PMID- 25052021
OWN - NLM
STAT- MEDLINE
DCOM- 20141013
LR  - 20211021
IS  - 1365-294X (Electronic)
IS  - 0962-1083 (Print)
IS  - 0962-1083 (Linking)
VI  - 23
IP  - 17
DP  - 2014 Sep
TI  - Assessing Symbiodinium diversity in scleractinian corals via next-generation 
      sequencing-based genotyping of the ITS2 rDNA region.
PG  - 4418-33
LID - 10.1111/mec.12869 [doi]
AB  - 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.
CI  - (c) 2014 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.
FAU - Arif, Chatchanit
AU  - Arif C
AD  - Red Sea Research Center, King Abdullah University of Science and Technology 
      (KAUST), 23955, Thuwal, Saudi Arabia.
FAU - Daniels, Camille
AU  - Daniels C
FAU - Bayer, Till
AU  - Bayer T
FAU - Banguera-Hinestroza, Eulalia
AU  - Banguera-Hinestroza E
FAU - Barbrook, Adrian
AU  - Barbrook A
FAU - Howe, Christopher J
AU  - Howe CJ
FAU - LaJeunesse, Todd C
AU  - LaJeunesse TC
FAU - Voolstra, Christian R
AU  - Voolstra CR
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20140818
PL  - England
TA  - Mol Ecol
JT  - Molecular ecology
JID - 9214478
RN  - 0 (DNA, Ribosomal Spacer)
SB  - IM
EIN - Mol Ecol. 2019 Jun;28(12):3135-3136. PMID: 31317608
MH  - Animals
MH  - *Anthozoa
MH  - DNA, Ribosomal Spacer/genetics
MH  - Dinoflagellida/classification/*genetics
MH  - Ecosystem
MH  - *Genetic Variation
MH  - Genotype
MH  - High-Throughput Nucleotide Sequencing
MH  - Sequence Analysis, DNA
MH  - *Symbiosis
PMC - PMC4285332
OTO - NOTNLM
OT  - Symbiodinium
OT  - coral reefs
OT  - dinoflagellates
OT  - internal transcribed spacer 2
OT  - next-generation sequencing
OT  - operational taxonomic unit
EDAT- 2014/07/24 06:00
MHDA- 2014/10/14 06:00
PMCR- 2015/01/06
CRDT- 2014/07/24 06:00
PHST- 2014/04/16 00:00 [received]
PHST- 2014/07/17 00:00 [revised]
PHST- 2014/07/18 00:00 [accepted]
PHST- 2014/07/24 06:00 [entrez]
PHST- 2014/07/24 06:00 [pubmed]
PHST- 2014/10/14 06:00 [medline]
PHST- 2015/01/06 00:00 [pmc-release]
AID - 10.1111/mec.12869 [doi]
PST - ppublish
SO  - Mol Ecol. 2014 Sep;23(17):4418-33. doi: 10.1111/mec.12869. Epub 2014 Aug 18.