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

S A Kitchen,K L Vasquez Kuntz,I B Baums,Nicole D Fogarty,W Miller,G Von Kuster,H G Reich,S Griffin

doi:10.1038/s41598-020-69101-z

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 Caribbean Acropora species 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 genera Breviolum, Cladocopium, and Durusdinium. Analytic tools to produce multi-locus genotypes of hosts based on these SNP markers were combined in a workflow called the Standard Tools for Acroporid Genotyping (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.

Highlights

Standardized identification of genotypes is necessary in animals that reproduce asexually and form large clonal populations such as coral
We identified 1.6 million high-quality coral single nucleotide polymorphisms (SNP) that varied between the genomes of 42 previously sequenced A. palmata and A. cervicornis from four locations (Belize, Curacao, Florida, and U.S Virgin Islands) using two variant callers, samtools m pileup[44] that uses likelihood scores and freebayes[45] that uses Bayesian posterior probabilities for variant calls
When comparing two deeply-sequenced A. palmata and A. cervicornis genomes to the reference S. tridanidornium genome, we identified 2,657 high-quality symbiont SNPs using samtools mpileup[44]

Summary

Introduction

Standardized identification of genotypes is necessary in animals that reproduce asexually and form large clonal populations such as coral. Hybridization-based SNP arrays tend to have lower error rates RADseq methods[5,6] and increased accuracy of genet identification and tracking Forgo discovery of new SNP loci in favor of assaying a standard set of probes across all samples resulting in some ascertainment bias[7,8,9] When it comes to the analysis of SNP genotyping data, familiarity with computer programming and access to high performance computing is typically required but not always available. Hermaphroditic corals species like the Caribbean acroporids are mainly self-incompatible, thereby requiring the presence of gametes from different genets for successful sexual reproduction[25,26] For these reasons, identification of genets and preservation of genotypic diversity are conservation priorities[27]

Objectives

Methods

Results

Conclusion