Coexpression enhances cross-species integration of single-cell RNA sequencing across diverse plant species

Abstract

Single-cell RNA sequencing is increasingly used to investigate cross-species differences driven by gene expression and cell-type composition in plants. However, the frequent expansion of plant gene families due to whole-genome duplications makes identification of one-to-one orthologues difficult, complicating integration. Here we demonstrate that coexpression can be used to trim many-to-many orthology families down to identify one-to-one gene pairs with proxy expression profiles, improving the performance of traditional integration methods and reducing barriers to integration across a diverse array of plant species. To enhance cross-species single-cell analysis, the authors find gene pairs with similar expression patterns across 13 species. These coexpression proxies serve as common features in datasets, improving integrative and comparative cell-type analysis.