{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Li X"],"funding":["United Soybean Board","National Science Foundation"],"pagination":["koaf279"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12679596"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["37(12)"],"pubmed_abstract":["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 and cis-regulatory landscapes of duplicated genes in cultivated soybean (Glycine max), which has undergone 2 rounds of whole-genome duplication. Our analysis revealed extensive diversity of transcriptional profiles within and across tissues among duplicated gene pairs. Within-tissue divergence was largely attributable to genetic variation in their associated accessible chromatin regions (ACRs), where cis-regulatory elements reside, whereas cross-tissue divergence was more likely shaped by dynamics in ACR chromatin accessibility profiles across tissues. Distinct duplication mechanisms also likely give rise to different types of cis-regulatory variants, contributing variably to transcriptional divergence. By comparing ACRs associated with gene sets derived from 2 rounds of whole-genome duplication and sharing a common ancestral gene, we found that most ACRs retained one or multiple corresponding duplicated sequences in which mutations gradually accumulated over time, while a subset likely arose de novo. Finally, we traced the evolution of cell-type-specific expression and cell-type-specific ACRs within duplicated gene sets, illustrating a powerful framework for identifying candidate regulatory regions driving cell-type-specific expression. Collectively, our findings highlight the important role of cis-regulatory evolution in shaping transcriptional divergence in a spatiotemporal manner, uncovered with the resolution of single-cell genomics."],"journal":["The Plant cell"],"pubmed_title":["From duplication to divergence: Single-cell insights into transcriptional and cis-regulatory landscapes in soybean."],"pmcid":["PMC12679596"],"funding_grant_id":["IOS-1856627","2432-201-0102"],"pubmed_authors":["Li X","Schmitz RJ","Zhang X"],"additional_accession":[]},"is_claimable":false,"name":"From duplication to divergence: Single-cell insights into transcriptional and cis-regulatory landscapes in soybean.","description":"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 and cis-regulatory landscapes of duplicated genes in cultivated soybean (Glycine max), which has undergone 2 rounds of whole-genome duplication. Our analysis revealed extensive diversity of transcriptional profiles within and across tissues among duplicated gene pairs. Within-tissue divergence was largely attributable to genetic variation in their associated accessible chromatin regions (ACRs), where cis-regulatory elements reside, whereas cross-tissue divergence was more likely shaped by dynamics in ACR chromatin accessibility profiles across tissues. Distinct duplication mechanisms also likely give rise to different types of cis-regulatory variants, contributing variably to transcriptional divergence. By comparing ACRs associated with gene sets derived from 2 rounds of whole-genome duplication and sharing a common ancestral gene, we found that most ACRs retained one or multiple corresponding duplicated sequences in which mutations gradually accumulated over time, while a subset likely arose de novo. Finally, we traced the evolution of cell-type-specific expression and cell-type-specific ACRs within duplicated gene sets, illustrating a powerful framework for identifying candidate regulatory regions driving cell-type-specific expression. Collectively, our findings highlight the important role of cis-regulatory evolution in shaping transcriptional divergence in a spatiotemporal manner, uncovered with the resolution of single-cell genomics.","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Dec","modification":"2026-05-23T03:16:36.605Z","creation":"2026-05-23T03:10:11.869Z"},"accession":"S-EPMC12679596","cross_references":{"pubmed":["41285681"],"doi":["10.1093/plcell/koaf279"]}}