Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region
Microsoft Word 2007
Microsoft Excel 2007
Daniels, Camille Arian
Banguera Hinestroza, Eulalia
Howe, Christopher J.
LaJeunesse, Todd C.
Voolstra, Christian R.
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Marine Science Program
Red Sea Research Center (RSRC)
Reef Genomics Lab
Online Publication Date2014-08-18
Print Publication Date2014-09
Permanent link to this recordhttp://hdl.handle.net/10754/550142
MetadataShow full item record
AbstractThe persistence of coral reef ecosystems relies on the symbiotic relationship between scleractinian corals and intracellular, photosynthetic dinoflagellates in the genus Symbiodinium. Genetic evidence indicates that these symbionts are biologically diverse and exhibit discrete patterns of environmental and host distribution. This makes the assessment of Symbiodinium diversity critical to understanding the symbiosis ecology of corals. Here, we applied pyrosequencing to the elucidation of Symbiodinium diversity via analysis of the internal transcribed spacer 2 (ITS2) region, a multicopy genetic marker commonly used to analyse Symbiodinium diversity. Replicated data generated from isoclonal Symbiodinium cultures showed that all genomes contained numerous, yet mostly rare, ITS2 sequence variants. Pyrosequencing data were consistent with more traditional denaturing gradient gel electrophoresis (DGGE) approaches to the screening of ITS2 PCR amplifications, where the most common sequences appeared as the most intense bands. Further, we developed an operational taxonomic unit (OTU)-based pipeline for Symbiodinium ITS2 diversity typing to provisionally resolve ecologically discrete entities from intragenomic variation. A genetic distance cut-off of 0.03 collapsed intragenomic ITS2 variants of isoclonal cultures into single OTUs. When applied to the analysis of field-collected coral samples, our analyses confirm that much of the commonly observed Symbiodinium ITS2 diversity can be attributed to intragenomic variation. We conclude that by analysing Symbiodinium populations in an OTU-based framework, we can improve objectivity, comparability and simplicity when assessing ITS2 diversity in field-based studies.
CitationAssessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region 2014, 23 (17):4418 Molecular Ecology
PubMed Central IDPMC4285332
- Patterns of Symbiodinium (Dinophyceae) diversity and assemblages among diverse hosts and the coral reef environment of Lizard Island, Australia.
- Authors: Ziegler M, Stone E, Colman D, Takacs-Vesbach C, Shepherd U
- Issue date: 2018 Aug
- Cohesive molecular genetic data delineate species diversity in the dinoflagellate genus Symbiodinium.
- Authors: Sampayo EM, Dove S, Lajeunesse TC
- Issue date: 2009 Feb
- SymPortal: A novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling.
- Authors: Hume BCC, Smith EG, Ziegler M, Warrington HJM, Burt JA, LaJeunesse TC, Wiedenmann J, Voolstra CR
- Issue date: 2019 Jul
- SymbioGBR: a web-based database of Symbiodinium associated with cnidarian hosts on the Great Barrier Reef.
- Authors: Tonk L, Bongaerts P, Sampayo EM, Hoegh-Guldberg O
- Issue date: 2013 Mar 13
- Host specificity of Symbiodinium variants revealed by an ITS2 metahaplotype approach.
- Authors: Smith EG, Ketchum RN, Burt JA
- Issue date: 2017 Jun