Code
This repository contains the code that was used in the following research article.
CELL REPORTS
A single-cell and spatial wheat root atlas with cross-species cluster annotations allows the delineation of 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* and Bert De Rybel*
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 evolutionary 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 transcriptomic 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.