Plant systems and spatial biology

While recent advances in plant single-cell RNA sequencing (scRNA-seq) have made numerous strides in identifying novel regulatory events, transcriptional profiling of certain cell types, such as phloem poles, has not yet been thoroughly investigated. A recent article by Otero et al. utilized cell-type specific marker lines and a second-generation single-cell approach to uncover transcriptomic landscapes specifying protophloem-adjacent cells, as well as identify a set of important transcription factors (TFs) signifying early phloem development.

In this Perspective, Diane Dickel and colleagues review recent progress and opportunities in applying single-cell sequencing and microfluidics methods to plants. The authors highlight the need for new tools developed with plants in mind, and advocate for the creation of a centralized, open-access database to house plant single-cell data.

This review highlights the importance of comprehending plant-pathogen interactions at the single-cell and spatial levels, while also providing an overview of relevant cutting-edge technologies.

Arabidopsis H3K9 methyltransferases directly interact with ASYMMETRIC LEAVES1 (AS1) and AS2 to repress KNOTTED-LIKE FROM ARABIDOPSIS THALIANA 1 (KNAT1) and KNAT2 in leaf development.

A host-viral interactome map demonstrates that turnip mosaic virus targets high information-spreading nodes, which are also hubs.

Ecological mechanisms governing inheritance of bacterial and fungal communities from seed to seed in rice are revealed. The inherited microbes dominate each community at the ripening stage, and parental seeds and stem endosphere are major sources.

Ian Ware et al. use reciprocal plant population by soil location feedback experiments to show how the soil microbiomes of the narrowleaf cottonwood are influenced by genetic and environmental variation, and how these factors affect foliar phenology. They find a landscape-level feedback between tree populations and their associated soil microbial counterparts. This study contributes to the understanding of the interplay between soil, climate, plant and microbial populations with climate warming.

A chromosome-level genome assembly for Onobrychis viciifolia (autotetraploid sainfoin) combined with transcriptomic data provides insights into how proanthocyanidins are synthesized and Onobrychis evolution.

A genome assembly for Rauvolfia tetraphylla combined with transcriptomic, metabolomic, and proteomic analyses as well as machine learning enables identification of enzymes involved in yohimbane monoterpene indole alkaloid biosynthesis.

A chromosome-level genome assembly for Angelica sinensis var. Qinggui1 combined with metabolomic and transcriptomic analyses provides insight into the pathways involved in the biosynthesis of pharmaceutically important compounds in roots of this plant.

Transcriptome, proteome, spatial metabolome, and spatial lipidome analyses provide insight into the mechanisms that regulate seed germination in the gymnosperm Taxus chinensis var mairei (Chinese yew).

A chromosome-scale genome assembly for rhubarb combined with transcriptomic data provides insight into the molecular mechanisms regulating anthraquinone biosynthesis in this plant.

A chromosome-level reference genome for chia together with transcriptomic, proteomic, and metabolomic datasets provide insight into the molecular basis for the unique characteristics of this plant’s seeds.

A high-quality genome assembly and phylogenetic analysis for the glasshouse plant, Rheum nobile, shed light on its evolutionary history and ability to adapt to intensive UV radiation in a low-temperature, alpine environment.

A broad survey of the metabolome over the growth curve of K. mikimotoi identifies glucose to glycine ratio as indicative of dinoflagellate cells entering the late stationary phase, predicting bloom demise.

Comparative phenotyping and genome-wide association study in a panel of 149 wheat genotypes reveal alleles associated with heat tolerance, which could be useful in future breeding programmes for wheat cultivars.

An integrated genomic and transcriptomic analysis of progeny from reciprocal crosses between tetraploid and hexaploid wheat species reveals parental contributions to gene expression during various stages of seed development.

A full-length transcriptome and expression atlas of protein-coding genes and long non-coding RNAs is generated in chickpea. Components of transcriptional regulatory networks and candidate tissue-specific transcripts associated with quantitative trait loci are identified.

A transcriptome time course of Puccinia striiformis f. sp. tritici (Pst) infection reveals nuclear genes encoding chloroplast-localized proteins are manipulated during infection and highlights TaCSP41a disruption as a target for resistance breeding.

Ko and Brandizzi use Arabidopsis thaliana to investigate the downstream regulators of two major endoplasmic reticulum (ER) stress-related transcription factors, bZIP60 and bZIP28. Their results provide further insight on how two modulators of the unfolded protein response contribute to growth recovery from ER stress.

Wang et al. report zaxinone as a global regulator of the transcriptome and metabolome, as well as of hormonal and cellular composition of rice roots. This study shows that zaxinone promotes rice growth by enhancing root sugar uptake and metabolism and modulation of cytokinin content, indicating the potential application of this compound in increasing rice performance.

Zhimin Hou, Yanhui Liu et al. used single cell RNA-seq to analyze the model organism, Arabidopsis thaliana, at three stages during female germline differentiation. They reconstructed the continuous trajectory of female germline differentiation, providing a valuable reference for future investigation of germline cell fate determination in A. thaliana.