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1. Acropra DNA extraction with Qiagen DNAease tissue kit V.1

   https://doi.org/10.17504/protocols.io.bcwuixew  

   Baums, I (March 2020, Protocolsio)

   null (Ed.)

   DNA extraction protocol for Acropora tissue based on Qiagen DNAeasy kit THIS PROTOCOL ACCOMPANIES THE FOLLOWING PUBLICATION Baums IB, Hughes CR, Hellberg MH (2005) Mendelian microsatellite loci for the Caribbean coral Acropora palmata. Mar Ecol Prog Ser 288:115-127. doi:10.3354/meps288115. dx.doi.org/10.17504/protocols.io.bcwuixew 

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2. Sampling strategies and sample preservation Acropora V.2

   https://doi.org/dx.doi.org/10.17504/protocols.io.bec8jazw  

   Baums, I (May 2020, Protocolsio)

   null (Ed.)

   Protocol describes sampling strategies, perservation and shipping of Acropora samples for Applied Biosystems™ Axiom™ Coral Genotyping Array – 550961 (384f) Applied Biosystems™ Axiom™ Coral Genotyping Array – 550962 (Mini 96) THIS PROTOCOL ACCOMPANIES THE FOLLOWING PUBLICATION Kitchen SA, Von Kuster G, Vasquez Kuntz KL, Reich HG, Miller W, Griffin S, Fogarty ND, Baums IB (2020) STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts. bioRxiv 10.1101/2020.01.21.914424:2020.2001.2021.914424. doi:10.1101/2020.01.21.914424. dx.doi.org/10.17504/protocols.io.bec8jazw 

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3. Genome assembly and annotation of Acropora pulchra from Mo’orea French Polynesia

   https://doi.org/10.46471/gigabyte.153  

   Conn, Trinity; Ashey, Jill; Cunning, Ross; Putnam, Hollie M (April 2025, Gigabyte)

   Reef-building corals are integral ecosystem engineers of tropical reefs but face threats from climate change. Investigating genetic, epigenetic, and environmental factors influencing their adaptation is critical. Genomic resources are essential for understanding coral biology and guiding conservation efforts. However, genomes of the coral genus Acropora are limited to highly-studied species. Here, we present the assembly and annotation of the genome and DNA methylome of Acropora pulchra from Mo’orea, French Polynesia. Using long-read PacBio HiFi and Illumina RNASeq, we generated the most complete Acropora genome to date (BUSCO completeness of 96.7% metazoan genes). The assembly size is 518 Mbp, with 174 scaffolds, and a scaffold N50 of 17 Mbp. We predicted 40,518 protein-coding genes and 16.74% of the genome in repeats. DNA methylation in the CpG context is 14.6%. This assembly of the A. pulchra genome and DNA methylome will support studies of coastal corals in French Polynesia, aiding conservation and comparative studies of Acropora and cnidarians. 

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4. Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata

   https://doi.org/10.7717/peerj.4077  

   Devlin-Durante, Meghann K.; Baums, Iliana B. (January 2017, PeerJ)

   null (Ed.)

   The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata , to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species. 

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5. Genome assembly and annotation of Acropora pulchra from Mo’orea, French Polynesia

   https://doi.org/10.1101/2025.03.27.645822  

   Conn, Trinity; Ashey, Jill; Cunning, Ross; Putnam, Hollie (April 2025, Gigabyte)

   Abstract Reef-building corals are integral ecosystem engineers in tropical coral reefs worldwide but are increasingly threatened by climate change and rising ocean temperatures. Consequently, there is an urgency to identify genetic, epigenetic, and environmental factors, and how they interact, for species acclimatization and adaptation. The availability of genomic resources is essential for understanding the biology of these organisms and informing future research needs for management and and conservation. The highly diverse coral genusAcroporaboasts the largest number of high-quality coral genomes, but these remain limited to a few geographic regions and highly studied species. Here we present the assembly and annotation of the genome and DNA methylome ofAcropora pulchrafrom Mo’orea, French Polynesia. The genome assembly was created from a combination of long-read PacBio HiFi data, from which DNA methylation data were also called and quantified, and additional Illumina RNASeq data forab initiogene predictions. The work presented here resulted in the most completeAcroporagenome to date, with a BUSCO completeness of 96.7% metazoan genes. The assembly size is 518 Mbp, with 174 scaffolds, and a scaffold N50 of 17 Mbp. Structural and functional annotation resulted in the prediction of a total of 40,518 protein-coding genes, and 16.74% of the genome in repeats. DNA methylation in the CpG context was 14.6% and predominantly found in flanking and gene body regions (61.7%). This reference assembly of theA. pulchragenome and DNA methylome will provide the capacity for further mechanistic studies of a common coastal coral in French Polynesia of great relevance for restoration and improve our capacity for comparative genomics inAcroporaand cnidarians more broadly. 

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