The genomic architecture of introgression during Rhododendron speciation

Han-Tao Qin; Alex D. Twyford; Wei Zheng; Richard I. Milne; Li-Jun Yan; Zhi-Qiong Mo; Ming-Shu Zhu; Hans Wilhelm Nützmann; De-Zhu Li; Hong-Tao Li; Lian-Ming Gao

doi:10.1111/nph.70794

The genomic architecture of introgression during Rhododendron speciation

Han-Tao Qin, Alex D. Twyford, Wei Zheng, Richard I. Milne, Li-Jun Yan, Zhi-Qiong Mo, Ming-Shu Zhu, Hans Wilhelm Nützmann, De-Zhu Li^*, Hong-Tao Li^*, Lian-Ming Gao^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

• Understanding how genomic architecture shapes patterns of gene flow is fundamental to unraveling the mechanisms of plant speciation. Here, we investigate whether differential gene flow dynamics between genomic spatial compartments play a role in speciation of Rhododendron subsect. Scabrifolia.
• We first present a chromosome-level genome assembly for R. spinuliferum, and use this to characterize large-scale chromatin organization including A and B compartments. We then use genome resequencing data for 139 individuals from 15 populations of all eight species of R. subsect. Scabrifolia endemic to Southwest China to investigate speciation history.
• We find significant disparities in the extent of genomic differentiation between A and B compartments. The B compartment, closely associated with centromeres, tends to exhibit higher genetic differentiation, whereas the gene-rich A compartment appears less differentiated and exhibits more extreme fdm values, suggesting more extensive localized introgression.
• We propose that the heterogeneous nature of gene flow across genomic compartments contributes to speciation in Rhododendron, and may play a critical yet underappreciated role in gene flow dynamics in plants.

Original language	English
Pages (from-to)	2085-2102
Number of pages	18
Journal	New Phytologist
Volume	249
Issue number	4
Early online date	2 Dec 2025
DOIs	https://doi.org/10.1111/nph.70794
Publication status	Published - Feb 2026

Keywords / Materials (for Non-textual outputs)

A/B compartments
gene flow
genomic architecture
population genomics
Rhododendron
speciation

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MS-Rho speciation-clean-20251107Accepted author manuscript, 540 KBLicence: Creative Commons: Attribution (CC-BY)

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@article{ad9810088b78411aa82553c4034e50d6,

title = "The genomic architecture of introgression during Rhododendron speciation",

abstract = "• Understanding how genomic architecture shapes patterns of gene flow is fundamental to unraveling the mechanisms of plant speciation. Here, we investigate whether differential gene flow dynamics between genomic spatial compartments play a role in speciation of Rhododendron subsect. Scabrifolia. • We first present a chromosome-level genome assembly for R. spinuliferum, and use this to characterize large-scale chromatin organization including A and B compartments. We then use genome resequencing data for 139 individuals from 15 populations of all eight species of R. subsect. Scabrifolia endemic to Southwest China to investigate speciation history. • We find significant disparities in the extent of genomic differentiation between A and B compartments. The B compartment, closely associated with centromeres, tends to exhibit higher genetic differentiation, whereas the gene-rich A compartment appears less differentiated and exhibits more extreme fdm values, suggesting more extensive localized introgression. • We propose that the heterogeneous nature of gene flow across genomic compartments contributes to speciation in Rhododendron, and may play a critical yet underappreciated role in gene flow dynamics in plants. ",

keywords = "A/B compartments, gene flow, genomic architecture, population genomics, Rhododendron, speciation",

author = "Han-Tao Qin and Twyford, \{Alex D.\} and Wei Zheng and Milne, \{Richard I.\} and Li-Jun Yan and Zhi-Qiong Mo and Ming-Shu Zhu and N{\"u}tzmann, \{Hans Wilhelm\} and De-Zhu Li and Hong-Tao Li and Lian-Ming Gao",

note = "We extend our gratitude to Profs. Jinyong Hu, Andan Zhu, Shuai Nie, Guannan Wen and Jing Wang for their valuable comments on this study. Molecular experiments and data analysis were performed at the Laboratory of Molecular Biology and iFlora High Performance Computing Center of Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences. \_Author Contributions\_ LMG, HTL and DZL conceived and designed this research. LJY, WZ, HTQ, ZQM and MSZ collected and sequenced the plant material. HTQ conducted data analysis. HTQ, LMG, HTL, RM, AT and HWN wrote the manuscript. All authors edited, read and approved the final manuscript. ",

year = "2026",

month = feb,

doi = "10.1111/nph.70794",

language = "English",

volume = "249",

pages = "2085--2102",

journal = "New Phytologist",

issn = "0028-646X",

publisher = "Wiley-Blackwell",

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TY - JOUR

T1 - The genomic architecture of introgression during Rhododendron speciation

AU - Qin, Han-Tao

AU - Twyford, Alex D.

AU - Zheng, Wei

AU - Milne, Richard I.

AU - Yan, Li-Jun

AU - Mo, Zhi-Qiong

AU - Zhu, Ming-Shu

AU - Nützmann, Hans Wilhelm

AU - Li, De-Zhu

AU - Li, Hong-Tao

AU - Gao, Lian-Ming

N1 - We extend our gratitude to Profs. Jinyong Hu, Andan Zhu, Shuai Nie, Guannan Wen and Jing Wang for their valuable comments on this study. Molecular experiments and data analysis were performed at the Laboratory of Molecular Biology and iFlora High Performance Computing Center of Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences. _Author Contributions_ LMG, HTL and DZL conceived and designed this research. LJY, WZ, HTQ, ZQM and MSZ collected and sequenced the plant material. HTQ conducted data analysis. HTQ, LMG, HTL, RM, AT and HWN wrote the manuscript. All authors edited, read and approved the final manuscript.

PY - 2026/2

Y1 - 2026/2

N2 - • Understanding how genomic architecture shapes patterns of gene flow is fundamental to unraveling the mechanisms of plant speciation. Here, we investigate whether differential gene flow dynamics between genomic spatial compartments play a role in speciation of Rhododendron subsect. Scabrifolia. • We first present a chromosome-level genome assembly for R. spinuliferum, and use this to characterize large-scale chromatin organization including A and B compartments. We then use genome resequencing data for 139 individuals from 15 populations of all eight species of R. subsect. Scabrifolia endemic to Southwest China to investigate speciation history. • We find significant disparities in the extent of genomic differentiation between A and B compartments. The B compartment, closely associated with centromeres, tends to exhibit higher genetic differentiation, whereas the gene-rich A compartment appears less differentiated and exhibits more extreme fdm values, suggesting more extensive localized introgression. • We propose that the heterogeneous nature of gene flow across genomic compartments contributes to speciation in Rhododendron, and may play a critical yet underappreciated role in gene flow dynamics in plants.

AB - • Understanding how genomic architecture shapes patterns of gene flow is fundamental to unraveling the mechanisms of plant speciation. Here, we investigate whether differential gene flow dynamics between genomic spatial compartments play a role in speciation of Rhododendron subsect. Scabrifolia. • We first present a chromosome-level genome assembly for R. spinuliferum, and use this to characterize large-scale chromatin organization including A and B compartments. We then use genome resequencing data for 139 individuals from 15 populations of all eight species of R. subsect. Scabrifolia endemic to Southwest China to investigate speciation history. • We find significant disparities in the extent of genomic differentiation between A and B compartments. The B compartment, closely associated with centromeres, tends to exhibit higher genetic differentiation, whereas the gene-rich A compartment appears less differentiated and exhibits more extreme fdm values, suggesting more extensive localized introgression. • We propose that the heterogeneous nature of gene flow across genomic compartments contributes to speciation in Rhododendron, and may play a critical yet underappreciated role in gene flow dynamics in plants.

KW - A/B compartments

KW - gene flow

KW - genomic architecture

KW - population genomics

KW - Rhododendron

KW - speciation

UR - https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA024499

UR - https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA024491

UR - https://doi.org/10.57760/sciencedb.17142

U2 - 10.1111/nph.70794

DO - 10.1111/nph.70794

M3 - Article

SN - 0028-646X

VL - 249

SP - 2085

EP - 2102

JO - New Phytologist

JF - New Phytologist

IS - 4

ER -

The genomic architecture of introgression during Rhododendron speciation

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