Assembly and comparative analysis of the four complete mitochondrial genomes in Rehmannia (Orobanchaceae): structural diversity and evolutionary insights
Abstract
Species within the genus Rehmannia Bunge ex Link (Orobanchaceae Vent.) are traditional Chinese medicinal plants with important therapeutic and horticultural values. Although bioactive ingredients and related metabolic pathways in Rehmannia species have been extensively studied, their mitochondrial genomes remain poorly explored. We successfully assembled the complete mitochondrial genomes of four Rehmannia species investigated in this study: R. glutinosa (Gaertn.) Libosch. ex Fisch. & C.A.Mey., R. henryi N.E.Br., R. piasezkii Maxim., and R. chingii (Prain) P.C.Tsoong. Structural characterization revealed distinct genome organizations: R. glutinosa (547,002 bp) and R. piasezkii (742,657 bp) exhibited typical single circular molecules, whereas R. chingii (662,985 bp) comprised one linear and two circular structures, and R. henryi (663,966 bp) contained four circular structures. Furthermore, repeat analysis revealed conserved SSR composition but quantitative variation in dispersed and tandem repeats among species, supporting the structural plasticity of Rehmannia mitogenomes. Despite this structural diversity, RNA editing profiles were highly conserved, with 394 C-to-U editing sites predicted across 31 protein-coding genes in each species. In addition, 21–28 MTPTs were identified in each mitogenome, including a conserved approximately 4.5-kb plastid-derived region containing complete sequences of ndhB (photosynthesis-related) and two plastid ribosomal protein genes ( rps7 and rps12 ). Phylogenetic analysis strongly supported the monophyly of Rehmannia , while nucleotide diversity and Ka/Ks analyses revealed overall conservation of mitochondrial protein-coding genes, with sdh3 , atp6 , and matR showing relatively higher sequence variation. These findings elucidate key characteristics of Rehmannia mitogenomes and highlight the coexistence of pronounced structural plasticity with conserved genomic features, providing insights into mitochondrial genome evolution and diversification within the genus.
