Exploring Plastome Diversity and Molecular Evolution Within Genus <i>Tortula</i> (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 <i>Tortula</i>. We performed a comprehensive comparative plastome analysis of nine species within the genus <i>Tortula</i>, using <i>Syntrichia princeps</i> 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 <i>Tortula acaulon</i> exhibiting the most pronounced deviation. Phyloplastomic analysis based on maximum likelihood identified two major clades, indicating that <i>Tortula</i> section <i>Tortula</i> is not monophyletic. Several highly informative loci were found to replicate the full plastome phylogenetic signal. Additionally, a subset of genes, including <i>atp</i>E and <i>mat</i>K, exhibited nonsynonymous-to-synonymous substitution (dN/dS) ratios that suggest possible positive selection. These findings provide new insights into chloroplast genome evolution within <i>Tortula</i>, 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.