Investigating the regulatory basis of C and C photosynthesis in grasses at single-cell resolution.

While considerable knowledge exists about the enzymes pivotal for C photosynthesis, much less is known about the regulation important for specifying their expression in distinct cell types. Here, we use single-cell-indexed ATAC-seq to identify cell-type-specific accessible chromatin regions (ACRs) associated with C enzymes for five different grass species. This study spans four C species, covering three distinct photosynthetic subtypes: and (NADP-dependent malic enzyme), (NAD-dependent malic enzyme), (phosphoenolpyruvate carboxykinase), along with the C outgroup .

Investigating the -Regulatory Basis of C and C Photosynthesis in Grasses at Single-Cell Resolution.

While considerable knowledge exists about the enzymes pivotal for C photosynthesis, much less is known about the -regulation important for specifying their expression in distinct cell types. Here, we use single-cell-indexed ATAC-seq to identify cell-type-specific accessible chromatin regions (ACRs) associated with C enzymes for five different grass species. This study spans four C species, covering three distinct photosynthetic subtypes: and (NADP-ME), (NAD-ME), (PEPCK), along with the C outgroup .

Exploring plant cis-regulatory elements at single-cell resolution: overcoming biological and computational challenges to advance plant research.

Cis-regulatory elements (CREs) are important sequences for gene expression and for plant biological processes such as development, evolution, domestication, and stress response. However, studying CREs in plant genomes has been challenging. The totipotent nature of plant cells, coupled with the inability to maintain plant cell types in culture and the inherent technical challenges posed by the cell wall has limited our understanding of how plant cell types acquire and maintain their identities and respond to the environment via CRE usage.

Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet.

Pearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here, we developed a graph-based pan-genome by assembling ten chromosomal genomes with one existing assembly adapted to different climates worldwide and captured 424,085 genomic structural variations (SVs). Comparative genomics and transcriptomics analyses revealed the expansion of the RWP-RK transcription factor family and the involvement of endoplasmic reticulum (ER)-related genes in heat tolerance.

Simple and accurate transcriptional start site identification using Smar2C2 and examination of conserved promoter features.

The precise and accurate identification and quantification of transcriptional start sites (TSSs) is key to understanding the control of transcription. The core promoter consists of the TSS and proximal non-coding sequences, which are critical in transcriptional regulation. Therefore, the accurate identification of TSSs is important for understanding the molecular regulation of transcription.

Leveraging histone modifications to improve genome annotations.

Accurate genome annotations are essential to modern biology; however, they remain challenging to produce. Variation in gene structure and expression across species, as well as within an organism, make correctly annotating genes arduous; an issue exacerbated by pitfalls in current in silico methods. These issues necessitate complementary approaches to add additional confidence and rectify potential misannotations.