Comparative plastome analysis reveals evolutionary dynamics and codon usage patterns in Bidens (Asteraceae)

Plastome evolution in species-rich angiosperm lineages remains poorly understood despite recent advances in phylogenomics, particularly regarding the mechanistic drivers of codon usage bias (CUB) and their relationship to adaptive evolution. The genus Bidens (Asteraceae), comprising approximately 280 species, represents a morphologically diverse lineage with significant medicinal and economic value. Here, we assembled the complete plastid genome (plastome) of Bidens alba and conducted comprehensive comparative analyses across 31 Bidens species, integrating structural characterization, simple sequence repeat (SSR) distribution, codon usage bias assessment, and selection pressure analysis through Ka/Ks ratios and phylogenomic reconstruction. All plastomes exhibited the canonical angiosperm quadripartite structure (150,490 − 151,856 bp) with consistent AT bias (average GC content: 37.48%) and mononucleotide SSR predominance (37.43%). Twenty-nine high-frequency codons displayed strong AT preference, with multiple analytical approaches confirming natural selection as the primary driver of codon usage bias. The non-synonymous (Ka) /synonymous (Ks) substitution ratios revealed that most protein-coding genes showed evidence of purifying selection (Ka/Ks < 0.5), though the ycf2 and accD genes displayed elevated ratios suggesting adaptive evolution. Phylogenomic reconstruction supported Bidens monophyly with high bootstrap values and resolved species relationships with high confidence. Comparative structural analysis revealed exceptional genomic conservation across the genus, suggesting that while sequence evolution has occurred, the fundamental genomic architecture remains stable. These findings provide crucial insights into significant structural conservation across Bidens plastomes while demonstrating active sequence-level evolution, providing crucial insights into plastome evolutionary mechanisms within rapidly diversifying lineages and establish a robust genomic framework for understanding ecological adaptation and phylogenetic relationships in this ecologically important lineage.