Plastome variation and phylogenetic relationships of Salsola species in China

The genus Salsola (Amaranthaceae) comprises approximately 130 species distributed across Asia, Africa, and Europe, many of which possess important medicinal, horticultural, and ecological significance. Known for its remarkable ecological plasticity, Salsola species thrive in arid, semi-arid, and saline-alkaline environments, serving as key components of desert plant communities. However, extreme environmental pressures have driven convergent evolution, resulting in morphological similarities that obscure phylogenetic relationships. While this structural complexity offers significant horticultural potential, the genus's evolutionary branching remains poorly understood. In this study, we analyzed complete plastomes of 14 well-defined Salsola species to resolve these primary phylogenetic lineages. The results show that Salsola plastomes range from 149,653 to 152,969 bp in length and harbor 130 annotated genes. These sequences exhibit high synteny, with inverted repeat (IR) regions showing greater conservation than single-copy regions. Our phylogenetic analysis resolved the genus into two basal clades. One clade predominantly consists of annual herbs (e.g., S. brachiata, S. collina, and S. ruthenica), while the other includes the shrub S. arbuscula and semi-shrubs such as S. orientalis, S. passerina, and S. abrotanoides. From the perspective of complete plastome data, our results appear to support Salsola as a well-supported monophyletic lineage. Nevertheless, this inference should be treated with caution because it is based solely on plastome evidence; broader taxon sampling and nuclear genomic data will be needed to further test this conclusion. By providing complete plastome resources for representative Salsola species, this study offers a genomic foundation for future taxonomic clarification, species identification, germplasm conservation, medicinal and horticultural utilization of the genus.