Genomic variants among threatened Acropora corals
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ABSTRACTGenomic sequence data for non-model organisms are increasingly available requiring the development of efficient and reproducible workflows. Here, we develop the first genomic resources and reproducible workflows for two threatened members of the reef-building coral genusAcropora. We generated genomic sequence data from multiple samples of the CaribbeanA. cervicornis(staghorn coral) andA. palmata(elkhorn coral), and predicted millions of nucleotide variants among these two species and the PacificA. digitifera. A subset of predicted nucleotide variants were verified using restriction length polymorphism assays and proved useful in distinguishing the two Caribbean Acroporids and the hybrid they form (A. prolifera). Nucleotide variants are freely available from the Galaxy server (usegalaxy.org), and can be analyzed there with computational tools and stored workflows that require only an internet browser. We describe these data and some of the analysis tools, concentrating on fixed differences betweenA. cervicornisandA. palmata. In particular, we found that fixed amino acid differences between these two species were enriched in proteins associated with development, cellular stress response and the hosts interactions with associated microbes, for instance in the Wnt pathway, ABC transporters and superoxide dismutase. Identified candidate genes may underlie functional differences in the way these threatened species respond to changing environments. Users can expand the presented analyses easily by adding genomic data from additional species as they become available.Article SummaryWe provide the first comprehensive genomic resources for two threatened Caribbean reef-building corals in the genusAcropora. We identified genetic differences in key pathways and genes known to be important in the animals response to the environmental disturbances and larval development. We further provide a list of candidate loci for large scale genotyping of these species to gather intra- and interspecies differences betweenA. cervicornisandA. palmataacross their geographic range. All analyses and workflows are made available and can be used as a resource to not only analyze these corals but other non-model organisms.
