High intraindividual, intraspecific, and interspecific variability in large-subunit ribosomal DNA in the heterotrophic dinoflagellates Protoperidinium, Diplopsalis, and Preperidinium (Dinophyceae)

Abstract

K.E. Gribble and D.M. Anderson. 2007. High intraindividual, intraspecific, and interspecific variability in large-subunit ribosomal DNA in the heterotrophic dinoflagellates Protoperidinium, Diplopsalis, and Preperidinium (Dinophyceae). Phycologia 46: 315–324. DOI: 10.2216/06-68.1Large-subunit ribosomal DNA (LSU rDNA) gene sequences are frequently used to infer the phylogeny and species identity of organisms. The many copies of the LSU rDNA found in the genome are thought to be kept homogeneous by concerted evolution. In this study, we found high intraindividual, intraspecific and interspecific diversity in the D1-D6 region of the LSU rDNA in eight species of thecate, heterotrophic dinoflagellates using single-cell PCR, cloning, and sequencing of many clones. For each species, the clone library was usually comprised of one highly represented copy and many unique sequences. Sequence differences were primarily characterized by single base pair substitutions, single base pair insertion/deletions (indels), and/or large indels. Phylogenetic analysis of all sequence clones gave strong support for monophyly of the polymorphic copies of each species and recovered the same species tree as an analysis using just one sequence per species. Analysis of LSU rDNA expression in three species by RT-PCR indicated that expressed copies have fewer substitutions and fewer and smaller indels and that 50% or more of the copies are pseudogenes. High intraspecific and intraindividual LSU rDNA sequence variability could lead to inaccurate species phylogenies and overestimation of species diversity in environmental sequencing studies.