The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis

Abstract

Dinoflagellates are important components of marine ecosystems and essential coral symbionts, yet little is known about their genomes. We report here on the analysis of a high-quality assembly from the 1180-megabase genome of Symbiodinium kawagutii. We annotated protein-coding genes and identified Symbiodinium-specific gene families. No whole-genome duplication was observed, but instead we found active (retro)transposition and gene family expansion, especially in processes important for successful symbiosis with corals. We also documented genes potentially governing sexual reproduction and cyst formation, novel promoter elements, and a microRNA system potentially regulating gene expression in both symbiont and coral. We found biochemical complementarity between genomes of S. kawagutii and the anthozoan Acropora, indicative of host-symbiont coevolution, providing a resource for studying the molecular basis and evolution of coral symbiosis.

Current Knowledge and Recent Advances in Marine Dinoflagellate Transcriptomic Research

“…However, analysis of the Symbiodinium spp. genome sequence revealed the presence of those transcription factors suggesting that some genes in dinoflagellates are under the control of sequence-specific transcription factors [14,15]. Transcription factors in dinoflagellates are less abundant in comparison to those present in other protists such as Plasmodium, and it has been suggested that this low abundance may be a genomic signature for dinoflagellates [28].…”

“…Numerous novel dinoflagellate genes that are involved in gene regulation at the transcriptional and post-transcriptional level have been discovered in the Alexandrium catenella transcriptome, including homologs for a forkhead box protein (FOXL1), multiprotein bridging factor type 1 (MBF1), RAP2.4 and two identified TATA box-binding protein interacting proteins (TBP-IP; RuvB-like 1 and 2) [30]. Interestingly, the genome sequence of Symbiodinium kawagutii possesses a TATA-box binding protein (TBP)-like factor instead of TBP, which has high affinity toward the TTTT promoter motif [15]. The authors also suggested that the typical eukaryotic TATA box promoter motif is replaced by TTT(T/G) in dinoflagellates.…”

“…To date, only three dinoflagellates draft genomes have been sequenced from the genus Symbiodinium. A complete genome sequence is not yet available for most dinoflagellates; therefore, attempts to study dinoflagellates at the genomic level are difficult [13][14][15][16]. Studies of the transcriptome can be a practical alternative in such cases [17], commonly being used in large-scale studies of gene expression using either microarrays or next-generation sequencing (NGS) RNA-seq [18].…”

Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics

“…Detailed understanding of dinoflagellate biology has been limited by a paucity of sequence data, especially unusual features such as the organization of their very large and complex nuclear genomes (9,10). Poorly resolved dinoflagellate trees have further complicated predictions of how specific metabolic pathways evolved and how they are distributed in uncultured members of the group.…”

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

“…Although recently draft genomes of the coral symbionts dinoflagellates from the genus Symbiodinium were obtained and may serve as key model organism for transcriptome assembly, it was found to not be densely covered by high-quality draft genome sequences [14,18,[58][59][60]. Moreover, dinoflagellates transcriptome exhibits complex alternative splicing patterns and RNA-seq samples genetically exhibit polymorphism [61,62].…”