A Snapshot of a Coral “Holobiont”: A Transcriptome Assembly of the Scleractinian Coral, Porites, Captures a Wide Variety of Genes from Both the Host and Symbiotic Zooxanthellae

Abstract

Massive scleractinian corals of the genus Porites are important reef builders in the Indo-Pacific, and they are more resistant to thermal stress than other stony corals, such as the genus Acropora. Because coral health and survival largely depend on the interaction between a coral host and its symbionts, it is important to understand the molecular interactions of an entire “coral holobiont”. We simultaneously sequenced transcriptomes of Porites australiensis and its symbionts using the Illumina Hiseq2000 platform. We obtained 14.3 Gbp of sequencing data and assembled it into 74,997 contigs (average: 1,263 bp, N50 size: 2,037 bp). We successfully distinguished contigs originating from the host (Porites) and the symbiont (Symbiodinium) by aligning nucleotide sequences with the decoded Acropora digitifera and Symbiodinium minutum genomes. In contrast to previous coral transcriptome studies, at least 35% of the sequences were found to have originated from the symbionts, indicating that it is possible to analyze both host and symbiont transcriptomes simultaneously. Conserved protein domain and KEGG analyses showed that the dataset contains broad gene repertoires of both Porites and Symbiodinium. Effective utilization of sequence reads revealed that the polymorphism rate in P. australiensis is 1.0% and identified the major symbiotic Symbiodinium as Type C15. Analyses of amino acid biosynthetic pathways suggested that this Porites holobiont is probably able to synthesize most of the common amino acids and that Symbiodinium is potentially able to provide essential amino acids to its host. We believe this to be the first molecular evidence of complementarity in amino acid metabolism between coral hosts and their symbionts. We successfully assembled genes originating from both the host coral and the symbiotic Symbiodinium to create a snapshot of the coral holobiont transcriptome. This dataset will facilitate a deeper understanding of molecular mechanisms of coral symbioses and stress responses.

Development of a Novel Reference Transcriptome for Scleractinian Coral Porites lutea Using Single-Molecule Long-Read Isoform Sequencing (Iso-Seq)

“…Mean GC content of the Symbiodinium transcripts (51.77%) was also consistent with previous reports (Bayer et al, 2012;Shinzato et al, 2014;Mansour et al, 2016). Interestingly, the GC content distribution of transcripts assigned to Symbiodinium transcriptome had a smaller peak at ∼42% (Figure 1), suggesting that a small fraction of the "Symbiodinium" transcripts share the GC content characteristic with coral transcripts.…”

“…Mean GC content of the coral-specific assembly was 42.04%, which was comparable to the numbers reported for other anthozoan transcriptomes (Figure 1) (Shinzato et al, 2014;Anderson et al, 2016;Mansour et al, 2016;Frazier et al, 2017;Kenkel and Bay, 2017). Mean GC content of the Symbiodinium transcripts (51.77%) was also consistent with previous reports (Bayer et al, 2012;Shinzato et al, 2014;Mansour et al, 2016).…”

“…Such information is crucial for understanding the adaptive capacity of the coral holobionts (Hughes et al, 2003). The availability of transcriptome data from a number of coral species and their associated Symbiodinium allows us to probe the molecular stress response of the organisms to heat stress (Traylor-Knowles et al, 2011;Moya et al, 2012;Kenkel et al, 2013;Shinzato et al, 2014;Kitchen et al, 2015;Anderson et al, 2016;Davies et al, 2016). Here, we report the first reference transcriptome for a scleractinian coral Porites lutea, one of the dominant reef-builders in the Indo-West Pacific (Yeemin et al, 2009).…”

Using Seawater to Document Coral-Zoothanthella Diversity: A New Approach to Coral Reef Monitoring Using Environmental DNA

“…Scleractinian corals, including Acropora, form obligate endosymbioses with photosynthetic dinoflagellates of the genus Symbiodinium (Yellowlees et al, 2008;Bourne et al, 2009;Shinzato et al, 2014a). The genus Symbiodinium displays tremendous taxonomic and physiological diversity (Lajeunesse, 2001;Stat et al, 2008).…”

Transcriptomic Resilience of the Montipora digitata Holobiont to Low pH

“…The N50 length was 1,101 bp for the coral and 744 bp for Symbiodinium sp. G+C content of both reference transcriptomes were 43.9 and 54.5%, consistent with previous reports for the Order Scleractinia and Symbiodinium spp., respectively (Bayer et al, 2012;Shoguchi et al, 2013;Sun et al, 2013;Shinzato et al, 2014). Summary quality statistics for both transcriptomes are summarized in Table 1.…”