Dissecting mitogenomic conflict to illuminate angiosperm deep phylogeny: Sequence and architectural evidence

Liyun Nie; Jie Wang; Lei Huang; Jiali Kong; Bao Nie; Luke R. Tembrock; Shanshan Dong; Ravi Tiwari; Hui Wang; Shenglong Kan; Xinhui Zou; Zhiqiang Wu

doi:10.1016/j.pld.2025.10.003

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Dissecting mitogenomic conflict to illuminate angiosperm deep phylogeny: Sequence and architectural evidence

Journal article

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Dissecting mitogenomic conflict to illuminate angiosperm deep phylogeny: Sequence and architectural evidence

Liyun Nie, Jie Wang, Lei Huang, Jiali Kong, Bao Nie, Luke R. Tembrock, Shanshan Dong, Ravi Tiwari, Hui Wang, Shenglong Kan, …

Plant diversity, Vol.48(1), pp.41-58

2025

DOI: https://doi.org/10.1016/j.pld.2025.10.003

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Abstract

Angiosperm phylogeny

Ceratophyllales

Chloranthales

Evolutionary correlation

Mitochondrial genomes

Deep relationships in the angiosperm tree of life remain highly controversial. To address this, we first assembled the complete mitochondrial genomes for Ceratophyllum demersum and Chloranthus sessilifolius, confirming a well-supported sister relationship that starkly conflicts with nuclear and plastid data. To dissect this classic cyto-nuclear conflict, we developed the ‘PhyloForensics’ framework, a novel diagnostic approach to systematically identify sources of phylogenetic instability. This framework revealed that signal heterogeneity (topological entropy variance) and information content (the proportion of informative sites) are the primary drivers of gene-tree conflict. Empirically validating this, we show that removing a small subset of “loudly conflicted” genes resolves deep-level incongruence, yielding a single, highly-supported topology previously obscured by noise. Finally, complementing this sequence-based resolution, we demonstrate that mitogenome architecture provides powerful phylogenetic signals, revealing predictable, mitogenome-wide evolutionary patterns, such as a significant negative correlation between branch length and both GC content and RNA editing sites. By integrating a validated conflict-resolution framework with architectural genomics, our study provides a comprehensive strategy for navigating the complexities of deep evolutionary histories.

Details

Title: Dissecting mitogenomic conflict to illuminate angiosperm deep phylogeny: Sequence and architectural evidence
Authors/Creators: Liyun Nie - Agricultural Genomics Institute at Shenzhen
Jie Wang - Agricultural Genomics Institute at Shenzhen
Lei Huang - Shaanxi Normal University
Jiali Kong - Agricultural Genomics Institute at Shenzhen
Bao Nie - Agricultural Genomics Institute at Shenzhen
Luke R. Tembrock - Colorado State University
Shanshan Dong - Fairy Lake Botanical Garden
Ravi Tiwari - Murdoch University
Hui Wang - Fairy Lake Botanical Garden
Shenglong Kan - Agricultural Genomics Institute at Shenzhen
Xinhui Zou - State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
Zhiqiang Wu - Agricultural Genomics Institute at Shenzhen
Publication Details: Plant diversity, Vol.48(1), pp.41-58
Publisher: Elsevier B.V.
Identifiers: 991005828144407891
Murdoch Affiliation: School of Medical, Molecular and Forensic Sciences
Language: English
Resource Type: Journal article

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