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The agarophyte  Ahnfeltia  (Ahnfeltiales, Rhodophyta) is a globally widespread genus with 11 accepted species names. Two of the most widespread species in this genus,  A. plicata  and  A. fastigiata , may have diverged genetically due to past geographic changes and subsequent geographic isolation. To investigate this genomic and genetic diversity, we generated new plastid (ptDNAs) and mitochondrial genomes (mtDNAs) of these  Ahnfeltia  species from four different regions ( A. plicata  - Chile and UK and  A. fastigiata  - Korea and Oregon). Two architecture variations were found in the  Ahnfeltia  genomes: in ptDNA of  A. fastigiata  Oregon, the hypothetical pseudogene region was translocated, likely due to recombination with palindromic repeats or a gene transfer from a red algal plasmid. In mtDNA of  A. fastigiata  Korea, the composition of the group II intronic ORFs was distinct from others suggesting different scenarios of gain and loss of group II intronic ORFs. These features resulted in genome size differences between the two species .  Overall gene contents of organelle genomes of  Ahnfeltia  were conserved. Phylogenetic analysis using concatenated genes from ptDNAs and mtDNAs supported the monophyly of the Ahnfeltiophycidae. The most probable individual gene trees showed that the  Ahnfeltia  populations were genetically diversified. These trees, the  cox 1 haplotype network, and a dN/dS analysis all supported the theory that these  Ahnfeltia  populations have diversified genetically in accordance with geographic distribution.

Organelle Genome Variation in the Red Algal Genus Ahnfeltia (Florideophyceae)