Research articles

Genome-wide comparative analysis of DNA binding for 200 transcription factors in two maize inbred lines reveals prevalent genotype-specific variation that is associated with gene expression differences and agronomic traits.

This study presents 11 telomere-to-telomere genomes of wild and domesticated pepper, highlights how transposable elements have shaped the evolution of genome structure and regulatory elements and identifies structural variations and introgressions associated with key traits in cultivated pepper.

The near-complete genome of hexaploid wild oat, along with 117 global wild and cultivated accessions, reveals genome divergence between wild and cultivated oats and a large fragment duplication event from chromosomes 4A to 4D during oat domestication.

This study reports a transcriptome atlas of the germinating Arabidopsis embryo at single-cell resolution. It demonstrates that the cells of the embryo transition from a common transcriptional state to cell type-specific states as germination progresses.

Parallel degradome sequencing and DMS-MaPseq pinpoint the first cleavage sites on bona fide pri-miRNAs, decode their in vivo structure and provide better interpretation of the cleavage modes and impact of DCL1 cofactors in the process in Arabidopsis.

Analyses of three newly sequenced modern cultivar cotton genomes revealed sequence and structural variation alongside traces of ancient and ongoing introgressions. Moreover, transcriptome analysis pointed at unique fibre quality traits of cultivars.

The authors integrate spatial (Stereo-seq) and single-cell transcriptomes of the developing maize ear to produce an atlas of maize ear cells and their developmental trajectories. They also identify a pair of transcription factors involved in inflorescence development.

Using a combination of single-cell and spatial transcriptomic analysis, Serrano et al. uncover transcriptional dynamics during the establishment of arbuscular mycorrhizal symbiosis.

The near telomere-to-telomere genome of Physcomitrium patens reveals 26 chromosomes and new genome structures, while also identifying new telomeres, an improved chromosomal karyotype model and intriguing differences in 3D genome models between the protonema and gametophore stages, which offer promising prospects for future research.

Using transcriptomic data from ~100,000 informative cells, this study constructed a dynamic cell atlas during the process of de-etiolation induced by light for Arabidopsis seedlings, revealing comprehensive development responses at single-cell resolution.

Chromosome-level genome reference sequence assemblies of the model and biofactory Nicotiana benthamiana line, and a wild relative, have been generated and annotated for gene models, tissue-specific transcriptomes, microRNAs and epigenetic landscapes.

A 2.2 Å cryo-electron microscopy structure of an actively translating 80S ribosome from tobacco reveals bound tRNA and mRNA, the nascent peptide and numerous cofactors, providing a basis for understanding the molecular mechanism of protein synthesis in plants.

The compartmentation of monoterpenoid indole alkaloid biosynthesis in periwinkle leaves was determined using single-cell RNA-seq, which reveals the spatial distribution of plant specialized metabolism at the single-cell resolution.

This study established a comprehensive poly(A) tail atlas comprising over 120 million full-length RNA reads from various tissues and plant species and found that plant poly(A) tails peaked at 20 and 45 nucleotides, except in pollen and seed where they peaked at longer sizes.

A large-scale comparison of transcriptome datasets from ten evolutionarily representative species identifies general patterns on the genomic evolution of various plant organs. Among various insights, the authors find that the origin of organ-specific gene families predate the origin of the organs themselves.

Microbes induce an immune response in plants that includes transcriptional changes and biosynthesis of defence molecules. Analysis of both transcriptome and metabolome output to multiple bacteria identifies a common non-self response to microorganisms.

Pseudomonas syringae is an endophytic plant pathogen. The authors analyse both the transcriptome and proteome of the bacteria while it infects leaves of wild-type and immune mutants of Arabidopsis.

The target of rapamycin (TOR) kinase, present in all eukaryotes, is a major regulator of growth and metabolism. Using quantitative phosphoproteomics and comprehensive interactome approaches, the authors reveal the TOR signalling network, including potential substrates.

In early Arabidopsis embryos, cell-type-specific labelling of the nuclear envelope, followed by affinity-based isolation of tagged nuclei, is used to build a temporal and spatial transcriptome atlas of the developing embryo.