Single-cell RNA-sequencing datasets of Arabidopsis roots have been generated,but related comprehensive gene co-expression network analyses are lacking.We conducted a single-cell gene co-expression network analysis wit...Single-cell RNA-sequencing datasets of Arabidopsis roots have been generated,but related comprehensive gene co-expression network analyses are lacking.We conducted a single-cell gene co-expression network analysis with publicly available scRNA-seq datasets of Arabidopsis roots using a SingleCellGGM algorithm.The analysis identified 149 gene co-expression modules,which we considered to be gene expression programs(GEPs).By examining their spatiotemporal expression,we identified GEPs specifically expressed in major root cell types along their developmental trajectories.These GEPs define gene programs regulating root cell development at different stages and are enriched with relevant developmental regulators.As examples,a GEP specific for the quiescent center(QC)contains 20 genes regulating QC and stem cell niche homeostasis,and four GEPs are expressed in sieve elements(SEs)from early to late developmental stages,with the early-stage GEP containing 17 known SE developmental regulators.We also identified GEPs for metabolic pathways with cell-type-specific expression,suggesting the existence of cell-type-specific metabolism in roots.Using the GEPs,we discovered and verified a columellaspecific gene,NRL27,as a regulator of the auxin-related root gravitropism response.Our analysis thus systematically reveals GEPs that regulate Arabidopsis root development and metabolism and provides ample resources for root biology studies.展开更多
基金supported by grants from the Strategic Priority Research Program of the Chinese Academy of Science(XDA24010303)the National Natural Science Foundation of China(31770268)+1 种基金the Fundamental Research Funds for the Central Universities(WK2070000091)the University of Science and Technology of China(start-up fund to S.M.)。
文摘Single-cell RNA-sequencing datasets of Arabidopsis roots have been generated,but related comprehensive gene co-expression network analyses are lacking.We conducted a single-cell gene co-expression network analysis with publicly available scRNA-seq datasets of Arabidopsis roots using a SingleCellGGM algorithm.The analysis identified 149 gene co-expression modules,which we considered to be gene expression programs(GEPs).By examining their spatiotemporal expression,we identified GEPs specifically expressed in major root cell types along their developmental trajectories.These GEPs define gene programs regulating root cell development at different stages and are enriched with relevant developmental regulators.As examples,a GEP specific for the quiescent center(QC)contains 20 genes regulating QC and stem cell niche homeostasis,and four GEPs are expressed in sieve elements(SEs)from early to late developmental stages,with the early-stage GEP containing 17 known SE developmental regulators.We also identified GEPs for metabolic pathways with cell-type-specific expression,suggesting the existence of cell-type-specific metabolism in roots.Using the GEPs,we discovered and verified a columellaspecific gene,NRL27,as a regulator of the auxin-related root gravitropism response.Our analysis thus systematically reveals GEPs that regulate Arabidopsis root development and metabolism and provides ample resources for root biology studies.
