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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. 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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3. Symbiodiniaceae Enumeration in Ground Coral Samples Using Countess™ II FL Automated Cell Counter

   https://doi.org/10.17504/protocols.io.bdc5i2y6  

   Mclachlan, R; Juracka, C; Grottoli, AG (March 2020, Protocolsio)

   null (Ed.)

   This protocol outlines a method for quantifying the density of Symbiodiniaceae cells in Scleractinian coral samples which have been previously ground into a homogenous paste consisting of aragonite skeleton, coral host tissue and endosymbiotic Symbiodiniaceae cells. There are four parts to quantifying Symbiodiniaceae cell density from ground corals: 1) grind and sub-sample the coral and store at -80 °C until ready to extract, 2) separate Symbiodiniaceae cells from the coral skeleton, 3) image Symbiodiniaceae fluorescence using Countess™ II FL Automated Cell Counter, and 4) quantify cells using the software ImageJ. Note: a CY5 EVOS™ light cube is required for this method. For instructions on installing the CY5 EVOS™ light cube to your Countess™ II FL Cell Counter, see page 40 of the Countess™ II FL Cell Counter user manual. This method was originally developed by Rowan McLachlan in February 2020. Claire Juracka assisted Rowan McLachlan by conducting tests to compare this method to the traditional method using a hemocytometer and microscope. The traditional cell counting method has been reported in several publications by Grottoli's team (e.g., Rodrigues & Grottoli 2007). This protocol was written by Rowan McLachlan with the guidance of Dr. Andréa Grottoli at The Ohio State University. dx.doi.org/10.17504/protocols.io.bdc5i2y6 

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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. STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts

   https://doi.org/10.1038/s41598-020-69101-z  

   Kitchen, S. A.; Von Kuster, G.; Kuntz, K. L. Vasquez; Reich, H. G.; Miller, W.; Griffin, S.; Fogarty, Nicole D.; Baums, I. B. (July 2020, Scientific Reports)

   Abstract Standardized identification of genotypes is necessary in animals that reproduce asexually and form large clonal populations such as coral. We developed a high-resolution hybridization-based genotype array coupled with an analysis workflow and database for the most speciose genus of coral,Acropora, and their symbionts. We designed the array to co-analyze host and symbionts based on bi-allelic single nucleotide polymorphisms (SNP) markers identified from genomic data of the two CaribbeanAcroporaspecies as well as their dominant dinoflagellate symbiont,Symbiodinium ‘fitti’.SNPs were selected to resolve multi-locus genotypes of host (called genets) and symbionts (called strains), distinguish host populations and determine ancestry of coral hybrids between Caribbean acroporids. Pacific acroporids can also be genotyped using a subset of the SNP loci and additional markers enable the detection of symbionts belonging to the generaBreviolum, Cladocopium, andDurusdinium. Analytic tools to produce multi-locus genotypes of hosts based on these SNP markers were combined in a workflow called theStandardTools forAcroporidGenotyping (STAG). The STAG workflow and database are contained within a customized Galaxy environment (https://coralsnp.science.psu.edu/galaxy/), which allows for consistent identification of host genet and symbiont strains and serves as a template for the development of arrays for additional coral genera. STAG data can be used to track temporal and spatial changes of sampled genets necessary for restoration planning and can be applied to downstream genomic analyses. Using STAG, we uncover bi-directional hybridization between and population structure within Caribbean acroporids and detect a cryptic Acroporid species in the Pacific. 

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