Species diversity of amphidomatacean dinoflagellates belonging to Azadinium and Amphidoma was examined by microscopic observation and ITS- and LSU rDNA-based phylogeny, using 81 culture strains and two uncultured cells from Japanese waters during 2016–2024. In total, 11 species were found in Japanese waters. Of these, Azadinium caudatum, Az. cuneatum, Az. dexteroporum, and Az. spinosum were newly found in the Northwest Pacific, Az. dalianense was the first report in Japan, and Azadinium inconspicuum sp. nov. was a new species described in this study. Azadinium inconspicuum independently branched in the clade of Az. dexteroporum/Az. galwayense/Az. perfusorium but differed from Az. dexteroporum in shape of the Po plate (absent vs. present of the finger-like protrusion), from Az. galwayense in shape of the 2a plate (four- vs. five-sided), and from Az. perfusorium in position of pyrenoid (in the episome vs. at the antapex). It had a close resemblance to Az. luciferelloides in thecal morphology, but differed in detailed position of the ventral pore and shape of the posterior sulcal plate. Azaspiracids (AZAs) were detected in Azadinium poporum and Az. spinosum, but no trace was found in other amphidomatacean cultures, including Az. dexteroporum. Among 81 cultures examined, 47 cultures were assigned to Az. poporum, and belonged to four intraspecific ribotypes. Major AZA components in Japanese Az. poporum strains were AZA-59 (ribotype A1), AZA-2 (ribotype A2), AZA-2, -11, -36, -40 (ribotype B), and AZA-2 (ribotype C1). These results suggested that Az. poporum, particularly in ribotype C1, where high AZA amounts were detected, is the major AZA-producer along the Japanese coastal waters.
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