Comparative analysis of the Pocillopora damicornis genome highlights role of immune system in coral evolution

Abstract

Comparative analysis of the expanding genomic resources for scleractinian corals may provide insights into the evolution of these organisms, with implications for their continued persistence under global climate change. Here, we sequenced and annotated the genome of Pocillopora damicornis, one of the most abundant and widespread corals in the world. We compared this genome, based on protein-coding gene orthology, with other publicly available coral genomes (Cnidaria, Anthozoa, Scleractinia), as well as genomes from other anthozoan groups (Actiniaria, Corallimorpharia), and two basal metazoan outgroup phlya (Porifera, Ctenophora). We found that 46.6% of P. damicornis genes had orthologs in all other scleractinians, defining a coral ‘core’ genome enriched in basic housekeeping functions. Of these core genes, 3.7% were unique to scleractinians and were enriched in immune functionality, suggesting an important role of the immune system in coral evolution. Genes occurring only in P. damicornis were enriched in cellular signaling and stress response pathways, and we found similar immune-related gene family expansions in each coral species, indicating that immune system diversification may be a prominent feature of scleractinian coral evolution at multiple taxonomic levels. Diversification of the immune gene repertoire may underlie scleractinian adaptations to symbiosis, pathogen interactions, and environmental stress.

Sequencing, de novo assembly and annotation of the genome of the scleractinian coral, Pocillopora acuta

“…predicted-genes encoding 79,506 alternatively spliced transcripts. The number of predicted genes using the experimental data is slightly higher to what was found for the two other sequenced symbiotic anthozoan (Shinzato et al 2011, Baumgarten et al 2015, Prada et al 2016, Voolstra et al 2017, Cunning et al 2018. However the number of putative transcripts encoded by these genes are in agreement with what was classically obtained in Anthozoan transcriptome assembly (Meyer et al 2009, Traylor-Knowles et al 2011, Lehnert et al 2012, Moya et al 2012, Shinzato et al 2014, Kitchen et al 2015.…”

“…However, there is still few reference genomes for the ecologically important hermatypic corals. To date four species were sequenced and assembled: Acropora digitifera (Shinzato et al 2011), Pocillopora damicornis (Cunning et al 2018), Stylophora pistillata (Voolstra et al 2017) and Orbicela faveolata (Prada et al 2016).…”

The past, present, and future of coral heat stress studies

“…Yet, only four fully sequenced genomes are currently available (Acropora digitifera (Shinzato et al, 2011), Acropora millepora (Ying et al, 2019), Pocillopora damicornis (Cunning, Bay, Gillette, Baker, & Traylor-Knowles, 2018), and Stylophora pistillata ). Yet, only four fully sequenced genomes are currently available (Acropora digitifera (Shinzato et al, 2011), Acropora millepora (Ying et al, 2019), Pocillopora damicornis (Cunning, Bay, Gillette, Baker, & Traylor-Knowles, 2018), and Stylophora pistillata ).…”

“…Reference genomes of a diverse range of corals will provide further insight into their biology and enable the development of new molecular tools. Yet, only four fully sequenced genomes are currently available (Acropora digitifera (Shinzato et al, 2011), Acropora millepora (Ying et al, 2019), Pocillopora damicornis (Cunning, Bay, Gillette, Baker, & Traylor-Knowles, 2018), and Stylophora pistillata ). The Reef Future Genomics Consortium recognized the urgency of this problem.…”

Population genetics of the coralAcropora millepora: Towards a genomic predictor of bleaching

“…We additionally sequenced two pools of aposymbiotic larvae and mapped these reads to our de novo assembly to remove symbiont contigs. In total, we assembled 475 Mb of sequence with chromosome-scale scaffolds for an N50 of 19.8 Mb and predicted 28,186 gene models, which include > 96% of core-eukaryotic single copy orthologs, making it the most complete coral genome constructed to date [24][25][26][27][28][29] .…”