Analysis of the plastid and mitochondrial genomes offer robust frameworks for identifying evolutionary relationships in red algae. The Solieriaceae is a family of red algae that includes the species of the economically important Kappaphycus and Eucheuma (eucheumatoids) that are valuable sources of carrageenan. Despite this, the composition and arrangement of retained and lost organelle genes remain underexplored in the Solieriaceae. Comparative genomic and phylogenetic analyses of the family Solieriaceae were performed with newly generated complete plastid and mitochondrial genome sequences from Kappaphycus alvarezii, K. striatus, and Eucheuma denticulatum, the three primary cultivated taxa. Results revealed that the plastid gene pbsA, which is broadly conserved across most red algal plastid genomes, and the more sparsely distributed gene ycf57, were both absent from Kappaphycus. This represents the first documented co-occurrence of plastid pbsA and ycf57 loss in K. alvarezii and K. striatus. However, Eucheuma denticulatum was shown to have pbsA (693 bp) and ycf57 (354 bp) with conserved synteny, matching arrangements in other Soliericeae members. Mitochondrial genomes were structurally conserved across the family, whereas plastid genomes showed greater evolutionary variability, including lineage-specific gene loss. Compared to single-locus markers like cox1 and rbcL, phylogenomic analyses based on concatenated plastid (197 protein-coding genes) and mitochondrial (22 protein-coding genes) datasets produced phylogenies with better resolution and stronger nodal support. The loss of plastid pbsA and ycf57, which are associated with heme and iron–sulfur–related processes in photosynthesis, suggests adaptive plastid genome streamlining in Kappaphycus rather than generalized genome degradation. Our results provide novel plastid and mitochondrial genome sequences and comparative genomic insights for the Solieriaceae, highlight contrasting evolutionary patterns, with lineage-specific plastid gene loss and localized structural variation, in contrast to the high conservation observed in mitochondrial genomes.

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