Cross-species single-cell annotation with orthologous marker gene groups
Chau, T.; Timilsena, P. R.; Bathala, S. P.; Bargmann, B.; Li, S.
Show abstract
Single-cell RNA sequencing (scRNA-seq) technology has been widely used in characterizing various cell types from in plant growth and development1-6. Applications of this technology in Arabidopsis have benefited from the extensive knowledge of cell-type identity markers7,8. Contrastingly, accurate labeling of cell types in other plant species remains a challenge due to the scarcity of known marker genes9. Various approaches have been explored to address this issue; however, studies have found many closest orthologs of cell-type identity marker genes in Arabidopsis do not exhibit the same cell-type identity across diverse plant species10,11. To address this challenge, we have developed a novel computational strategy called Orthologous Marker Gene Groups (OMGs). We demonstrated that using OMGs as a unit to determine cell type identity enables assignment of cell types by comparing 15 distantly related species. Our analysis revealed 14 dominant clusters with substantial conservation in shared cell-type markers across monocots and dicots.
Matching journals
The top 9 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- PlantConnectome: knowledge graph encompassing >70,000 plant articles 95%
- Species-specific gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection 94%
- Identification and Functional Annotation of Long Intergenic Non-coding RNAs in the Brassicaceae 94%
Similar papers in this journal
- MINI-AC: Inference of plant gene regulatory networks using bulk or single-cell accessible chromatin profiles 94%
- Systematic analysis of 1,298 RNA-Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas 94%
- The Soybean Expression Atlas v2: a comprehensive database of over 5000 RNA-seq samples 93%
Similar papers in this journal
Similar papers in this journal
- Spatial and single-cell expression analyses reveal complex expression domains in early wheat spike development 93%
- Endogenous virus sRNA regulates gene expression following genome shock in tomato hybrids 93%
- Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing 93%
Similar papers in this journal
- Telomere-to-telomere, gap-free genome of mung beans (Vigna radiata) provides insights into domestication under structural variation 93%
- Genomic insights into longan evolution from a chromosome-level genome assembly and population genomics of longan accessions 93%
- Redirecting DNA repair for efficient CRISPR-Cas-based gene targeting in tomato 92%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.