Recent Posts

The Marchantia transcription factor atlas

Marchantia’s power as a model organism continues to grow! Here, Ramoni et al. have investigated the expression pattern of the proximal promoters of most of its 450 transcription factor (TF)-encoding genes. The promoter elements were fused to nuclear-localized fluorescent reporters and introduced into…

JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom

Functional genomic studies across plants are incomplete without deciphering the putative gene functions in model as well as non-model plants. With an aim to facilitate gene function identification and cross-species expression analysis, Sreedasyam et al. describe the Joint Genome Institute (JGI) Plant…

eINTACT – An effective system for isolating effector-recipient cells in plant tissues

Bacteria can cause plant diseases by secreting small molecules called effectors. Studies of these effectors on host plants mostly have not accounted for the cellular complexity of plant tissues. The difficulty of detecting and isolating effector-recipient cells means that scientists mostly use bulk-infected…

Identifying thousands of RNA genes in Brassicaceae

Palos et al. identify thousands of new long intergenic noncoding RNAs using public data.  By Kyle Palos and Andrew Nelson  Background: All plants have thousands of genes in their genomes that contribute to plant form and function. While the functional “end-state” of many of these genes are…

Update: Toward a data infrastructure for the Plant Cell Atlas (Plant Physiol)

The ability to analyze the information contained within a single cell, for example through single-cell RNA sequening (scRNA-seq) presents exciting possibilities to biologists. Building on this and similar technologies, the Plant Cell Atlas (PCA) (www.plantcellatlas.org/) has the goal of creating an information…

Single seeds exhibit transcriptional heterogeneity during secondary dormancy induction (Plant Physiol)

Secondary dormancy (SD) of seeds is a natural strategy that allows survival of the plant in environments with unfavourable climatic conditions. However, in Arabidopsis, a variance of dormancy depth in between identical seeds can be explained by population-based threshold models. This single-seed variability…

Robust transcriptional indicators of immune cell death revealed by spatio-temporal transcriptome analyses (Mol Plant)

Many plants trigger a form of cell death, known as the hypersensitive response (HR), immediately upon pathogen recognition. To minimize damage to the plant, this cell death must be highly localized to the site of attack, while more distal cells survive and activate other immune responses. However, the…

ATTED-II v11: A plant gene coexpression database using a sample balancing technique by subagging of principal components (Plant Cell Physiol)

Genes are generally expressed in concert with one another with data often represented by gene co-expression networks. Gene co-expression data may be useful in identifying genes with unknown functions and are generally utilized in exploring molecular processes occurring during normal development as well…

A single-cell Arabidopsis root atlas reveals developmental trajectories in WT and cell identity mutants (Dev. Cell)

Single-cell RNA sequencing (scRNA-seq) is a powerful tool to identify rare and novel cell types, characterize multiple cell types, and more accurately understand their functions across their life cycles. The Arabidopsis root is a perfect system in which to investigate cellular differentiation due to…