Description

Gene expression visualization in Arabidopsis leaf single-cell dataset (leaf #3, 14DAS, updated 08.03.20).

As the main photosynthetic instrument of vascular plants, leaves are crucial and complex plant organs. A strict organization of leaf mesophyll and epidermal cell layers orchestrate photosynthesis and gas-exchange. In addition, water and nutrients supporting photosynthesis and leaf growth are provided through the vascular tissue.

Defining the cell-type-specific transcriptomic landscape in leaf tissues is essential to understand its cell heterogeneity and functions. To unravel unique leaf cell type transcriptional features, we isolated cells from the third leaf at 14 DAS at single-cell level using microfluidics followed by high-throughput sequencing of the transcriptome of each individual cell.

Single-Cell RNA-Sequencing of ~19.000 different transcripts in over ~1800 high-quality leaf cells revealed leaf cell diversity, enabling us to identify fourteen cell populations composing a young Arabidopsis leaf.

Besides the core leaf tissues; mesophyll, epidermis and vasculature; we identified 14 distinct leaf subpopulations, pooling cells with distinct identity or metabolic stage. In addition, we describe the effect of mild drought stress applied to young developing leaves, starting at 8 DAS, on the main cell types.



Abbreviations:

  • XP-1: Xylem Parenchyma 1

  • XP-2: Xylem Parenchyma 2

  • PP-1: Phloem Parenchyma 1

  • PP-2: Phloem Parenchyma 2

  • GC: Guard Cell

  • CC: Companion Cell

  • MI: Myrosin Idioblast

  • G1S Synth: G1S Replication

  • G1S Comp: G1S Compactation

  • Adaxial PC: Adaxial pavement cell

  • Abaxial PC: Abaxial pavement cell

Gene Selection

Main Tissue

Gene expression visualization in Arabidopsis leaf single-cell dataset (leaf #3, 14DAS, updated 08.03.20).

Epidermis

Gene expression visualization in Arabidopsis leaf single-cell dataset (leaf #3, 14DAS, updated 08.03.20). Download as PNG

Mesophyll

Gene expression visualization in Arabidopsis leaf single-cell dataset (leaf #3, 14DAS, updated 08.03.20). Download as PNG

Vasculature

Gene expression visualization in Arabidopsis leaf single-cell dataset (leaf #3, 14DAS, updated 08.03.20). Download as PNG

Drought Response

Gene expression visualization in Arabidopsis leaf single-cell dataset (leaf #3, 14DAS, updated 08.03.20). Download as PNG

Co-expression

Gene expression visualization in Arabidopsis leaf single-cell dataset (leaf #3, 14DAS, updated 08.03.20).
Download as PNG

Find correlated genes

Calculation of gene expression correlations in Arabidopsis leaf single-cell dataset (leaf #3, 14DAS, updated 12.03.21).

Top 1000 positively and negatively correlated genes based on PCC (not significance)

Download positively correlated genes Download negatively correlated genes

Contact

For questions related to the data and annotation, please contact Ruben Tenorio Berrio or Marieke Dubois.

For technical questions regarding this tool, please contact Julie Pevernagie.