Exploring Plastome Diversity and Molecular Evolution Within Genus (Family Pottiaceae, Bryophyta).

The Pottiaceae family represents one of the most diverse and ecologically adaptable bryophytes; however, its chloroplast genome diversity remains largely unexplored. This study aimed to investigate plastome variation and identify evolutionary informative loci within the moss genus . We performed a comprehensive comparative plastome analysis of nine species within the genus , using as an outgroup within the family Pottiaceae. High-quality chloroplast genomes were assembled and annotated based on next-generation sequencing (NGS) data. All plastomes exhibited conserved quadripartite structures with genome size ranging from 121,889 to 122,697 bp. Adenine-thymine (AT)-rich dinucleotide repeats were the most abundant simple sequence repeats (SSRs), and several genes contained unique higher-order SSRs, suggesting potential utility as population-level markers. Codon usage analysis revealed species-specific biases, particularly in leucine, serine, and threonine codons, with exhibiting the most pronounced deviation. Phyloplastomic analysis based on maximum likelihood identified two major clades, indicating that section is not monophyletic. Several highly informative loci were found to replicate the full plastome phylogenetic signal. Additionally, a subset of genes, including E and K, exhibited nonsynonymous-to-synonymous substitution (dN/dS) ratios that suggest possible positive selection. These findings provide new insights into chloroplast genome evolution within , while identifying candidate loci for future phylogenetic and evolutionary studies. This study contributes to a more robust understanding of plastome-based studies in Pottiaceae and highlights efficient molecular markers for broader bryophyte phylogenomics.