ArticleBMC plant biology2026
Integrative chloroplast genomics of Polygonaceae: evolutionary dynamics, codon optimization, and phylogenetic resolution.
Article in BMC plant biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
2 citing papers in PubMed.
- Article
- Plastome evidence repositionsFrontiers in plant science · 2026Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
backgroundThe Polygonaceae family comprises approximately 1,200 species of pharmacological, economic, and ecological importance, including medicinal genera such as Rheum, Polygonum, and Fagopyrum, which produce bioactive anthraquinones, stilbenes, and flavonoids. Despite their therapeutic importance, comprehensive analyses of chloroplast genomes across this family remain limited. Chloroplast genomes provide valuable molecular markers for evolutionary studies, phylogenetic reconstruction, and quality control of herbal medicines.
resultsThis study comprehensively analyzed chloroplast genomes across 48 Polygonaceae species, focusing on genome architecture, gene content, codon usage patterns, selection pressures, simple sequence repeats (SSRs), and phylogenetic relationships. All chloroplast genomes exhibited conserved quadripartite structures, with genome sizes ranging from 155,838 − 179,064 bp and GC contents ranging from 36.59 to 38.22%, demonstrating AT enrichment and a consistent bias toward A/U-ending codons. RSCU analysis revealed six universally optimal codons (AGA, GAU, GCU, UAU, UCU, and UUA) conserved across the family. ENC values (46.36–48.28) indicated weak overall codon bias; however, ENC-GC3 plots, neutrality, and PR2 analyses confirmed that natural selection, rather than mutational pressure, predominantly shaped synonymous codon usage. Ka/Ks analysis revealed that 89.1% of gene pairs were under strong purifying selection, with photosystem-related genes the most conserved. A total of 4,593 SSR loci were identified, predominantly mononucleotide repeats concentrated in intergenic regions. Collinearity analyses demonstrated high structural conservation within genera, with coding regions more conserved than noncoding sequences. Phylogenetic reconstruction delineated major lineages and suggested that subfamily-specific codon usage patterns correlate with ecological adaptation.
conclusionsThis study provides comprehensive insights into chloroplast genome evolution in Polygonaceae, highlighting the predominant role of natural selection in codon usage bias and identifying conserved genomic features, SSR resources, and phylogenetic relationships. These findings establish a foundation for molecular marker development, quality control of medicinal species, and evolutionary investigations of this pharmacologically important plant family.
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