Mitochondrial cob and cox1 Genes and Editing of the Corresponding mRNAs in Dinophysis acuminata from Narragansett Bay, with Special Reference to the Phylogenetic Position of the Genus Dinophysis

Abstract

Dinophysis acuminata cells were isolated from Narragansett Bay water samples in June 2005 using flow cytometry. Dinoflagellate-specific PCR primers were used to isolate small-subunit rRNA (18S rRNA), mitochondrial cytochrome b (cob), and cytochrome c oxidase I (cox1) genes and the encoded cDNAs. Maximumlikelihood analysis of a concatenated data set of ribosomal DNA and cDNA sequences of cob and cox1 showed that D. acuminata was sister to Gonyaulacoids, but without strong bootstrap support. The approximately unbiased test could not reject alternative positions of D. acuminata. To gain better resolution, mRNA editing of cob and cox1 was inferred for D. acuminata and 13 other dinoflagellate species. The location and type of editing as well as the distribution pattern in D. acuminata were generally similar to those in other dinoflagellates except for two edited sites that are unique to this species. Bayesian analyses of a matrix that recorded the location and type of editing, and of a matrix that included the protein sequences of COB and COX1 with the editing data yielded tree topologies similar to the three-gene tree but again failed to resolve the phylogenetic position of D. acuminata. However, the density of edited sites in the D. acuminata mitochondrial genes, consistent with phylogenetic trees, indicated that Dinophysis is a derived dinoflagellate lineage, diverging after other lineages such as Oxyrrhis, Amphidinium, and Symbiodinium. We demonstrate that dinoflagellate-specific PCR coupled with flow cytometry can be a useful tool to analyze genes and their transcripts from a natural dinoflagellate population.

Exploring the identity of the Greek Dinophysis cf. acuminata

“…Recently, the mitochondrial phylogenetic markers cob and cox1, widely used for animal barcoding (Hebert et al, 2003), have proved very useful in delimiting Dinophysis species, at least within the D. acuminata complex (Raho et al, 2008;Zhang et al, 2008;Lin et al, 2009). Raho et al (2008) demonstrated the capacity of cox1 to distinguish D. acuminata from D. ovum.…”

“…Single or couplets of cells were used for all molecular work, a practice also successfully used in the past (Janson and Graneli, 2003;Raho et al, 2008;Zhang et al, 2008). In the phylogenetic analysis of the rDNA gene region, the sequences obtained in this study co-resided with most sequences assigned to species of the D. acuminata complex onto the well-supported Cluster I.…”

“…However, using well-established molecular markers from the ribosomal DNA (rDNA) regions has proved largely unfruitful in this attempt (Marín et al, 2001;Guillou et al, 2002). More recently, research on dinoflagellate taxonomy has turned to mitochondrial DNA (mtDNA) regions (Lin et al, 2002;Zhang et al, 2005;Lin et al, 2009) and molecular markers corresponding to conserved regions of the cytochrome b (cob) and cox1 genes have been successfully used in Dinophysis (Raho et al, 2008;Zhang et al, 2008).…”

Peculiarities within peculiarities – dinoflagellates and their mitochondrial genomes

“…The editing intensity increases from basal phylogenetic lineages, where it is absent, e.g. in Oxyrrhis marina, to the later branching ones known as the core dinoflagellates (Figure 1; Zhang et al 2008). Although RNA editing occurs in other organisms, the versatility and scale of changes is unprecedented in dinoflagellates.…”

Cloning, characterization, and expression of Cytochrome b (Cytb)—a key mitochondrial gene from Prorocentrum donghaiense

“…Genes of mitochondria can act like a molecular clock, and the evolution of mitochondria parallels that of the nucleus; therefore, Cytb has been widely used in studies of phylogenetic analysis in many species, including microalgae (Benne et al, 1986;Bernasconi et al, 2001;Lin et al, 2006). Moreover, Cytb of some species is subject to the phenomenon of RNA editing, which is signifi ed by changes in an RNA sequence compared to that of its encoding DNA (Zanlungo et al, 1993;Islas-Osuna et al, 2006;Zhang et al, 2008).…”