Pan-genome Analysis of Angiosperm Plastomes using PGR-TK

Abstract

We present a novel approach for taxonomic analysis of chloroplast genomes in angiosperms using the Pan-genome Research Toolkit (PGR-TK). Comparative plots generated by PGR-TK across diverse angiosperm genera reveal a wide range of structural complexity, from straightforward to highly intricate patterns. Notably, the characteristic quadripartite plastome structure, comprising the large single copy (LSC), small single copy (SSC), and inverted repeat (IR) regions, is clearly identifiable in over 75% of the genera analyzed. Our findings also underscore several occurrences of species mis-annotations in public genomic databases, which are readily detected through visual anomalies in the PGR-TK plots. While more complex plot patterns remain difficult to interpret, they likely reflect underlying biological variation or technical inconsistencies in genome assembly. Overall, this approach effectively integrates classical botanical visualization with modern molecular taxonomy, providing a powerful tool for genome-based classification in plant systematics.