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Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region.


Type

Article

Change log

Authors

Arif, Chatchanit 
Daniels, Camille 
Bayer, Till 
Banguera-Hinestroza, Eulalia 

Abstract

The 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.

Description

Keywords

Symbiodinium, coral reefs, dinoflagellates, internal transcribed spacer 2, next-generation sequencing, operational taxonomic unit, Animals, Anthozoa, DNA, Ribosomal Spacer, Dinoflagellida, Ecosystem, Genetic Variation, Genotype, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Symbiosis

Journal Title

Mol Ecol

Conference Name

Journal ISSN

0962-1083
1365-294X

Volume Title

23

Publisher

Wiley
Sponsorship
We would like to thank the KAUST BioScience Core Lab and S. Neelamegam for 454 library generation and sequencing. We would also like to thank Y. Sawall and A. Al-Sofyani for provision and collection of coral samples, and three anonymous reviewers for helpful comments. This project was funded by a KAUST Academic Excellence Alliance (AEA) Award to CRV and CJH, baseline research funds to CRV and a National Science Foundation grant to TCL (OCE-09287664).