Proof that dinoflagellate spliced leader (DinoSL) is a useful hook for fishing dinoflagellate transcripts from mixed microbial samples: Symbiodinium kawagutii as a case study

Abstract

The ability to analyze dinoflagellate lineage-specific transcriptomes in the natural environment would be powerful for gaining understanding on how these organisms thrive in diverse environments and how they form harmful algal blooms and produce biotoxins. This can be made possible by lineage-specific mRNA markers such as the dinoflagellate-specific trans-spliced leader (DinoSL). By constructing and sequencing a 5'-cap selective full-length cDNA library for a monoculture of the coral reef endosymbiotic dinoflagellate Symbiodinium kawagutii and a DinoSL-based cDNA library for a mixture of S. kawagutii and other phytoplankton, we found DinoSL in essentially all full-length cDNAs in the 5'-cap selective library. We also discovered that the DinoSL-based library contained functionally diverse transcripts all belonging to dinoflagellates with no evidence of biases toward certain groups of functional genes. The results verified that DinoSL is specific to dinoflagellate mRNAs and is ubiquitous in the dinoflagellate transcriptomes. Annotation of the unigene dataset generated from the two libraries combined indicated high functional diversity of the transcriptome and revealed some biochemical pathways previously undocumented in Symbiodinium such as an mRNA splicing machinery potentially serving both cis- and trans-splicing. The protocol will be useful for transcriptomic studies of Symbiodinium in hospite and other dinoflagellates in natural environments.

Keywords: DinoSL; Dinoflagellates; full-length cDNA; lineage-specific; metatranscriptomics..