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1. Acropora DNA extraction with Qiagen DNeasy tissue kit V.2

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

   Baums, I; Kitchen, SA (May 2020, Protocolsio)

   null (Ed.)

   DNA extraction protocol for Acropora or other coral tissue based on Qiagen DNAeasy kit. This extraction protocol works well for the Acropora SNPchip and other coral genotyping applications (such as microsatellite genotyping). It preferrentially extracts coral host DNA but some Symbiodiniacea DNA will be present. 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.bgjqjumw 

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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. Whole genome assembly and annotation of the endangered Caribbean coral Acropora cervicornis

   https://doi.org/10.1093/g3journal/jkad232  

   Selwyn, Jason D; Vollmer, Steven V (October 2023, G3: Genes, Genomes, Genetics)

   Vogel, K (Ed.)

   Abstract Coral species in the genus Acropora are key ecological components of coral reefs worldwide and represent the most diverse genus of scleractinian corals. While key species of Indo-Pacific Acropora have annotated genomes, no annotated genome has been published for either of the two species of Caribbean Acropora. Here we present the first fully annotated genome of the endangered Caribbean staghorn coral, Acropora cervicornis. We assembled and annotated this genome using high-fidelity nanopore long-read sequencing with gene annotations validated with mRNA sequencing. The assembled genome size is 318 Mb, with 28,059 validated genes. Comparative genomic analyses with other Acropora revealed unique features in A. cervicornis, including contractions in immune pathways and expansions in signaling pathways. Phylogenetic analysis confirms previous findings showing that A. cervicornis diverged from Indo-Pacific relatives around 41 million years ago, with the closure of the western Tethys Sea, prior to the primary radiation of Indo-Pacific Acropora. This new A. cervicornis genome enriches our understanding of the speciose Acropora and addresses evolutionary inquiries concerning speciation and hybridization in this diverse clade. 

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4. Phenotyping 3D coral models in MeshLab

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

   Million, WC; Kenkel, C (July 2020, Protocolsio)

   null (Ed.)

   This protocol describes the process of phenotyping branching coral using the 3D model editing software, MeshLab. MeshLab is a free, straightforward software to analyze 3D models of corals that is especially useful in its ability to import color from Agisoft Metashape models. This protocol outlines the steps used by the Kenkel lab to noninvasively phenotype Acropora cervicornis colonies for total linear extension (TLE), surface area, volume, and volume of interstitial space. We incorporate Agisoft Metashape markers with our Tomahawk scaling system (see Image Capture Protocol) in our workflow which is useful for scaling and to improve model building. Other scaling objects can be used, however these markers provide a consistent scale that do not obstruct the coral during image capture. MeshLab measurements of TLE have been groundtruthed to field measures of TLE. 3D surface area and volume have not yet been compared to traditional methods of wax dipping, for surface area, and water displacement, for volume. However, in tests with shapes of known dimensions, i.e. cubes, MeshLab produced accurate measures of 3D surface area and volume when compared to calculated surface area and volume. For directions to photograph coral for 3D photogrammetry see our Image Capture Protocol. For a walkthrough and scripts to run Agisoft Metashape on the command line, see https://github.com/wyattmillion/Coral3DPhotogram. These protocols, while created for branching coral, can be applied to 3D models of any coral morphology or any object really. Our goal is to make easy-to-use protocols using accessible softwares in the hopes of creating a standardized method for 3D photogrammetry in coral biology. Go to http://www.meshlab.net/#download to download the appropriate software for your operating system. P. Cignoni, M. Callieri, M. Corsini, M. Dellepiane, F. Ganovelli, G. Ranzuglia MeshLab: an Open-Source Mesh Processing Tool Sixth Eurographics Italian Chapter Conference, page 129-136, 2008 DOI dx.doi.org/10.17504/protocols.io.bgbpjsmn 

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5. 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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