Towards an in-depth characterization of Symbiodiniaceae in tropical giant clams via metabarcoding of pooled multi-gene amplicons

Development and preliminary validation of a multi-trophic metabarcoding biotic index for monitoring benthic organic enrichment

(2018) Nigel Keeley et al.   ECOLOGICAL INDICATORS

The impact of artificial surfaces on marine bacterial and eukaryotic biofouling assemblages: A high-throughput sequencing analysis

(2018) Ulla von Ammon et al.   MARINE ENVIRONMENTAL RESEARCH

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

Metabarcoding using multiplexed markers increases species detection in complex zooplankton communities

(2018) Guang K. Zhang et al.   Evolutionary Applications

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

(2018) Johan Decelle et al.   CURRENT BIOLOGY

Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring

(2018) Vasco Elbrecht et al.   FRESHWATER BIOLOGY

Host specificity of Symbiodinium variants revealed by an ITS2 metahaplotype approach

(2017) Edward G Smith et al.   ISME Journal

New barcoded primers for efficient retrieval of cercozoan sequences in high-throughput environmental diversity surveys, with emphasis on worldwide biological soil crusts

(2017) Anna Maria Fiore-Donno et al.   Molecular Ecology Resources

Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment

(2017) Michael Stat et al.   Scientific Reports

Genetic diversity of giant clams (Tridacna spp.) and their associated Symbiodinium in the central Red Sea

(2017) Melissa K. Pappas et al.   Marine Biodiversity

Zooxanthellal genetic varieties in giant clams are partially determined by species-intrinsic and growth-related characteristics

(2017) Shota Ikeda et al.   PLoS One

Metabarcoding improves detection of eukaryotes from early biofouling communities: implications for pest monitoring and pathway management

(2016) Anastasija Zaiko et al.   BIOFOULING

A simple and rapid determination method for zooxanthellal genetic diversity in giant clams using multiplex PCR

(2016) Shota Ikeda et al.   FISHERIES SCIENCE

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

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae

(2016) Vanessa Rossetto Marcelino et al.   Scientific Reports

The ecological significance of giant clams in coral reef ecosystems

(2015) Mei Lin Neo et al.   BIOLOGICAL CONSERVATION

Dinoflagellate diversity among nudibranchs and sponges from French Polynesia: Insights into associations and transfer

(2015) Patricia Wecker et al.   COMPTES RENDUS BIOLOGIES

Symbiodinium tridacnidorumsp. nov., a dinoflagellate common to Indo-Pacific giant clams, and a revised morphological description ofSymbiodinium microadriaticumFreudenthal, emended Trench & Blank

(2015) Sung Yeon Lee et al.   EUROPEAN JOURNAL OF PHYCOLOGY

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

(2015) Ross Cunning et al.   PLoS One

Long-term changes in Symbiodinium communities in Orbicella annularis in St. John, US Virgin Islands

(2014) PJ Edmunds et al.   MARINE ECOLOGY PROGRESS SERIES

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

(2014) L. Thomas et al.   MOLECULAR ECOLOGY

Illuminating Choices for Library Prep: A Comparison of Library Preparation Methods for Whole Genome Sequencing of Cryptococcus neoformans Using Illumina HiSeq

(2014) Johanna Rhodes et al.   PLoS One

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

(2014) Xavier Pochon et al.   PeerJ

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet

(2013) M. De Barba et al.   Molecular Ecology Resources

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Identifying and Characterizing Alternative Molecular Markers for the Symbiotic and Free-Living Dinoflagellate Genus Symbiodinium

(2012) Xavier Pochon et al.   PLoS One

Genetic diversity of free-living Symbiodinium in surface water and sediment of Hawai‘i and Florida

(2011) M. Takabayashi et al.   CORAL REEFS

Patterns of Symbiodinium distribution in three giant clam species across the biodiverse Bird’s Head region of Indonesia

(2011) TS DeBoer et al.   MARINE ECOLOGY PROGRESS SERIES

GeoSymbio: a hybrid, cloud-based web application of global geospatial bioinformatics and ecoinformatics for Symbiodinium-host symbioses

(2011) ERIK C. FRANKLIN et al.   Molecular Ecology Resources

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

(2010) Anna Engelbrektson et al.   ISME Journal

COMPARISON OF ENDOSYMBIOTIC AND FREE-LIVING SYMBIODINIUM (DINOPHYCEAE) DIVERSITY IN A HAWAIIAN REEF ENVIRONMENT1

(2010) Xavier Pochon et al.   JOURNAL OF PHYCOLOGY

Diversity in populations of free-living Symbiodinium from a Caribbean and Pacific reef

(2010) Mackenzie M. Manning et al.   LIMNOLOGY AND OCEANOGRAPHY

Host-symbiont recombination versus natural selection in the response of coral-dinoflagellate symbioses to environmental disturbance

(2010) T. C. LaJeunesse et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Effects of coral transplantation and giant clam restocking on the structure of fish communities on degraded patch reefs

(2008) Patrick C. Cabaitan et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Latitudinal symbiont zonation in Stylophora pistillata from southeast Africa

(2008) Angus H. H. Macdonald et al.   MARINE BIOLOGY