Shoot and root single cell sequencing reveals tissue- and daytime-specific transcriptome profiles.

Area of Science:

• Plant biology
• Genomics
• Molecular biology

Background:

• Previous single-cell RNA sequencing (scRNAseq) studies in Arabidopsis thaliana primarily focused on root tissues.
• A comprehensive reference map for both root and above-ground cell types, considering daily transcriptome fluctuations, is lacking.

Purpose of the Study:

• To generate a de novo reference cell atlas for Arabidopsis thaliana, encompassing both root and above-ground tissues.
• To investigate diurnal transcriptome changes and identify cell-specific gene expression patterns.
• To explore non-annotated and di-cistronic transcripts and their potential functions.

Main Methods:

• Single-cell RNA sequencing (scRNAseq) was performed on Arabidopsis thaliana root and above-ground tissues at distinct times of day (end of day and end of night).
• Tissue-specific reporter lines were utilized for root analysis.
• Bioinformatic analyses were conducted to identify cell types, markers, and novel transcripts.

Main Results:

• A high-resolution cell atlas of nearly 70,000 cells from Arabidopsis thaliana was created for both below- and above-ground tissues.
• Common cell types and markers between root and shoot were identified.
• Significant transcriptome changes in above-ground tissues were observed depending on the time of day.
• Novel non-annotated and di-cistronic transcripts were identified and experimentally validated.
• The function of a novel marker gene for dividing cells was investigated.

Conclusions:

• This study provides a valuable resource for understanding spatial gene expression control in Arabidopsis thaliana at single-cell resolution.
• The findings highlight the dynamic nature of the plant transcriptome and its regulation by the circadian clock.
• The identification and validation of novel transcripts expand our knowledge of the Arabidopsis thaliana genome and gene regulation.