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Comparative plastid genomics of Elaeagnaceae: Resolving phylogeny and revealing structural evolution
Wei Gu1, Ji-Gui Yuan2, Li-Bo Zhao1
1Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 101408, China; Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing 100093, China.
Genomics
|March 11, 2026
Summary
This study analyzed 71 plastomes from 62 Elaeagnaceae species, revealing conserved plastome structure but unresolved Elaeagnus relationships due to rapid evolution. Protein-coding genes offered the best phylogenetic resolution for Hippophae.
Area of Science:
- Plant genomics
- Phylogenetics
- Evolutionary biology
Background:
- The Elaeagnaceae family has an established backbone phylogeny, but intrageneric relationships within the genus Elaeagnus remain unclear.
- Family-wide plastome evolution in Elaeagnaceae is not well understood.
Purpose of the Study:
- To reconstruct phylogenies within Elaeagnaceae using plastome data.
- To explore family-wide plastome evolution.
- To investigate the phylogenetic complexity and adaptive evolution of Elaeagnaceae.
Main Methods:
- Analysis of 71 plastomes from 62 species, including four newly sequenced Elaeagnus L. samples.
- Phylogenetic reconstruction using protein-coding genes (PCGs), intergenic spacers (IGS), and complete plastome sequences.
- Identification of repeat sequences and signals of positive selection.
Main Results:
- Protein-coding genes (PCGs) provided the strongest phylogenetic resolution, clarifying relationships within Hippophae L.
- Elaeagnus topologies remained poorly resolved across all datasets, suggesting rapid evolutionary radiation.
- Plastome structure was highly conserved, with lineage-specific IR expansion observed in Hippophae.
- Repeat sequences and signals of positive selection were identified.
Conclusions:
- This study provides crucial plastomic resources for the Elaeagnaceae family.
- The findings highlight the phylogenetic complexity within Elaeagnus, likely due to rapid radiation.
- Conserved plastome structure with specific exceptions (Hippophae IR expansion) provides insights into evolutionary patterns.
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