De Novo Sequencing of Drymaria villosa and Comparative Analysis of Plastome in Caryophyllaceae Across 23 Species.

Abstract

Plant plastome are well studied due to their essential roles in photosynthesis and plant development. Comparative studies among plastome of closely related genera or families are limited, hindering our understanding of evolutionary changes and adaptation. This study presents a comparative analysis of 23 Caryophyllaceae plastome revealing a dynamic interplay of conserved and variable features. The genome size exhibited a moderate coefficient of variation (CV) of 2.58%. The large single-copy (LSC) and small single-copy (SSC) regions were highly conserved, with CVs of 2.55% and 2.00%, respectively. In contrast, the inverted repeat (IR) regions displayed greater variability, with a CV of 4.23%, indicating dynamic evolutionary processes. Exon counts varied significantly (CV 17.20%), while intron counts showed some variability (CV 7.79%), reflecting diverse gene structures. Coding sequences had moderate variability (CV 3.67%), while non-coding sequences varied more (CV 5.05%). tRNA counts were slightly variable (CV 2.67%), and GC content was notably consistent (CV 0.40%). This study includes the newly sequenced plastome of Drymaria villosa (GenBank accession OR790517), confirming its placement within Caryophyllaceae with significant diversification through phylogenetic analysis. Correlations (> 0.6) among plastome components and genome size reflect their tight evolutionary linkage, enhancing our understanding of plastome evolution in Caryophyllaceae and aiding future investigations into the ecological and medicinal potential of D. villosa and related species.