e-journal

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

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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 OTUbased
framework, we can improve objectivity, comparability and simplicity when
assessing ITS2 diversity in field-based studies.

Keywords: coral reefs, dinoflagellates, internal transcribed spacer 2, next-generation sequencing,
operational taxonomic unit, Symbiodinium

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Informasi Detail

Judul Seri

Molecular Ecology

No. Panggil

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Penerbit

New York : John Wiley & Sons, Ltd.., 2014

Deskripsi Fisik

Molecular Ecology (2014) 23, 4418–4433

Bahasa

English

ISBN/ISSN

doi: 10.1111/mec.128

Klasifikasi

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Tipe Isi

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Tipe Media

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Tipe Pembawa

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Edisi

(2014) 23, 4418–4433

Subjek

EKOLOGI

Info Detail Spesifik

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Pernyataan Tanggungjawab

agus

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