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.
Highlights
Scleractinian corals serve the critical ecological role of building reefs that provide billions of dollars annually in goods and services[1] and sustain high levels of biodiversity[2]
We address these questions based on orthology of protein-coding genes, which generalizes the approaches taken by Bhattacharya et al.[10] and Voolstra et al.[17] to a larger set of complete genomes to describe both shared and unique adaptations in the Scleractinia
Total non-repetitive 31mer content was estimated at 262 Mb and the sum of contigs was 226 Mb, indicating that up to 14% of non-repetitive content may be missing from the assembly, likely due to high heterozygosity (Dovetail Genomics, personal communication)
Summary
Scleractinian corals serve the critical ecological role of building reefs that provide billions of dollars annually in goods and services[1] and sustain high levels of biodiversity[2]. We present the genome of Pocillopora damicornis, one of the most abundant and widespread reef-building corals in the world[18] This ecologically important coral is a model species and is commonly used in experimental biology and physiology. We address the following critical questions: (1) which genes are specific to or diversified within the scleractinian lineage, (2) which genes are specific to or diversified within individual scleractinian coral species, and (3) which features distinguish the P. damicornis genome from those of other corals We address these questions based on orthology of protein-coding genes, which generalizes the approaches taken by Bhattacharya et al.[10] and Voolstra et al.[17] to a larger set of complete genomes to describe both shared and unique adaptations in the Scleractinia. We reveal prominent diversification and expansion of immune-related genes, demonstrating that immune pathways are the subject of diverse evolutionary adaptations in corals
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