The Axiom Coral-Algae Genotyping array (Axiom AcropSNP) was designed in collaboration with Dr. Iliana Baums and the Baums laboratory at Pennsylvania State University. The array was designed to co-analyze the coral host (Acropora) and algal symbionts (Symbiodiniaceae) based on the single nucleotide polymorphism (SNP) loci selected to resolve multi-locus genotypes of host (genets) and symbionts (strains). SNPs were also selected to distinguish host populations and to determine ancestry of the coral hybrids in Caribbean acroporids. A subset of SNP loci can be used to genotype Pacific acroporids.

The array consists of 53,589 SNPs from the coral host and 4,021 SNPs from algal symbionts. This array is also available in mini-96 format.

Analytic tools to produce multi-locus genotypes of hosts based on these SNP markers have been combined by the Baums laboratory in a workflow called the Standard Tools for Acroporid Genotyping (STAG). The STAG workflow and database are contained within a customized Galaxy environment , which allows for consistent identification of host genet and symbiont strains and can serve as a template for the development of future arrays for additional coral genera.

References
1. Kitchen SA, Ratan A, Bedoya-Reina OC, et al. Genomic Variants Among Threatened Acropora Corals. G3 (Bethesda). 2019;9(5):1633-1646.

2. Kitchen SA, Von Kuster G, Kuntz KLV, et al. STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts. Sci Rep. 2020;10(1):12488.

Required products
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument
Axiom Analysis Suite Software