A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data

Abstract

Cellular heterogeneity in growth and differentiation results in organ patterning. Single-cell transcriptomics allows characterization of gene expression heterogeneity in developing organs at unprecedented resolution. However, the original physical location of the cell is lost during this methodology. To recover the original location of cells in the developing organ is essential to link gene activity with cellular identity and function in plants. Here, we propose a method to reconstruct genome-wide gene expression patterns of individual cells in a 3D flower meristem by combining single-nuclei RNA-seq with microcopy-based 3D spatial reconstruction. By this, gene expression differences among meristematic domains giving rise to different tissue and organ types can be determined. As a proof of principle, the method is used to trace the initiation of vascular identity within the floral meristem. Our work demonstrates the power of spatially reconstructed single cell transcriptome atlases to understand plant morphogenesis. The floral meristem 3D gene expression atlas can be accessed at http://threed-flower-meristem.herokuapp.com.

Large-scale single-cell profiling of stem cells uncovers redundant regulators of shoot development and yield trait variation

“…To recover stem cells that were largely missed in previous shoot single-cell studies (Conde et al, 2022; Neumann et al, 2022; Satterlee et al, 2020; Xu et al, 2021; Zhang et al, 2021b; Zong et al, 2022), we finely dissected the tips of developing maize ear primordia (wild type B73), comprising the inflorescence meristem and early stage spikelet pair meristems (Figure 1A). Additionally, we optimized our cell sorting protocol (Xu et al, 2021) using OptiPrep Gradient Medium (Sigma-Aldrich, OptiPrep™ Application Sheet C18), or by modifying the cell isolation steps based on (Satterlee et al, 2020) (see STAR methods for details).…”

“…To recover stem cells that were largely missed in previous shoot single-cell studies (Conde et al, 2022;Neumann et al, 2022;Satterlee et al, 2020;Xu et al, 2021;Zhang et al, 2021b;Zong et al, 2022), we finely dissected the tips of developing maize ear primordia (wild type B73), comprising the inflorescence meristem and early stage spikelet pair meristems (Figure 1A).…”

“…However, this approach relied on transgenic lines and low-throughput isolation protocols that cannot be easily applied to crop plants. In recent years, single-cell transcriptomic analysis has been extensively used to profile shoot meristems in arabidopsis (Neumann et al, 2022; Zhang et al, 2021b), maize (Satterlee et al, 2020; Xu et al, 2021), rice (Zong et al, 2022), and Populus (Conde et al, 2022). However, these studies failed to recover cells expressing CLV3 and/ or WUS, presumably due to their scarcity, inaccessibility, fragility, or low expression level of these markers.…”

Comparative transcriptome analyses reveal insights into catkin bloom patterns in pecan protogynous and protandrous cultivars

“…In comparison, during the month of June 2017, there were 36 differentially expressed genes between ‘Wichita’ (protogynous) non-fruiting and fruiting samples ( S1 Fig ). These genes, listed in Table 3 , include genes that have been described in other species as necessary for initiation of both pistillate and staminate flowers [ 15 – 20 ]. From these 36 genes, 10 genes were upregulated in ‘Wichita’ non-fruiting sample and 26 were upregulated in ‘Wichita’ fruiting sample.…”

Contemplation on wheat vernalization

“…VanGessel et al (2022) recently demonstrated transcriptional signatures of inflorescent development in the tetraploid wheat variety Kronos. The gene expression atlas of the floral meristem based on single nucleus RNA-seq data was developed latterly in barley (Neumann et al, 2022). Adapting the new techniques of targeted mutagenesis could help to develop the new alleles for functional studies.…”