Phylogeny and ultrastructure of a non-toxigenic dinoflagellate Amphidoma fulgens sp. nov. (Amphidomataceae, Dinophyceae), with a wide distribution across Asian Pacific

•A marine thecate dinoflagellate Amphidoma fulgens sp. nov., widely distributed across the Asian Pacific, is described.•The marine lipophilic toxin azaspiracids (AZAs) were not detected from Amphidoma fulgens, despite its close relationship to the AZA-producer Amphidoma languida.•Cells of Amphidoma fulgens possess vesicles containing crystalline structure, which are visible as refractile bodies by light microscopy.•Flagellar apparatus of Amphidoma fulgens lacks the striated root connective, which has been observed from gonyaulacoid and gymnodinioid dinoflagellates.•Environmental rDNAs related to Amphidoma languida, previously reported from the Asian Pacific, are identical to those of Amphidoma fulgens. Amphidoma languida, a marine thecate dinoflagellate that produces the lipophilic toxin azaspiracids (AZAs), is primarily found in the Atlantic. Although this species has not been recorded in the Asian Pacific, environmental DNAs related to Am. languida have been widely detected in the region by metabarcoding analysis. Their morphology and AZA production remain unclear. In this study, the morphology, ultrastructure, phylogeny, and AZA production of nine Amphidoma strains isolated from Japan, Malaysia, and Philippines were investigated. Phylogenetic trees inferred from rDNAs (SSU, ITS, and LSU rDNA) showed monophyly of the nine Pacific strains and were sister to the Am. languida clade, including the toxigenic strains from the Atlantic. Cells were ellipsoid, 8.7–16.7 µm in length and 7.4–14.0 µm in width, with a conspicuous apical pore complex. A large nucleus in the hyposome, parietal chloroplast with a spherical pyrenoid in the episome, and refractile bodies were observed. Thecal tabulation was typical of Amphidoma, Po, cp, X, 6ʹ, 6ʹʹ, 6C, 5S, 6ʹʹʹ, 2ʹʹʹʹ. A ventral pore was located on the anterior of 1ʹ plate, beside the suture to 6ʹ plate. The presence of a ventral depression, on the anterior of anterior sulcal plate, was different from Am. languida. A large antapical pore, containing approximately 10 small pores, was observed. Cells were apparently smaller than Am. trioculata, a species possessing three pores (ventral pore, ventral depression, and antapical pore). TEM showed the presence of crystalline structures, resembling guanine crystals, and cytoplasmic invaginations into the pyrenoid matrix. Flagellar apparatus lacking the striated root connective is similar to peridinioids and related dinoflagellates. AZAs were not detected from the Pacific strains