Phylogenomic and comparative analyses of plastomes of the tribe Marsdenieae (Apocynaceae: Asclepiadoideae): insights into plastome characteristics and generic relationships with an emphasis on Asian genera

BACKGROUND: The tribe Marsdenieae is one of the five tribes within the subfamily Asclepiadoideae of the Apocynaceae. To date, the evolutionary dynamics of plastomes and phylogenetic relationships within the tribe Marsdenieae (Apocynaceae) remain poorly understood, particularly regarding the structural diversity driven by variations in the boundary of inverted repeat (IR). This study aimed to elucidate the evolutionary history of plastome structure and refine the taxonomic framework of Marsdenieae by analyzing IR boundary dynamics, repeat sequence features, and phylogenetic signals. RESULTS: In this study, 76 plastomes of tribe Marsdenieae were analyzed using phylogenomic approaches and ancestral state reconstruction to investigate plastome structural variation and its evolutionary trajectory. Phylogenetic signals associated with variations of IR boundary were evaluated using EM Mantel tests and Delta statistics. Although Marsdenieae plastomes retain a conserved quadripartite structure, they exhibit substantial size variation (156,364-179,121 bp), primarily driven by IR expansion. Five types of the IR boundary (I-V) were identified, with Type III inferred as ancestral state; Type IV further diversified into three subtypes (Ⅳa, Ⅳb, and Ⅳc) corresponding to distinct clades (Clades A1, A2, and A5). Plastome phylogenetic analyses supported two major clades within Marsdenieae but revealed non-monophyly in genera Hoya, Marsdenia, and Dregea, and two Asian monotypic genera, Sinomarsdenia and Dolichopetalum, were supported as distinct genera. Moreover, based on molecular and morphological evidence, we propose merging Gongreos into Sinomarsdenia. Moreover, Asian Marsdenia species resolved into two subclades, while Dregea sinensis formed a represented lineage clearly separated from core Dregea taxa, indicating a well-supported phylogenetic divergence between these groups. CONCLUSIONS: IR boundary dynamics were central to plastome diversity in Marsdenieae, and IR structural variations were strongly consistent with phylogenetic signals, thus supporting relevant taxonomic revisions. However, complex relationships within Hoya and allied genera underscore the limitations of plastome data alone, highlighting the need for future integration of nuclear genomic data together with morphological and biogeographical evidence. This study advances our understanding of plastome evolution in Apocynaceae and highlights the urgency of resolving polyphyly and refining generic boundaries of Asian genera in the tribe Marsdenieae.