A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators
Yuji Ke,
Vincent Pujol,
Jasper Staut,
Lotte Pollaris,
Ruth Seurinck,
Thomas Eekhout,
Carolin Grones,
Maite Saura-Sanchez,
Michiel Van Bel,
Marnik Vuylsteke,
Andrea Ariani,
Christophe Liseron-Monfils,
Klaas Vandepoele,
Yvan Saeys,
Bert De Rybel
Affiliations
Yuji Ke
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
Vincent Pujol
Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium; VIB Center for Inflammation Research, Ghent, BE, Belgium
Jasper Staut
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
Lotte Pollaris
Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium; VIB Center for Inflammation Research, Ghent, BE, Belgium
Ruth Seurinck
Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium; VIB Center for Inflammation Research, Ghent, BE, Belgium
Thomas Eekhout
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; VIB Single Cell Core, VIB, Ghent/Leuven, Belgium
Carolin Grones
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
Maite Saura-Sanchez
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
Michiel Van Bel
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
Marnik Vuylsteke
Gnomixx, Melle, Belgium
Andrea Ariani
BASF Belgium Coordination Center CommV, Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Ghent, Belgium
Christophe Liseron-Monfils
BASF Belgium Coordination Center CommV, Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Ghent, Belgium
Klaas Vandepoele
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; Corresponding author
Yvan Saeys
Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium; VIB Center for Inflammation Research, Ghent, BE, Belgium; Corresponding author
Bert De Rybel
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; Corresponding author
Summary: Despite the broad use of single-cell/nucleus RNA sequencing in plant research, accurate cluster annotation in less-studied plant species remains a major challenge due to the lack of validated marker genes. Here, we generated a single-cell RNA sequencing atlas of soil-grown wheat roots and annotated cluster identities by transferring annotations from publicly available datasets in wheat, rice, maize, and Arabidopsis. The predictions from our orthology-based annotation approach were next validated using untargeted spatial transcriptomics. These results allowed us to predict evolutionarily conserved tissue-specific markers and generate cell type-specific gene regulatory networks for root tissues of wheat and the other species used in our analysis. In summary, we generated a single-cell and spatial transcriptomics resource for wheat root apical meristems, including numerous known and uncharacterized cell type-specific marker genes and developmental regulators. These data and analyses will facilitate future cell type annotation in non-model plant species.
