Transcriptome Profiling of a Toxic Dinoflagellate Reveals a Gene-Rich Protist and a Potential Impact on Gene Expression Due to Bacterial Presence

Abstract

BackgroundDinoflagellates are unicellular, often photosynthetic protists that play a major role in the dynamics of the Earth's oceans and climate. Sequencing of dinoflagellate nuclear DNA is thwarted by their massive genome sizes that are often several times that in humans. However, modern transcriptomic methods offer promising approaches to tackle this challenging system. Here, we used massively parallel signature sequencing (MPSS) to understand global transcriptional regulation patterns in Alexandrium tamarense cultures that were grown under four different conditions.Methodology/Principal FindingsWe generated more than 40,000 unique short expression signatures gathered from the four conditions. Of these, about 11,000 signatures did not display detectable differential expression patterns. At a p-value < 1E-10, 1,124 signatures were differentially expressed in the three treatments, xenic, nitrogen-limited, and phosphorus-limited, compared to the nutrient-replete control, with the presence of bacteria explaining the largest set of these differentially expressed signatures.Conclusions/SignificanceAmong microbial eukaryotes, dinoflagellates contain the largest number of genes in their nuclear genomes. These genes occur in complex families, many of which have evolved via recent gene duplication events. Our expression data suggest that about 73% of the Alexandrium transcriptome shows no significant change in gene expression under the experimental conditions used here and may comprise a “core” component for this species. We report a fundamental shift in expression patterns in response to the presence of bacteria, highlighting the impact of biotic interaction on gene expression in dinoflagellates.

Functional group-specific traits drive phytoplankton dynamics in the oligotrophic ocean

“…The dominance of dinoflagellates in the 5-μm size fraction, confirmed in historic surface pigment analyses at Station ALOHA (29), stands in contrast to previous eukaryotic metatranscriptome studies in the oligotrophic ocean, where they accounted for <5% of reads (16). Although clearly present and important to the community, dinoflagellate read abundance here and in sediment trap data collected during the same cruise series (30) may be magnified by their large transcript pool (31,32).…”

“…The lack of change in the QMF of dinoflagellates (Fig. 2B) likely reflects their range of life strategies (32) and minimal transcriptional regulation of gene expression as observed in culture studies (31).…”

Metatranscriptome analyses indicate resource partitioning between diatoms in the field

“…Studies focused on nutrient geochemistry and phytoplankton quotas or uptake have emphasized the importance of nutrients to community dynamics, but these studies do not generally examine resource partitioning between individual species (30,31). Transcriptional studies provide speciesspecific resolution, but few studies have examined the global expression of nutrient metabolism pathways in the field (32) or in organisms lacking a fully sequenced genome (33,34), and as a result, the mechanistic underpinnings of phytoplankton resource metabolism in situ are not well understood. In situ global gene expression analyses (metatranscriptome profiling) are a means for elucidating a species' metabolic capacity and examining Significance Nutrient availability plays a central role in driving the activities and large-scale distributions of phytoplankton, yet there are still fundamental gaps in understanding how phytoplankton metabolize nutrients, like nitrogen (N) and phosphorus (P), and how this metabolic potential is modulated in field populations.…”

RNA-Seq as an Emerging Tool for Marine Dinoflagellate Transcriptome Analysis: Process and Challenges

“…Coyne et al [37] developed a novel approach to facilitate the construction of SAGE libraries for dinoflagellates which require a lower amount of RNA to identify genes expressed during toxic zoospores stages of Pfiesteria shumwayae. Apparently, the SAGE method did not get too much attention and this method was soon replaced by Massively Parallel Signature Sequencing (MPSS) which covers a deeper sequencing depth and more sensitive to low abundance genes compared to SAGE [2,38]. Utilization of the MPSS method has proven useful for Alexandrium spp.…”

“…Dinoflagellates have been studied extensively for their role in maintaining coral reefs and their toxin production especially during the event of Harmful algae blooms (HABs) in the ocean [2][3][4]. HABs caused by dinoflagellates has been associated with water discoloration and accumulation of toxins through the marine food chain, gave a severe negative impact toward economic and health [5,6].…”