Deciphering the plastome of Bergenia ciliata: comprehensive analysis of structure, codon usage pattern, and phylogenetic relationships within the medicinal family Saxifragaceae

Abstract

Although the biogeography and systematics of Saxifragaceae taxa have advanced, the plastome structure, evolution, and phylogeny of Bergenia ciliata remain to be investigated. The plastid genome comprises 131 genes, which include 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. Nucleotide diversity (Pi) analysis unveils significant variability in specific protein-coding genes, such as rps12_copy, matK, clpP, ndhF, and ccsA, that could be used as potential biomarkers. The IRb/SSC junction analysis reveals consistent transcription of ycf1 and ndhF across species. Exploration of Ka/Ks ratios in 89 protein-coding genes reveals that 73 genes are under purifying selection, while petL demonstrated positive selection. Codon usage bias analysis revealed variable ENC values (25.61–61), indicating preferences in codon usage, with neutrality plots indicating a GC-rich bias influenced by natural selection and mutation pressure. RSCU analysis demonstrates distinct preferences for certain codons, particularly A/T (U)-ending codons in B. ciliata. The phylogenetic analysis establishes a robust relationship, with B. ciliata and B. scopulosa forming a closely related cluster (BS=100) indicative of a shared recent common ancestor. This study provides a foundational genomic resource for exploring evolutionary dynamics and ecological interactions of B. ciliata within Saxifragaceae.