Research Data

Coral metagenome: multiple Symbiodinium types isolated from multiple coral species

Details

Print this Page Print this Page
Show all sections
General
Title
Coral metagenome: multiple Symbiodinium types isolated from multiple coral species
Type
Dataset
Date Record Created
2017-12-12
Date Record Modified
2018-01-03
Language
English
Coverage
Date Coverage
(no information)
Time Period
(no information)
Geospatial Location
(no information)
Description
Descriptions
  1. Type: full

    Multiple Symbiodinium types isolated from multiple coral species, from the National Center for Biotechnology Information (NCBI) BioProject number PRJNA238605. Submitted by James Cook University.

    Description: 454 NGS sequencing of Symbiodinium types in a dilution series.

    Data type: Targeted locus (loci)

    Abstract [Related Publication]: The capacity of reef-building corals to associate with environmentally-appropriate types of endosymbionts from the dinoflagellate genus Symbiodinium contributes significantly to their success at local scales. Additionally, some corals are able to acclimatize to environmental perturbations by shuffling the relative proportions of different Symbiodinium types hosted. Understanding the dynamics of these symbioses requires a sensitive and quantitative method of Symbiodinium genotyping. Electrophoresis methods, still widely utilized for this purpose, are predominantly qualitative and cannot guarantee detection of a background type below 10% of the total Symbiodinium population. Here, the relative abundances of four Symbiodinium types (A13, C1, C3, and D1) in mixed samples of known composition were quantified using deep sequencing of the internal transcribed spacer of the ribosomal RNA gene (ITS-2) by means of Next Generation Sequencing (NGS) using Roche 454. In samples dominated by each of the four Symbiodinium types tested, background levels of the other three types were detected when present at 5%, 1%, and 0.1% levels, and their relative abundances were quantified with high (A13, C1, D1) to variable (C3) accuracy. The potential of this deep sequencing method for resolving fine-scale genetic diversity within a symbiont type was further demonstrated in a natural symbiosis using ITS-1, and uncovered reef-specific differences in the composition of Symbiodinium microadriaticum in two species of acroporid corals (Acropora digitifera and A. hyacinthus) from Palau. The ability of deep sequencing of the ITS locus (1 and 2) to detect and quantify low-abundant Symbiodinium types, as well as finer-scale diversity below the type level, will enable more robust quantification of local genetic diversity in Symbiodinium populations. This method will help to elucidate the role that background types have in maximizing coral fitness across diverse environments and in response to environmental change.

    The full methodology (including a detailed pipeline for sequencing) is available in the Open Access publication from the Related Publication links below.

Related Publications
  1. Quigley, Kate M., Davies, Sarah W., Kenkel, Carly D., Willis, Bette L., Matz, Mikhail V., and Bay, Line K. (2014) Deep-sequencing method for quantifying background abundances of Symbiodinium types: exploring the rare Symbiodinium biosphere in reef-building corals. PLoS One, 9 (4). pp. 1-15.
    Open Access
  2. Detailed pipeline for Symbiodinium 454 Next Generation Sequencing data from a single locus (i.e. ITS-1 or ITS-2)
    Open Access
Related Websites
(no information)
Related Data
  1. Has part: >> SRA Experiments (26)
    • ID: https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=238605 (EXTERNAL)
    • Publish to RDA: This related object (and relationship) is NOT being published to RDA.
  2. Has part: >> BioSamples (26)
    • ID: https://www.ncbi.nlm.nih.gov/biosample?Db=biosample&DbFrom=bioproject&Cmd=Link&LinkName=bioproject_biosample&LinkReadableName=BioSample&ordinalpos=1&IdsFromResult=238605 (EXTERNAL)
    • Publish to RDA: This related object (and relationship) is NOT being published to RDA.
Related Services
(no information)
Technical metadata
(no information)
People
Creators
  1. Managed by: Ms Kate Quigley , katemarie.quigley@jcu.edu.au , ARC Centre of Excellence for Coral Reef Studies
  2. Associated with: Prof Bette Willis , bette.willis@jcu.edu.au , ARC Centre of Excellence for Coral Reef Studies, Marine Biology & Aquaculture
Primary Contact
Ms Kate Quigley, katemarie.quigley@jcu.edu.au
Supervisors
(no information)
Collaborators
  1. Sarah W. Davies, University of Texas - Austin, USA
  2. Carly D. Kenkel, University of Texas - Austin, USA
  3. Mikhail V. Matz, University of Texas - Austin, USA
  4. LIne K. Bay, Australian Institute of Marine Science
Subject
Fields of Research
  1. 060205 - Marine and Estuarine Ecology (incl. Marine Ichthyology) (060205)
  2. 060411 - Population, Ecological and Evolutionary Genetics (060411)
Socio-Economic Objective
  1. 960305 - Ecosystem Adaptation to Climate Change (960305)
  2. 970106 - Expanding Knowledge in the Biological Sciences (970106)
Keywords
  1. Symbiodinium
  2. corals
  3. metagenomics
  4. ARC Centre of Excellence for Coral Reef Studies
Research Activity
(no information)
Research Themes
Tropical Ecosystems, Conservation and Climate Change
Rights
License
(no information)
License - Other
(no information)
Access Rights/Conditions
NCBI places no restrictions on the use or distribution of data.
Type
open
Rights
(no information)
Data
Data Location
Online Locations
  1. https://www.ncbi.nlm.nih.gov/bioproject/238605
Stored At
(no information)
Citation
Cite:
Quigley, K.; Davies, S.; Kenkel, C.; Willis, B.; Matz, M.; Bay, L. (2014). Coral metagenome: multiple Symbiodinium types isolated from multiple coral species. James Cook University. (dataset). e00cbfc1b5fe575a8f61adb0da5aa1b9