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

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

doi:10.1038/s41598-020-69101-z

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

2020
By Kitchen, S. A. ; Von Kuster, G. ; Kuntz, K. L. Vasquez ; ...
Source: Sci Rep. 2020 Jul 27;10(1):12488.

[PDF-2.04 MB]

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Journal Title:

Scientific Reports
Personal Author:

Kitchen, S. A. ; Von Kuster, G. ; Kuntz, K. L. Vasquez ; Reich, H. G. ; Miller, W. ; ... More +

Kitchen, S. A. ; Von Kuster, G. ; Kuntz, K. L. Vasquez ; Reich, H. G. ; Miller, W. ; Griffin, S. ; Fogarty, Nicole D. ; Baums, I. B. Less -
NOAA Program & Office:

NOS (National Ocean Service) ; OCM (Office for Coastal Management) ; OHC (Office of Habitat Conservation) ; NMFS (National Marine Fisheries Service) ; CoRIS (Coral Reef Information System)

NOS (National Ocean Service) ; OCM (Office for Coastal Management) ; OHC (Office of Habitat Conservation) ; NMFS (National Marine Fisheries Service) ; CoRIS (Coral Reef Information System) Less -
Description:

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.
Keywords:

[+]

Corals Identification
Source:

Sci Rep. 2020 Jul 27;10(1):12488.
DOI:

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

32719467
Pubmed Central ID:

PMC7385180
Document Type:

Journal Article
Funding:

Grant no. NA17NOS4820083
Rights Information:

CC BY
Compliance:

PMC
Main Document Checksum:

[+]

urn:sha256:5eef3eadf032536319d7af657f8f5287cff59e9cc0cce1353021b0cab1c8379b
Download URL:

https://repository.library.noaa.gov/view/noaa/27534/noaa_27534_DS1.pdf
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STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts

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