Plastid Phylogenomics of Elatostemateae (Urticaceae): Insights Into Structural Variation and Phylogenetic Relationships

Abstract

ABSTRACT The tribe Elatostemateae, with approximately 1300 species, is the most species‐rich group within Urticaceae, yet plastome evolution and several intergeneric relationships remain incompletely resolved. We analyzed 40 species representing the major extant lineages of Elatostemateae using complete plastomes and nuclear ribosomal DNA (nrDNA); Metapilea was excluded because suitable DNA material was unavailable. Plastomes retained the typical angiosperm quadripartite structure and ranged from 143,738 to 163,969 bp. Comparative analyses revealed large inversions in the large single‐copy (LSC) region, pronounced inverted‐repeat (IR) boundary shifts, and a rare plastid mitochondrial DNA‐derived sequence (PTMT) insertion. Seven highly variable regions were identified as candidate markers for DNA barcoding. Plastome, protein‐coding sequence (CDS), nrDNA, and combined analyses recovered the same three major Elatostemateae clades, although several internal nrDNA nodes had lower support. Plastid and nrDNA data placed Gyrotaenia as sister to Pilea s.l. within Elatostemateae, whereas recent low‐copy nuclear evidence places Gyrotaenia + Myriocarpa sister to core Elatostemateae, revealing cytonuclear discordance. These results provide a framework for Elatostemateae systematics and document substantial plastome structural variation; denser low‐copy nuclear or whole‐genome sampling will be needed to distinguish incomplete lineage sorting from historical introgression.