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

Apelt, F., Mavrothalassiti, E., Gupta, S., Machin, F., Olas, J. J., Annunziata, M. G., et al. (2021). Shoot and root single cell sequencing reveals tissue- and daytime-specific transcriptome profiles. Plant Physiology. doi:10.1093/plphys/kiab537.

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 Creators:
Apelt, Federico1, Author              
Mavrothalassiti, E.1, Author              
Gupta, S.1, Author              
Machin, F.1, Author              
Olas, Justyna Jadwiga2, Author
Annunziata, Maria Grazia3, Author              
Schindelasch, D.1, Author              
Kragler, F.1, Author              
Affiliations:
1Intercellular Macromolecular Transport, Department Köhler, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_3338335              
2external, ou_persistent22              
3System Regulation, Department Stitt, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753327              

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 Abstract: Although several large-scale single-cell RNA sequencing (scRNAseq) studies addressing the root of Arabidopsis (Arabidopsis thaliana) have been published, there is still need for a de novo reference map for both root and especially above-ground cell types. As the plants’ transcriptome substantially changes throughout the day, shaped by the circadian clock, we performed scRNAseq on both Arabidopsis root and above-ground tissues at defined times of the day. For the root scRNAseq analysis, we used tissue-specific reporter lines grown on plates and harvested at the end of the day (ED). In addition, we submitted above-ground tissues from plants grown on soil at ED and end of the night to scRNAseq, which allowed us to identify common cell types/markers between root and shoot and uncover transcriptome changes to above-ground tissues depending on the time of the day. The dataset was also exploited beyond the traditional scRNAseq analysis to investigate non-annotated and di-cistronic transcripts. We experimentally confirmed the predicted presence of some of these transcripts and also addressed the potential function of a previously unidentified marker gene for dividing cells. In summary, this work provides insights into the spatial control of gene expression from nearly 70,000 cells of Arabidopsis for below- and whole above-ground tissue at single-cell resolution at defined time points.

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Language(s): eng - English
 Dates: 2021-11-19
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1093/plphys/kiab537
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Title: Plant Physiology
  Other : Plant Physiol.
Source Genre: Journal
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Publ. Info: Bethesda, Md. : American Society of Plant Biologists
Pages: - Volume / Issue: - Sequence Number: - Start / End Page: - Identifier: ISSN: 0032-0889
CoNE: https://pure.mpg.de/cone/journals/resource/991042744294438