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Plastome Evolution and Codon Usage Dynamics in Argentina (Rosaceae): Phylogenomic Resolution and Adaptive Signatures
Guang-Nan Zhang1, Li-Zhen Ling2, Jie Tian1
1Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education Academy of Agriculture and Forestry Sciences of Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences) Xining China.
Ecology and Evolution
|July 28, 2026
Summary
The chloroplast genomes of the *Argentina* genus are highly stable, but synonymous codon usage shows variation. Natural selection, not mutation, drives these codon changes, suggesting adaptation to diverse environments.
Area of Science:
- Plant genomics and phylogenetics
- Molecular evolution and population genetics
Background:
- The *Argentina* genus (Rosaceae) presents taxonomic challenges due to morphological plasticity.
- Understanding chloroplast genome evolution and codon usage bias is crucial for resolving phylogenetic relationships and inferring adaptive processes.
Purpose of the Study:
- To analyze the chloroplast genome architecture, phylogenetic relationships, and synonymous codon usage bias (CUB) in the genus *Argentina*.
- To investigate the evolutionary forces shaping CUB and their potential role in adaptation to environmental heterogeneity.
Main Methods:
- Sequencing and analysis of complete chloroplast genomes from three *Argentina* species.
- Integration with existing congeneric plastome data for phylogenomic reconstruction.
- Analysis of synonymous codon usage bias using effective number of codons (ENC), codon adaptation index (CAI), and relative synonymous codon usage (RSCU).
Main Results:
- All *Argentina* plastomes exhibit conserved quadripartite structure and gene content, indicating high architectural stability.
- Phylogenomic analysis supports the monophyly of *Argentina* and clarifies the taxonomic placement of transferred species.
- Weak overall codon bias was observed, with natural selection identified as the primary driver of CUB variation (>95%).
- Interspecific variation in optimal codons suggests independent modulation by ecological selection.
Conclusions:
- The *Argentina* genus displays a decoupled evolutionary architecture: ultraconserved genome organization alongside dynamic synonymous codon usage.
- Reciprocal fine-tuning between plastid translational machinery and environmental selection likely shapes codon choice for adaptation.
- This study provides insights into how *Argentina* modulates organellar gene expression to cope with diverse environments across its range.
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