Spatial transcriptomic atlas of shoot organogenesis in tomato callus

Abstract

Callus is a reprogrammed transitional cell mass during plant regeneration. Pluripotent callus cells develop into fertile shoots through de novo shoot organogenesis. This study represents a pioneering effort in exploring the spatial transcriptome of tomato callus during shoot regeneration, using technologies including BGI Stereo-seq, BMKMANU S1000, and 10x Visium. The results indicate that the callus comprises highly heterogeneous cells, classified into various cell types based on spatial gene expression and histological observation, including epidermis, shoot primordium, vascular tissue, inner callus, and outgrowth shoots. The developmental trajectories from shoot primordium to outgrowth shoot are traced, and vascular tissue development is characterized. The single-cell resolution spatial approach reveals the origin of shoot primordia from the sub-epidermis. The spatial full length RNA sequencing shows high incompletely spliced (IS) ratios in the shoot primordium cells. These findings enhance our knowledge of plant organogenesis and highlight the significance of spatial biology in plant research.

Spatially resolved transcriptomic analysis of the germinating barley grain

“…Most recently, researchers combined Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH) and slide-seq spatial technologies to validate newly discovered marker genes and aid in cluster annotation of complex organs such as germinating Arabidopsis seeds and siliques ( 22 ). A combined approach using single-nuclei RNA-seq, BGI single-cell Stereo-seq, 10x Visium spatial RNA-seq and BMKMANUS1000 RNA-seq has also been used to profile tomato callus during shoot regeneration, revealing callus displays a high level of cellular heterogeneity and that the shoot primordia originates from the sub-epidermis ( 23 ).…”