Abstract
BackgroundThe most diverse marine ecosystems, coral reefs, depend upon a functional symbiosis between cnidarian hosts and unicellular dinoflagellate algae. The molecular mechanisms underlying the establishment, maintenance, and breakdown of the symbiotic partnership are, however, not well understood. Efforts to dissect these questions have been slow, as corals are notoriously difficult to work with. In order to expedite this field of research, we generated and analyzed a collection of expressed sequence tags (ESTs) from the sea anemone Aiptasia pallida and its dinoflagellate symbiont (Symbiodinium sp.), a system that is gaining popularity as a model to study cellular, molecular, and genomic questions related to cnidarian-dinoflagellate symbioses.ResultsA set of 4,925 unique sequences (UniSeqs) comprising 1,427 clusters of 2 or more ESTs (contigs) and 3,498 unclustered ESTs (singletons) was generated by analyzing 10,285 high-quality ESTs from a mixed host/symbiont cDNA library. Using a BLAST-based approach to predict which unique sequences derived from the host versus symbiont genomes, we found that the contribution of the symbiont genome to the transcriptome was surprisingly small (1.6–6.4%). This may reflect low levels of gene expression in the symbionts, low coverage of alveolate genes in the sequence databases, a small number of symbiont cells relative to the total cellular content of the anemones, or failure to adequately lyse symbiont cells. Furthermore, we were able to identify groups of genes that are known or likely to play a role in cnidarian-dinoflagellate symbioses, including oxidative stress pathways that emerged as a prominent biological feature of this transcriptome. All ESTs and UniSeqs along with annotation results and other tools have been made accessible through the implementation of a publicly accessible database named AiptasiaBase.ConclusionWe have established the first large-scale transcriptomic resource for Aiptasia pallida and its dinoflagellate symbiont. These data provide researchers with tools to study questions related to cnidarian-dinoflagellate symbioses on a molecular, cellular, and genomic level. This groundwork represents a crucial step towards the establishment of a tractable model system that can be utilized to better understand cnidarian-dinoflagellate symbioses. With the advent of next-generation sequencing methods, the transcriptomic inventory of A. pallida and its symbiont, and thus the extent of AiptasiaBase, should expand dramatically in the near future.
Highlights
The most diverse marine ecosystems, coral reefs, depend upon a functional symbiosis between cnidarian hosts and unicellular dinoflagellate algae
We report the generation and analysis of 10,285 high-quality expressed sequence tags (ESTs) from a Symbiodinium clade Ahosting clonal population of Aiptasia pallida that was likely derived from an individual originating from the Florida Keys lineage, which were processed through a software pipeline [36] resulting in a user-friendly, queryable, web-accessible database named AiptasiaBase
Because of the possibility that two unique sequences (UniSeqs) originated from the same transcript, we estimated the number of unique genes in our dataset by assembling only the reverse reads of the directionally cloned cDNAs
Summary
The most diverse marine ecosystems, coral reefs, depend upon a functional symbiosis between cnidarian hosts and unicellular dinoflagellate algae. The dinoflagellates are classified in a single genus, Symbiodinium, but molecular methods have revealed a high genetic diversity in this genus [1,2] The onset of these symbioses has been shown to display flexibility, but a range of specificity, i.e. from highly flexible to highly specific, is apparent during its maintenance [3,4,5,6,7,8]. This process is likely to involve early recognition mechanisms [9,10] and an evasion of the hosts' digestive and immune systems [11], as well as adaptations to diverse ecological niches [12,13] and physiological acclimation [14,15]. Our knowledge of the underlying cellular and molecular mechanisms that facilitate the recognition between the partners, and determine the specificity, dynamics, and collapse of cnidarian-dinoflagellate symbioses, is limited
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