Using single-cell genomics to explore transcriptional divergence andcis-regulatory dynamics of duplicated genes

Gene duplication is a major source of evolutionary innovation, enabling the emergence of novel expression patterns and functions. Leveraging single-cell genomics, we investigated the transcriptional dynamics andcis-regulatory evolution of duplicated genes in cultivated soybean (Glycine max), a species that has undergone two rounds of whole-genome duplication. Our analysis revealed extensive transcriptional divergence among these duplicated gene pairs, including dosage balanced, paralogue dominance, divergence, specialization, and widespread mono-expressed pattern. These expression divergences are correlated with sequence variation in their associated accessible chromatin regions (ACRs), wherecis-regulatory elements reside. Moreover, different duplication mechanisms, including whole-genome duplication and small-scale duplication, likely give rise to distinct types ofcis-regulatory variants, leading to varying effects on transcriptional divergence. To further explore the evolution ofcis-regulatory elements and their impact on gene expression, we focused on gene sets in which duplicated genes are derived from two rounds of whole-genome duplication and share a common ancestral gene, ascis-regulatory elements are typically co-duplicated with genes during whole-genome duplication. Most ACRs were retained after duplication whereas a subset likely arosede novo. Both mutations in duplicated elements and the emergence ofde novoevolved elements contribute to widespread expression divergence within these gene sets. We also characterized the evolution of cell-type-specific expression and cell-type-specific ACRs among these sets. Collectively, our findings highlight the important role ofcis-regulatory evolution in shaping transcriptional divergence and facilitating the retention of duplicated genes, offering a high-resolution view through the lens of single-cell genomics.