SymPortal

A novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling

Benjamin C.C. Hume, Edward G. Smith, Maren Ziegler, Hugh J.M. Warrington, John A. Burt, Todd C. Lajeunesse, Joerg Wiedenmann, Christian R. Voolstra

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

We present SymPortal (SymPortal.org), a novel analytical framework and platform for genetically resolving the algal symbionts of reef corals using next-generation sequencing (NGS) data of the ITS2 rDNA. Although the ITS2 marker is widely used to genetically characterize taxa within the family Symbiodiniaceae (formerly the genus Symbiodinium), the multicopy nature of the marker complicates its use. Commonly, the intragenomic diversity resultant from this multicopy nature is collapsed by analytical approaches, thereby focusing on only the most abundant sequences. In contrast, SymPortal employs logic to identify within-sample informative intragenomic sequences, which we have termed ‘defining intragenomic variants' (DIVs), to identify ITS2-type profiles representative of putative Symbiodiniaceae taxa. By making use of this intragenomic ITS2 diversity, SymPortal is able to resolve genetic delineations using the ITS2 marker at a level that was previously only possible by using additional genetic markers. We demonstrate this by comparing this novel approach to the most commonly used alternative approach for NGS ITS2 data, the 97% similarity clustering to operational taxonomic units (OTUs). The SymPortal platform accepts NGS raw sequencing data as input to provide an easy-to-use, standardization-enforced, and community-driven framework that integrates with a database to gain resolving power with increased use. We consider that SymPortal, in conjunction with ongoing large-scale sampling and sequencing efforts, should play an instrumental role in making future sampling efforts more comparable and in maximizing their efficacy in working towards the classification of the global Symbiodiniaceae diversity.

Original languageEnglish (US)
Pages (from-to)1063-1080
Number of pages18
JournalMolecular Ecology Resources
Volume19
Issue number4
DOIs
StatePublished - Jul 1 2019

Fingerprint

Coral Reefs
Anthozoa
analytical framework
Ribosomal DNA
symbiont
Genetic Markers
symbionts
Cluster Analysis
corals
coral
Databases
Symbiodinium
sampling
genetic marker
standardization
coral reefs
coral reef
genetic markers
Symbiodiniaceae
marker

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Hume, Benjamin C.C. ; Smith, Edward G. ; Ziegler, Maren ; Warrington, Hugh J.M. ; Burt, John A. ; Lajeunesse, Todd C. ; Wiedenmann, Joerg ; Voolstra, Christian R. / SymPortal : A novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling. In: Molecular Ecology Resources. 2019 ; Vol. 19, No. 4. pp. 1063-1080.
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abstract = "We present SymPortal (SymPortal.org), a novel analytical framework and platform for genetically resolving the algal symbionts of reef corals using next-generation sequencing (NGS) data of the ITS2 rDNA. Although the ITS2 marker is widely used to genetically characterize taxa within the family Symbiodiniaceae (formerly the genus Symbiodinium), the multicopy nature of the marker complicates its use. Commonly, the intragenomic diversity resultant from this multicopy nature is collapsed by analytical approaches, thereby focusing on only the most abundant sequences. In contrast, SymPortal employs logic to identify within-sample informative intragenomic sequences, which we have termed ‘defining intragenomic variants' (DIVs), to identify ITS2-type profiles representative of putative Symbiodiniaceae taxa. By making use of this intragenomic ITS2 diversity, SymPortal is able to resolve genetic delineations using the ITS2 marker at a level that was previously only possible by using additional genetic markers. We demonstrate this by comparing this novel approach to the most commonly used alternative approach for NGS ITS2 data, the 97{\%} similarity clustering to operational taxonomic units (OTUs). The SymPortal platform accepts NGS raw sequencing data as input to provide an easy-to-use, standardization-enforced, and community-driven framework that integrates with a database to gain resolving power with increased use. We consider that SymPortal, in conjunction with ongoing large-scale sampling and sequencing efforts, should play an instrumental role in making future sampling efforts more comparable and in maximizing their efficacy in working towards the classification of the global Symbiodiniaceae diversity.",
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SymPortal : A novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling. / Hume, Benjamin C.C.; Smith, Edward G.; Ziegler, Maren; Warrington, Hugh J.M.; Burt, John A.; Lajeunesse, Todd C.; Wiedenmann, Joerg; Voolstra, Christian R.

In: Molecular Ecology Resources, Vol. 19, No. 4, 01.07.2019, p. 1063-1080.

Research output: Contribution to journalArticle

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T2 - A novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling

AU - Hume, Benjamin C.C.

AU - Smith, Edward G.

AU - Ziegler, Maren

AU - Warrington, Hugh J.M.

AU - Burt, John A.

AU - Lajeunesse, Todd C.

AU - Wiedenmann, Joerg

AU - Voolstra, Christian R.

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