Mitochondrial genomes from two red tide forming raphidophycean algae Heterosigma akashiwo and Chattonella marina var. marina

Chattonella marina (Subrahmanyan) Hara et Chihara var. marina and Heterosigma akashiwo Hada (Hada) are members of raphidophycean algae responsible for large-scale red tides resulting in mass mortality of cultured fishes. For accurate monitoring and controlling the ecological dynamics of these harmful algae, sensitive genetic markers are indispensable. Since mitochondrial (mt) DNA sequences have been used for biogeographical and population studies of various eukaryotic species, we expect that mt genomes of C. marina and H. akashiwo may contain useful sequence information that can be used to examine their ecological dynamics. The present study characterizes the complete mt genomes of C. marina var. marina and H. akashiwo. The mt genomes of C. marina var. marina and H. akashiwo are 44,772 bp and 38,690 bp in length, respectively. Curiously, C. marina and H. akashiwo mt genomes have independently experienced partial genome duplication. For in-depth investigation of the evolution of the partially duplicated regions in the C. marina mt genome, we further determined the corresponding region in the mt genomes of eight additional Chattonella strains sampled from C. marina and close relatives. Our sequence comparison revealed that the duplicated regions accumulated multiple deletions as well as substitutions and repeats. Significantly, the nine Chattonella strains can be distinguished from each other based on the characteristics of these regions.