Comparative Analysis of the Plastid Genomes of Zephyranthes bagnoldii, Zephyranthes sarae, and Paposoa laeta from the Flowering Desert of the Atacama Region, Chile

Background: The Atacama “flowering desert” offers a natural setting to investigate plant genomic diversity and lineage differentiation in endemic geophytes shaped by long-term aridity, fragmented habitats, and ENSO-linked winter rains. We assembled, annotated, and compared complete plastid genomes for three Chilean taxa ( Zephyranthes bagnoldii , Zephyranthes sarae , and Paposoa laeta ) with two objectives: (i) to clarify their relationships within Hippeastreae, and (ii) to identify genome regions and repeat features that can be applied to species identification, population studies, and conservation planning in northern Chile and comparable deserts. Results: All three genomes showed the canonical quadripartite organization with broadly similar sizes (158,144 to 158,678 bp) and gene complements. Whole-genome alignments and synteny comparisons indicated overall collinearity, while boundary visualizations revealed modest shifts at the junctions between the large single-copy, small single-copy, and inverted repeat regions, most often involving rpl22 and ycf1 . Analyses of repetitive elements and simple sequence repeats (microsatellites) identified predominantly adenine/thymine-rich motifs and regions of elevated sequence variability in the single-copy portions, indicating multiple loci as suitable for DNA barcoding and population-level studies. Both subtribes within Hippeastreae are resolved as monophyletic, however, within subtribe Hippeastrinae , Zephyranthes is recovered as polyphyletic. Conclusions: These plastid genomes demonstrate strong architectural stability while revealing informative boundary differences and clear contrasts in repeat and microsatellite profiles. The identified regions of elevated variability provide usable markers for species delimitation, phylogeography, and monitoring of genetic connectivity in Amaryllidaceae Atacama geophytes. The recovered relationships confirm subtribal relationships between Traubiinae and Hippeastrinae and establish a plastid reference framework that supports integrative studies and conservation efforts in the flowering-desert system.