Assessing the utility of mitochondrial gene markers in the family Suessiaceae (Dinophyta) with phylogenomic validation

[Display omitted] •We assessed mitochondrial genes to develop robust molecular markers of the family Suessiaceae.•Phylogenetic relationships were inferred from nuclear and mitochondrial genes with a large collection of isolates.•The validity of molecular markers was evaluated using phylogenomic analysis.•The cob gene can be a novel marker reflecting topology at the genome-scale within the family. The dinoflagellate family Suessiaceae comprises cosmopolitan species distributed across polar and tropical waters in both marine and freshwater ecosystems, encompassing free-living forms, symbionts, and parasites. Recently, species diversity within the family has rapidly expanded, now including a few species reported to cause red tides. Despite their ecological and evolutionary importance, classifying them within Suessiaceae is difficult due to the limitations of the existing molecular markers—the highly conserved small subunit ribosomal gene (SSU rDNA) and the presence of two indel regions of sequence fragments of the large subunit ribosomal gene (LSU rDNA)—resulting in poorly resolved phylogenetic relationships. We assessed mitochondrial cytochrome b (cob) and cytochrome c oxidase 1 (cox1) genes to develop robust molecular markers that can reveal the genetic diversity of the family Suessiaceae. The divergences of cob and cox1 sequences among the species in the family were greater than the SSU rDNA but less than the LSU rDNA and the ITS region. Moreover, the distinctive topology inferred from the mitochondrial genes provided high resolution among the suessiacean species. We examined the validity of the genetic markers using phylogenomics based on 2,023 core proteins. The divergence of the cob phylogeny was most consistent with that of the phylogenomic results. Taken together, the cob gene can be a novel marker reflecting topology at the genome-scale within the family Suessiaceae.