Comparative plastome analyses and phylogenetic insights of Elatostema

Elatostema, one of the largest genera in Urticaceae, comprises approximately 570 species. The taxonomic delimitation of Elatostema and its closely related genera, Elatostematoides and Procris and the infrageneric classification of Elatostema, have historically been challenging. Previous studies have been limited by insufficient molecular data, hindering our understanding of species-level relationships and the evolution of plastid genomes in this group. To address these limitations, we assembled and analyzed a comprehensive plastome analysis of 42 species across Elatostema and its allied genera. Our study focused on plastome structure, sequence diversity, and phylogenetic relationships to elucidate the evolutionary history of these taxa.

Our findings reveal that Elatostema plastomes exhibit a typical quadripartite structure, with genome sizes ranging from 149,152 bp to 164,019 bp. Comparative analysis of plastome structures across Elatostema and its related genera indicates high conservation in genome size, structure, gene content, and inverted repeat boundary configuration. Our findings indicate a strong association between the length of small single-copy (SSC) regions and phylogenetic grouping within Elatostema and between Elatostema, Elatostematoides and Procris. The length variations in the ndhF-rpl32, rpl32-trnL, and rps15-SSC/IRa regions may account for this observed correlation, highlighting the utility of SSC sequences in resolving phylogenetic relationships within this genus. Furthermore, we identified seven highly variable regions with potential as DNA barcodes for species identification and phylogenetic analysis. Our phylogenomic analysis provides robust support for the taxonomic delimitation of Elatostema s.l. into three distinct genera: Elatostema, Procris, and Elatostematoides. We also reconfirm the infrageneric classification of Elatostema into four major clades.

The utilization of plastome sequences has enabled a highly resolved phylogenetic framework, shedding light on the evolutionary history and speciation mechanism within Elatostema, particularly its species-rich core Elatostema clade. These findings provide a valuable foundation for future taxonomic revisions and evolutionary studies within this challenging plant group.