Biology subjects

Millsteed, T.

Publications and source records attributed to Millsteed, T..

3 recordsLinked to original sources

bioRxiv2026

Poly Pipeline: A Polyvalent Spatial Transcriptomics Workflow Validated Across Polyploid and Diploid Organisms

Spatial transcriptomics (ST) has emerged as a transformative approach for visualizing tissue landscapes, yet it faces significant challenges regarding data standardization, sparsity, and the analysis of complex genomes, particularly polyploid plants. To address these limitations, we introduce Poly Pipeline, a robust and universal bioinformatic workflow designed to streamline analysis across diverse plant and animal genomes. The pipeline integrates a comprehensive converter for proprietary formats, clustering algorithms, and hdWGCNA co-expression networks, which indirectly preserves the expression signatures of low-expressed duplicated genes. Benchmarking across datasets from wheat, rice, Arabidopsis, and mouse demonstrated the broad applicability of the pipeline in identifying relevant clusters, showing effectiveness across diverse organisms and data types. By providing a unified and reproducible framework, Poly Pipeline addresses a critical gap in analyzing genomic redundancy, especially that related to polyploidy, and promotes FAIR data principles for the broader scientific community.

bioinformatics↗

bioRxiv2025

Going Against the Grain: Investigating the C4 Wheat Hypothesis with Spatial Transcriptomics

The possibility of a C4 photosynthetic pathway present in the developing grain of wheat, a C3 plant, has been the source of scientific debate. Wheat is critical to food security and may benefit greatly from the biological advantages conferred by C4 photosynthesis under heat and drought stress. Therefore, significant research has gone towards engineering wheat to use C4 biochemistry, resulting in the discovery of a unique photosynthetic pathway in the grain that has been suggested to be C4 specific. Here, we employed a spatial transcriptomics analysis of the developing wheat grain to further investigate the spatial expression patterns of C4 specific genes. Our results showed that most of the genes related to C4 photosynthesis were expressed in the grain in the theorised tissue locations, including phosphoenolpyruvate carboxylase (ppc) and pyruvate orthophosphate dikinase (ppdk). The photosynthetic pericarp cells were the site of ppc synthesis while the endosperm was the site of ppc carboxylation activity. Notably, isoforms of aspartate aminotransferase, alanine aminotransferase and malate dehydrogenase exhibited spatially distinct expression patterns, with tissue specificity, possibly linked to the unique functions of individual isoforms. As wheat performance under stress has been associated with the levels of expression of these C4 genes, confirmation of an active C4 pathway in the grain would have significant agronomic implications. Our results provide novel gene expression data for key genes related to photosynthesis, which could contribute to future development of highly productive, climate change resilient wheat varieties.

genetics↗

bioRxiv2025

Spatial transcriptomics of developing wheat seed reveals radial expression patterns in endosperm and subgenome biased expression of key genes

Gene expression of developing seeds drives essential processes such as nutrient storage, stress tolerance and germination. However, the spatial organisation of gene expression within the complex structure of the seed remains largely unexplored. Here we report the use of the STOmics spatial transcriptomics platform to visualise spatial expression patterns in the wheat (Triticum aestivum) seed at the critical period of grain filling in mid seed development. We analysed >4,000,000 spatially resolved transcripts, achieving subcellular resolution of transcript localization across multiple tissue domains, and identified gene expression clusters linked to eight functional cellular groups. Notably, our analysis characterised four distinct clusters within the endosperm, which exhibited radial expression patterns from the inner to outer regions of the grain, and identified novel marker gene candidates for the clusters found. We further investigated known tissue-specific genes and identified subgenome biased expression between paralogs of puroindoline-B, metallothionein protein, and -amylase/subtilisin inhibitor. These findings provide new detail about gene expression across and within different functional cellular groups of the developing seed and demonstrate that spatial transcriptomics could further our understanding of subgenome differences in polyploid plants.

plant biology↗