Genome Size, rDNA Copy, and qPCR Assays for Symbiodiniaceae

Development of a quantitative PCR–high-resolution melting assay for absolute measurement of coral-Symbiodiniaceae associations and its application to investigating variability at three spatial scales

(2019) Anne-Leila Meistertzheim et al.   MARINE BIOLOGY

SymPortal: a novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling

(2019) B. C. C. Hume et al.   Molecular Ecology Resources

DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions

(2019) Lucie Zinger et al.   MOLECULAR ECOLOGY

Climate change promotes parasitism in a coral symbiosis

(2018) David M. Baker et al.   ISME Journal

An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region

(2018) Benjamin C.C. Hume et al.   PeerJ

Systematic Revision of Symbiodiniaceae Highlights the Antiquity and Diversity of Coral Endosymbionts

(2018) Todd C. LaJeunesse et al.   CURRENT BIOLOGY

Worldwide Occurrence and Activity of the Reef-Building Coral Symbiont Symbiodinium in the Open Ocean

(2018) Johan Decelle et al.   CURRENT BIOLOGY

Host specificity of Symbiodinium variants revealed by an ITS2 metahaplotype approach

(2017) Edward G Smith et al.   ISME Journal

Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula

(2017) Maren Ziegler et al.   JOURNAL OF BIOGEOGRAPHY

An updated assessment ofSymbiodiniumspp. that associate with common scleractinian corals from Moorea (French Polynesia) reveals high diversity among background symbionts and a novel finding of clade B

(2017) Héloïse Rouzé et al.   PeerJ

Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin Islands

(2017) Ross Cunning et al.   PeerJ

Low symbiont diversity as a potential adaptive strategy in a marginal non-reefal environment: a case study of corals in Hong Kong

(2016) Tsz Yan Ng et al.   CORAL REEFS

A quantitative PCR approach for determining the ribosomal DNA copy number in the genome of Agave tequila Weber

(2016) Jorge Rubio-Piña et al.   ELECTRONIC JOURNAL OF BIOTECHNOLOGY

Exploring the Symbiodinium rare biosphere provides evidence for symbiont switching in reef-building corals

(2016) Nadine M Boulotte et al.   ISME Journal

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies

(2015) Matthew Perisin et al.   ISME Journal

An Improved DNA Extraction Method for Efficient and Quantitative Recovery of Phytoplankton Diversity in Natural Assemblages

(2015) Jian Yuan et al.   PLoS One

The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis

(2015) S. Lin et al.   SCIENCE

Variability of Symbiodinium Communities in Waters, Sediments, and Corals of Thermally Distinct Reef Pools in American Samoa

(2015) Ross Cunning et al.   PLoS One

A tool for design of primers for microRNA-specific quantitative RT-qPCR

(2014) Peter K Busk   BMC BIOINFORMATICS

Change in algal symbiont communities after bleaching, not prior heat exposure, increases heat tolerance of reef corals

(2014) Rachel N. Silverstein et al.   GLOBAL CHANGE BIOLOGY

AssessingSymbiodiniumdiversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region

(2014) Chatchanit Arif et al.   MOLECULAR ECOLOGY

ExploringSymbiodiniumdiversity and host specificity inAcroporacorals from geographical extremes of Western Australia with 454 amplicon pyrosequencing

(2014) L. Thomas et al.   MOLECULAR ECOLOGY

Deep-Sequencing Method for Quantifying Background Abundances of Symbiodinium Types: Exploring the Rare Symbiodinium Biosphere in Reef-Building Corals

(2014) Kate M. Quigley et al.   PLoS One

Guidelines for validation of qualitative real-time PCR methods

(2014) S. Broeders et al.   TRENDS IN FOOD SCIENCE & TECHNOLOGY

Not just who, but how many: the importance of partner abundance in reef coral symbioses

(2014) Ross Cunning et al.   Frontiers in Microbiology

Multi-gene analysis ofSymbiodiniumdinoflagellates: a perspective on rarity, symbiosis, and evolution

(2014) Xavier Pochon et al.   PeerJ

DNA barcoding species in Alexandrium tamarense complex using ITS and proposing designation of five species

(2013) Lu Wang et al.   HARMFUL ALGAE

Genetics and Morphology Characterize the DinoflagellateSymbiodinium voratum, n. sp., (Dinophyceae) as the Sole Representative ofSymbiodiniumClade E

(2013) Hae Jin Jeong et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Population genetic data of a model symbiotic cnidarian system reveal remarkable symbiotic specificity and vectored introductions across ocean basins

(2013) Daniel J. Thornhill et al.   MOLECULAR ECOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Multiple Symbiont Acquisition Strategies as an Adaptive Mechanism in the Coral Stylophora pistillata

(2013) Kristen A. Byler et al.   PLoS One

The distribution of the thermally tolerant symbiont lineage (Symbiodiniumclade D) in corals from Hawaii: correlations with host and the history of ocean thermal stress

(2013) Michael Stat et al.   Ecology and Evolution

Alkaline phosphatase gene sequence characteristics and transcriptional regulation by phosphate limitation in Karenia brevis (Dinophyceae)

(2012) Xin Lin et al.   HARMFUL ALGAE

MFEprimer-2.0: a fast thermodynamics-based program for checking PCR primer specificity

(2012) Wubin Qu et al.   NUCLEIC ACIDS RESEARCH

Major Cellular and Physiological Impacts of Ocean Acidification on a Reef Building Coral

(2012) Paulina Kaniewska et al.   PLoS One

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Molecular Detection, Quantification, and Diversity Evaluation of Microalgae

(2011) Vinitha Ebenezer et al.   MARINE BIOTECHNOLOGY

Variation in Symbiodinium ITS2 Sequence Assemblages among Coral Colonies

(2011) Michael Stat et al.   PLoS One

Improved Resolution of Reef-Coral Endosymbiont (Symbiodinium) Species Diversity, Ecology, and Evolution through psbA Non-Coding Region Genotyping

(2011) Todd C. LaJeunesse et al.   PLoS One

Do corals select zooxanthellae by alternative discharge?

(2010) Hiroshi Yamashita et al.   MARINE BIOLOGY

A new Symbiodinium clade (Dinophyceae) from soritid foraminifera in Hawai’i

(2010) Xavier Pochon et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Serious Overestimation in Quantitative PCR by Circular (Supercoiled) Plasmid Standard: Microalgal pcna as the Model Gene

(2010) Yubo Hou et al.   PLoS One

The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments

(2009) S. A. Bustin et al.   CLINICAL CHEMISTRY

Strain-Dependent Variation in 18S Ribosomal DNA Copy Numbers in Aspergillus fumigatus

(2009) M. L. Herrera et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Development of clade-specific Symbiodinium primers for quantitative PCR (qPCR) and their application to detecting clade D symbionts in Caribbean corals

(2009) Adrienne M. S. Correa et al.   MARINE BIOLOGY

Specificity in communities of Symbiodinium in corals from Johnston Atoll

(2009) M Stat et al.   MARINE ECOLOGY PROGRESS SERIES

Quantification of algal endosymbionts (Symbiodinium) in coral tissue using real-time PCR

(2009) J. C. MIEOG et al.   Molecular Ecology Resources

MFEprimer: multiple factor evaluation of the specificity of PCR primers

(2008) Wubin Qu et al.   BIOINFORMATICS