Comparative mitogenomics reveals extensive structural diversity and evolutionary dynamics in Dioscorea

Dioscorea (yam) is an economically and medicinally important monocotyledonous genus. While the nuclear and chloroplast genomes of several yam species have been characterized, mitochondrial genomic resources remain limited. Comparative mitochondrial genomes can reveal structural variation and provide complementary evidence for comparisons among closely related accessions. We assembled and compared mitochondrial genomes from ten Dioscorea species. Nonredundant genome sizes ranged from 475,742 to 584,909 bp, with conserved gene complements but substantial structural variation. Decomposition of the complex D. esculenta and D. sansibarensis graphs identified three and two candidate paths, respectively, and long-read in silico PCR supported the tested node connections. Rearrangements among several left-handed lineages remained after circular start and strand normalization, whereas focal D. polystachya and D. japonica assemblies were collinear across aligned mitochondrial blocks. Mitochondrial, chloroplast and nuclear phylogenies used 40, 74 and 2,259 CDS, respectively. High mitochondrial identity and low nuclear divergence indicated that the analyzed data from SRA project PRJNA766491, submitted under D. japonica , closely resemble the sampled D. polystachya datasets. The independent D. japonica dataset DRR822998 showed greater nuclear differentiation. These comparisons raise the possibility of an error in the species label or sample association of the analyzed PRJNA766491 records, although ITS differences leave this interpretation unresolved. Dioscorea mitochondrial genomes combine conserved coding content with diverse arrangements. The genomic comparison also identifies a possible discrepancy between the analyzed PRJNA766491 data and their submitted species label that warrants checking against the original sample and submission records.