Biology subjects

Deng, X. W.

Publications and source records attributed to Deng, X. W..

4 recordsLinked to original sources

bioRxiv2026

WheatPanRef: a unified linear pan-reference genome for wheat genomics

Linear reference genomes provide coordinates for read mapping, variant discovery and multi-omics data integration, yet assembly-specific coordinate systems limit data reuse, particularly in the large, repetitive and polyploid wheat genome. Here, we present WheatPanRef, a scalable linear pan-reference and coordinate framework that integrates wheat sequence diversity within a stable coordinate system. We reconciled independent Chinese Spring assemblies by resolving structural and sequences discrepancies to constructed a 14.50-Gb consensus sequences CS-NP. Using CS-NP as backbone, we incorporated 4.37 Gb of non-redundant non-CS sequences from 37 diverse wheat accessions, generating WheatPanRef (18.87 Gb). WheatPanRef improves read-alignment performance and captures putative wild-relative introgressions and sequences absent or unanchored in conventional references. Bidirectional coordinate-translation system enables accurate projection between WheatPanRef and individual assemblies without remapping, facilitating genomic resource integration and reuse. WheatPanRef provides a common sequence and coordinate foundation for population-scale wheat genomics, with potential utility for genomic resource integration in other complex crops.

genomics↗

bioRxiv2026

Super-resolution single-cell spatial atlas of plant de novo regeneration

Plant de novo regeneration, a capacity absent in animals, relies on stem-cell-niche formation rather than pre-existing reservoirs. Growth hormones such as auxin and cytokinin, together with numerous genetic regulators, participate in regeneration, but the architectural principles coordinating extensive cellular reprogramming at the individual-cell scale remain elusive. Using super-resolution multimodal spatial transcriptomics to 1.16 million cells, we tracked tomato regeneration across temporal intervals from wounding to organogenesis. Datasets are available at http://www.single-cell-spatial.com.

cell biology↗

bioRxiv2023

Amyloplast sedimentation repolarizes LAZYs to achieve gravity sensing in plants

Gravity controls directional growth of plants, and the classical starch-statolith hypothesis proposed more than a century ago postulates that amyloplast sedimentation in specialized cells initiates gravity sensing, but the molecular mechanism remains mysterious. Here, we report that gravistimulation by reorientation triggers the Mitogen-Activated Protein Kinase (MAPK) signaling-mediated phosphorylation of LAZY proteins, the key regulators of gravitropism accumulated more on the lower side of the plasma membrane in columella cells in regular growth Arabidopsis. Phosphorylation of LAZY increases its interaction with several TOC proteins on the surface of amyloplasts, facilitating the translocation of LAZY proteins from the plasma membrane to the amyloplasts. Amyloplast sedimentation subsequently guides LAZY to relocate to the new lower side of the plasma membrane in columella cells, where LAZY induces asymmetrical auxin distribution and differential growth. Together, this study provides a molecular interpretation for the starch-statolith hypothesis: the organelle movement-triggered molecular polarity formation.

plant biology↗

bioRxiv2019

PhyB induces intron retention and uORF-mediated translational inhibition of PIF3

The phytochrome B (phyB) photoreceptor stimulates light responses in plants in part by inactivating repressors of light responses such as phytochrome-interacting factor 3 (PIF3). It has been established that activated phyB inhibits PIF3 by rapid protein degradation and decreased transcription. PIF3 protein degradation has been shown to be mediated by EIN3-BINDING F-BOX PROTEIN (EBF) and LIGHT-RESPONSE BTB (LRB) E3 ligases, the latter simultaneously targeting phyB for degradation. In this study, we show that PIF3 level is additionally regulated by alternative splicing and protein translation. Overaccumulation of photo-activated phyB, which occur in the mutant defective for LRB genes under continuous red light (Rc), induces a specific alternative splicing of PIF3 that results in retention of an intron in the 5UTR of PIF3 mRNA. In turn, the upstream opening reading frames (uORF) contained within this intron inhibit PIF3 protein synthesis. The phyB-dependent alternative splicing of PIF3 is diurnally regulated under the short-day light cycle. We hypothesize that this reversible regulatory mechanism may be utilized to fine-tune the level of PIF3 protein in light-grown plants, and may contribute to the oscillation of PIF3 protein abundance under the short-day environment.\n\nOne Sentence SummaryLight down-regulates PIF3 by multiple mechanisms. We show that phyB induces an alternative splicing event that inhibits PIF3 protein translation, and that is regulated by short-day diurnal cycle.

plant biology↗