The multichromosomal structure evolution of Dendrobium mitogenomes and new insights into interrelationships of recently radiated tribes in Epidendroideae (Orchidaceae)

Introduction Epidendroideae is the largest subfamily in Orchidaceae, comprising over 20,000 species in 16 tribes, which are renowned for their remarkable morphological diversity and beautiful flowers. Although phylogenetic relationships have been well-resolved in most tribes of Epidendroideae, controversies remain among some recently radiated tribes. To advance the knowledge of Epidendroideae relationships, we used complete mitochondrial sequences to reconstruct the phylogeny of 10 orchid species from the six recently radiated tribes of Epidendroideae. Methods We first de novo assembled the complete mitogenome of Dendrobium chrysanthum using Illumina and Nanopore data. A comparative analysis was then conducted on nine mitogenomes from three orchid subfamilies. Additionally, we newly assembled 10 mitochondrial genomes of orchid species from six Epidendroideae tribes for phylogeny reconstruction and reconstructed both the mitochondrial and plastid phylogenies for these tribes. Results and discussion The mitogenome of D. chrysanthumwas was 638,041 bp long with a multichromosomal structure. The comparative analysis of nine orchid mitogenomes revealed great variations in the structure and genome size, while sequence similarities among these mitogenomes were closely related to the phylogenetic affinity. Most clades were resolved in mitochondrial and plastid phylogenies. Moreover, the comparative analysis of phylogenetic topology showed discordances between the plastid and mitochondrial phylogenies. Our findings enriched the mitogenome database and the knowledge of evolutionary features of orchid mitogenomes. The whole genomic sequences of mitogenomes provided new insights into the interrelationships of Epidendroideae (Orchidaceae).