Utility of mitochondrial‐encoded cytochrome c oxidase I gene for phylogenetic analysis and species identification of the planktonic diatom genus Skeletonema

SUMMARY Small subunit ( SSU ) and large subunit ( LSU ) r DNA sequences have been commonly used to delineate the taxonomy and biogeography of the planktonic diatom genus Skeletonema , but the genes occur as multiple copies and are therefore not suitable for barcoding purposes. Here, we analyzed phylogenetic relationships of Skeletonema using the mitochondrial‐encoded cytochrome c oxidase I gene ( cox 1), as well as partial LSU r DNA ( D 1– D 3) and SSU r DNA , to identify the factors that define species and to evaluate the utility of these three markers for this taxon. Twelve Skeletonema species were divided into six clades, I–VI , each of which comprised the same species by the three markers: clades I ( S. japonicum , S. grethae , S. pseudocostatum , and S. tropicum ), II ( S. menzelii ), III ( S. dohrnii and S. marinoi ), IV ( S. costatum , S. potamos , and S. subsalsum ), V ( S. grevillei ), and VI ( S. ardens ). However, the branching order among these clades was incongruent among the markers. In clade III , six S. marinoi strains had identical cox 1 sequences. These S. marinoi strains branched along with S. dohrnii , except for strains from the G ulf of N aples, with high support in cox 1. Species delimitation between S. dohrnii and S. marinoi was therefore not supported. In clade IV , S. costatum and S. subsalsum were robustly clustered, with S. potamos as a sister clade in the cox 1 tree, not in the LSU and SSU trees. In clade II , cox 1 also confirmed that S. menzelii includes three subclades potentially distinguishable from each other by morphological features. Cox 1 proved to be the most useful marker for the identification of Skeletonema species because it gave a tree with highly supported clades, has sufficient variation within and among species, encodes a protein in a single copy, and requires relatively few primers.