title: High-level diversity of dinoflagellates in the natural environment, revealed by assessment of mitochondrial cox1 and cob genes for dinoflagellate DNA barcoding.
abstract: DNA barcoding is a diagnostic technique for species identification using a short, standardized DNA. An effective DNA barcoding marker would be very helpful for unraveling the poorly understood species diversity of dinoflagellates in the natural environment. In this study, the potential utility for DNA barcoding of mitochondrial cytochrome c oxidase 1 (cox1) and cytochrome b (cob) was assessed. Among several primer sets examined, the one amplifying a 385-bp cob fragment was most effective for dinoflagellates. This short cob fragment is easy to sequence and yet possess reasonable taxon resolution. While the lack of a uniform gap between interspecific and intraspecific distances poses difficulties in establishing a phylum-wide species-discriminating distance threshold, the variability of cob allows recognition of species within particular lineages. The potential of this cob fragment as a dinoflagellate species marker was further tested by applying it to an analysis of the dinoflagellate assemblages in Long Island Sound (LIS) and Mirror Lake in Connecticut. In LIS, a highly diverse assemblage of dinoflagellates was detected. Some taxa can be identified to the species and some to the genus level, including a taxon distinctly related to the bipolar species Polarella glacialis, and the large number of others cannot be clearly identified, due to the inadequate database. In Mirror Lake, a Ceratium species and an unresolved taxon were detected, exhibiting a temporal transition from one to the other. We demonstrate that this 385-bp cob fragment is promising for lineage-wise dinoflagellate species identification, given an adequate database.
authors.affiliation: Department of Marine Sciences, University of Connecticut, Groton, Connecticut 06340, USA. senjie.lin@uconn.edu
authors.forename: Senjie
authors.initials: S
authors.lastname: Lin
authors.forename: Huan
authors.initials: H
authors.lastname: Zhang
authors.forename: Yubo
authors.initials: Y
authors.lastname: Hou
authors.forename: Yunyun
authors.initials: Y
authors.lastname: Zhuang
authors.forename: Lilibeth
authors.initials: L
authors.lastname: Miranda
mesh_terms: D000818:Animals; D044822:Biodiversity; D045303:Cytochromes b / Q000235:genetics*; D017931:DNA Primers / Q000235:genetics; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics; D004141:Dinoflagellida / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D003576:Electron Transport Complex IV / Q000235:genetics*; D004783:Environmental Microbiology; D024101:Mitochondrial Proteins / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D014481:United States
chemical_list: D017931:DNA Primers; D004272:DNA, Mitochondrial; D024101:Mitochondrial Proteins; D045303:Cytochromes b; D003576:Electron Transport Complex IV