Biology subjects

Stata, M.

Publications and source records attributed to Stata, M..

3 recordsLinked to original sources

bioRxiv2025

Single-cell-level response to drought in Sorghum bicolor reveals novel targets for improving water use efficiency

Increasing drought threatens global agriculture, especially in water-limited regions. Sorghum bicolor, a drought-tolerant C4 grass, is a promising bioenergy crop for cultivation on marginal lands, yet its molecular drought responses remain poorly understood. To uncover single-cell-level transcriptional responses to drought, we performed single-nucleus RNA sequencing on mature sorghum leaves under well-watered and drought conditions. We identified major cell types and analyzed differential gene expression across mesophyll, bundle sheath, epidermal, vascular, and stomatal cells. Surprisingly, drought effects on transcriptomes exceeded differences due to cell identity, revealing a shared response across cell types. We leveraged this convergence to identify candidate regulators of drought-responsive gene expression. These findings advance our understanding of sorghum drought adaptation and offer new targets for engineering enhanced water use efficiency in bioenergy crops.

plant biology↗

bioRxiv2024

UnigeneFinder: An automated pipeline for gene calling from transcriptome assemblies without a reference genome

For most species in nature, transcriptome data is much more readily available than genome data. Without a reference genome, however, gene calling is cumbersome and inaccurate due to the high degree of redundancy in de novo transcriptome assemblies. To simplify and increase the accuracy of de novo transcriptome assembly in the absence of a reference genome, we developed UnigeneFinder. Combining several clustering methods, UnigeneFinder substantially reduces the redundancy typical of raw transcriptome assemblies. This pipeline offers an effective solution to the problem of inflated transcript numbers, achieving a closer representation of the actual underlying genome. UnigeneFinder performs comparably or better, compared to existing tools, on plant species with varying genome complexities. UnigeneFinder is the only available transcriptome redundancy solution that fully automates the generation of primary transcript, coding region, and protein sequences, analogous to those available for high quality reference genomes. These features, coupled with the pipelines cross-platform implementation and focus on automation and an accessible user interface, make UnigeneFinder a useful tool for many downstream sequence-based analyses in non-model organisms lacking a reference genome, including differential gene expression analysis, accurate ortholog identification, functional enrichments, and evolutionary analyses. UnigeneFinder also runs efficiently both on high-performance computing (HPC) systems and personal computers, further reducing barriers to use.

bioinformatics↗

bioRxiv2023

Photosynthetic acclimation mediates exponential growth of a desert plant in Death Valley summer

Heat waves, now more frequent and longer due to climate change, devastate plant productivity. Although rare, thermophilic plants could hold keys to engineering heat resilience in crop plants. Tidestromia oblongifolia is a thermophilic flowering plant that thrives at temperatures above 45{degrees}C. When exposed to Death Valley summer conditions, T. oblongifolia increased its thermal optimum of photosynthesis within a day and accelerated growth within 10 days. The physiological changes were accompanied by morphological, anatomical, and gene expression changes revealed by a newly sequenced genome. In bundle sheath cells where Rubisco fixes CO2, mitochondria relocated to chloroplasts and novel, cup-shaped chloroplasts appeared. Understanding how this plant acclimates under heat may afford new ways of engineering heat tolerance in crop plants. One-Sentence SummaryTidestromia oblongifolias acclimation to Death Valley is accompanied by changes in gene expression, organellar dynamics, and photosynthesis.

plant biology↗