Pervasive historical introgression across oak phylogeny shapes gene expression
- 1Zhejiang University
Abstract
Oaks were once described as the "worst-case scenario" for the biological species concept because of the presumed pervasive hybridization and introgression among species. However, we still lack a full picture of genome-wide introgression across the eight sections of the Quercus phylogeny. Furthermore, we still do not have a complete characterization of what is introgressed and how it functionally influences the recipient species. Firstly, we used 168 whole genomes from 67 Quercus species belonging to the eight sections of the Quercus phylogeny and a super pan-genome to generate a phylogeny and test for ILS and introgression. Introgression was widespread: ancient introgression occurred between ancestors of the eight sections and more recent introgression took place within sections. Secondly, using genome-wide transcriptome, methylome, and chromatin accessibility data from a subset of 19 species sampled from four sections we demonstrated that introgressed genes are more highly and uniformly expressed than non-introgressed ones. This difference in expression level between introgressed and non-introgressed genes mostly results from cis-regulation, and is most likely due to DNA methylation decay in promoter ACRs. In summary, introgression has been a major evolutionary force during the whole evolutionary history of Quercus and had a significant impact on fundamental processes such as gene regulation and expression.
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BibTeX
@misc{zhu2026pervasive,
title = {{Pervasive historical introgression across oak phylogeny shapes gene expression}},
author = {Y. Zhu and R. Fu and M. Zhang and Y. Li and X. Teng and J. Wu and Y. Liu and Y. Zhang and Y. Lin and Z. Zhang and C. Pang and H. Wu and A. KREMER and M. Lascoux and J. Chen},
howpublished = {bioRxiv},
year = {2026},
month = jul,
doi = {10.64898/2026.07.16.739029},
url = {https://www.biorxiv.org/content/10.64898/2026.07.16.739029v2},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Pervasive historical introgression across oak phylogeny shapes gene expression
AU - Y. Zhu
AU - R. Fu
AU - M. Zhang
AU - Y. Li
AU - X. Teng
AU - J. Wu
AU - Y. Liu
AU - Y. Zhang
AU - Y. Lin
AU - Z. Zhang
AU - C. Pang
AU - H. Wu
AU - A. KREMER
AU - M. Lascoux
AU - J. Chen
PY - 2026
DA - 2026/07/16
PB - bioRxiv
DO - 10.64898/2026.07.16.739029
UR - https://www.biorxiv.org/content/10.64898/2026.07.16.739029v2
AB - Oaks were once described as the "worst-case scenario" for the biological species concept because of the presumed pervasive hybridization and introgression among species. However, we still lack a full picture of genome-wide introgression across the eight sections of the Quercus phylogeny. Furthermore, we still do not have a complete characterization of what is introgressed and how it functionally influences the recipient species. Firstly, we used 168 whole genomes from 67 Quercus species belonging to the eight sections of the Quercus phylogeny and a super pan-genome to generate a phylogeny and test for ILS and introgression. Introgression was widespread: ancient introgression occurred between ancestors of the eight sections and more recent introgression took place within sections. Secondly, using genome-wide transcriptome, methylome, and chromatin accessibility data from a subset of 19 species sampled from four sections we demonstrated that introgressed genes are more highly and uniformly expressed than non-introgressed ones. This difference in expression level between introgressed and non-introgressed genes mostly results from cis-regulation, and is most likely due to DNA methylation decay in promoter ACRs. In summary, introgression has been a major evolutionary force during the whole evolutionary history of Quercus and had a significant impact on fundamental processes such as gene regulation and expression.
ER -