New tool for identifying endangered corals could aid conservation
efforts

Date:
August 25, 2020
Source:
Penn State
Summary:
A newly developed genotyping 'chip' -- the first of its kind for
corals - - allows researchers to genetically identify corals and
the symbiotic algae that live within the coral's cells, a vital
step for establishing and maintaining genetic diversity in reef
restoration efforts.



FULL STORY ========================================================================== Coral conservation efforts could get a boost from a newly developed
genotyping "chip" -- the first of its kind for corals. The chip allows researchers to genetically identify corals and the symbiotic algae
that live within the coral's cells, a vital step for establishing and maintaining genetic diversity in reef restoration efforts. The chip
and its accompanying online analysis pipeline help to democratize the
genetic identification of coral biodiversity, making it accessible to conservation biologists who might not have access to the laboratory and computational resources needed to extract DNA and analyze the data.


==========================================================================
A paper describing the new chip appears in the journal Scientific Reports.

"Corals around the world are endangered due to warming oceans," said
Iliana Baums, professor of biology at Penn State and leader of the
research team. "We designed this genotyping chip to help restoration
and conservation efforts.

There is very little overhead needed to use the chip, so small restoration operations can access coral genetic identification to help them maximize
reef health by ensuring coral populations are genetically diverse."
The chip, also called a microarray, uses more than 30,000 single
nucleotide polymorphisms (SNPs) -- locations in the coral genome where
at each of the locations a single letter in the DNA alphabet can vary
among different corals in the Acroporid family. The Acroporid family of
corals contains the largest number of different species of any coral
family and are common in the Caribbean Sea and the Pacific Ocean. The
chip was designed using Caribbean corals but can also be used to analyze Pacific species and allows researchers to identify the symbiotic algae
that reside in the coral cells.

Corals can reproduce asexually by fragmentation, so Caribbean reefs are
often dominated by corals that all can be traced back to a single origin
and are therefore genetically nearly identical -- researchers refer to
these related corals as a "genet." The chip is sensitive enough to allow researchers to reliably distinguish members of different genets within
the same coral species.

"One way to increase genetic diversity in a reef is to make sure it is
built by individuals of more than one genet," said Baums. "Because all
of the corals on a reef could be members of the same genet, it is vital
to have a reliable way to identify them and our chip provides this to researchers in the field." To use the SNP chip, which was developed at
Penn State and licensed to Thermo Fisher Scientific who produces the
Affymetrix microarrays, researchers can simply send a sample of coral
to a commercial laboratory. At the lab, DNA is extracted and run on the
chip and the resulting data is returned to the researcher. The researcher
can then upload the data files into the online analysis pipeline called
the Standard Tools for Acroporid Genotyping (STAG).

The analysis is performed and data maintained in a customized "Science
Gateway" in the open-source web-based Galaxy platform, a resource for
data-rich biomedical research also developed at Penn State.

"With the SNP chip and STAG pipeline we can help ensure that researchers
around the world can genetically identify corals in a standardized way,"
said Baums.

"The database maintained in the Science Gateway allows researchers
to compare samples, identify novel strains, and track coral diversity
through time." In addition to Baums, the research team includes Sheila
A. Kitchen, who designed the chip, Greg Von Kuster, Kate L. Vasquez
Kuntz, Hannah G. Reich, and Webb Miller at Penn State; Sean Griffin at
the NOAA Restoration Center; and Nicole D. Fogarty at the University of
North Carolina Wilmington. The research was funded by the NOAA Office
for Coastal Management and the U.S. National Science Foundation.


========================================================================== Story Source: Materials provided by Penn_State. Original written by Sam Sholtis. Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. S. A. Kitchen, G. Von Kuster, K. L. Vasquez Kuntz, H. G. Reich, W.

Miller, S. Griffin, Nicole D. Fogarty, I. B. Baums. STAGdb: a 30K
SNP genotyping array and Science Gateway for Acropora corals and
their dinoflagellate symbionts. Scientific Reports, 2020; 10 (1)
DOI: 10.1038/ s41598-020-69101-z ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/08/200825124631.htm

--- up 1 day, 6 hours, 50 minutes
* Origin: -=> Castle Rock BBS <=- Now Husky HPT Powered! (1337:3/111)