Mitochondrial genome of the North American Morus rubra L. (red mulberry) reveals plastome gene transfer and essence of RNA editing

Abstract Morus rubra L. (Family: Moraceae), native to eastern North America, is distributed in the heart of pristine riparian forests and holds important ethnobotanical and ecological values. The species is severely threatened by introgressive hybridization with the introduced congener Morus alba , which is native to Asia. Insights into the mitochondrial (mito) genome of M. rubra along with comparative analyses against M. alba could potentially bridge the current knowledge gaps in understanding the genome architecture and hybridization patterns. The objectives of this study were to (1) sequence and assemble the draft mitogenome of M. rubra , and (2) perform a comparative mitogenomic phylogenetic analysis with the other 36 angiosperm taxa. M. rubra leaf sample from Waubonsie State Park (Fremont County, Iowa) was sequenced for mitogenome analysis within the scope of the species’ whole genome project. The mitogenome of M. rubra was 359,221 base pairs (bp) long with 45.8% GC content, comprising 57 genes: 32 protein-coding, 21 transfer, and four ribosomal RNAs. The chloroplast-to-mitogenome DNA transfer analysis revealed genes being synchronized with 17 homologous fragments from the chloroplast, accounting for 3.63% of the mitogenome. A total of 372 C to U RNA editing sites were detected in the mitochondrial protein-coding genes (mtPCGs) – responsible for the preprocessing of rpl16 and rps4 by adding a start codon, while postprocessing atp9 , ccmFN , and sdh4 by introducing a stop codon. The phylogenetic analysis of 37 species based on 23 shared mtPCGs revealed a tree topology identical to that proposed by the Angiosperm Phylogeny Group (APG) IV. This study is the first to report on the mitogenome of M. rubra , elucidating the mitogenome-based phylogeny and providing insights into the population genetics and evolution of mulberries. The publicly available M. rubra mitogenome enriches genomic resources for Moraceae and highlights the roles of SSRs, RNA editing, and inter-organellar DNA transfer in shaping mitogenome architecture.