Mitochondrial phylogenomics of eucheumatoids (Solieriaceae, Rhodophyta) from the Indo-Pacific

Eucheumatoid seaweeds are highly valued globally for their carrageenan. Members of this group are widely distributed and cultivated throughout the Indo-Pacific. Despite various molecular studies on this group, mitogenome research in eucheumatoids has only recently explored a limited number of species, leaving overall diversity largely unexplored. In this study, 26 complete mitogenomes of eucheumatoids from the Indo-Pacific were sequenced, including the first complete sequences for wild genotypes of <i>Eucheuma platycladum</i>, <i>Kappaphycus striatus</i>, <i>Kappaphycopsis cottonii,</i> and an unidentified species of <i>Kappaphycus</i> from Africa. The eucheumatoid mitogenomes range from 25.1 to 25.5 kb in size, containing 50 genes (24 protein-coding genes, 24 tRNA genes, two rRNA genes, and a single intron) bearing extensive gene synteny across species. Phylogenetic analyses using concatenated mitochondrial genes recovered strong clades for each group, with the exception of the genus <i>Eucheuma</i>. Apart from <i>atp</i>9, gene marker evaluations showed that all genes could be used for species identification. The utility of four genes, <i>atp</i>4, <i>nad</i>3, <i>nad</i>4, and <i>nad</i>6, was found to be effective for resolving intergeneric relationships. These findings provide a foundation for comparative analysis useful for resolving phylogenetic relationships and outstanding taxonomic issues, cultivar development, and conservation efforts. Expanding species coverage and incorporating plastome analyses would contribute to a more complete understanding of the genomic diversity and evolutionary history of this economically important group of seaweeds.<h4>Supplementary information</h4>The online version contains supplementary material available at 10.1007/s10811-026-03784-1.