylogenetically conserved and should be considered in conjunction with current techniques in future phylogenomic studies. Furthermore, the phylogenetic conservation of codon pairing indicates that codon pairing plays a greater role in the speciation process than previously acknowledged.\n\nAvailabilityAll scripts used to recover and compare phylogenies, including documentation and test files, are freely available on GitHub at https://github.com/ridgelab/codon_pairing.

evolutionary biology↗