SymPortal: A novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling
SymPortal: A novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling
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.
ITS2, molecular ecology, multicopy, phylogentics, Symbiodiniaceae, SymPortal
1063-1080
Hume, Benjamin C.C.
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Smith, Edward G.
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Ziegler, Maren
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Warrington, Hugh J.M.
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Burt, John A.
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LaJeunesse, Todd C.
1b4c7871-1dbd-44a6-8b5c-ea7877249e1e
Wiedenmann, Joerg
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Voolstra, Christian R.
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July 2019
Hume, Benjamin C.C.
dab8d735-3726-4193-9058-c2c1cfac349d
Smith, Edward G.
fc355d48-9c28-41dc-a191-0c33308be0ed
Ziegler, Maren
b5b7e437-5042-4077-9fd1-a5ae57f93b20
Warrington, Hugh J.M.
fe4ab76a-9729-4a9a-8e98-03327d83541b
Burt, John A.
9640a507-caa5-4ee3-a8bf-bec34d6a4fb8
LaJeunesse, Todd C.
1b4c7871-1dbd-44a6-8b5c-ea7877249e1e
Wiedenmann, Joerg
ad445af2-680f-4927-90b3-589ac9d538f7
Voolstra, Christian R.
e9c8ec10-db0a-40a2-805b-2cfadfbd55cd
Hume, Benjamin C.C., Smith, Edward G., Ziegler, Maren, Warrington, Hugh J.M., Burt, John A., LaJeunesse, Todd C., Wiedenmann, Joerg and Voolstra, Christian R.
(2019)
SymPortal: A novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling.
Molecular Ecology Resources, 19 (4), .
(doi:10.1111/1755-0998.13004).
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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Hume_et_al-2019-Molecular_Ecology_Resources
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Accepted/In Press date: 31 January 2019
e-pub ahead of print date: 11 February 2019
Published date: July 2019
Keywords:
ITS2, molecular ecology, multicopy, phylogentics, Symbiodiniaceae, SymPortal
Identifiers
Local EPrints ID: 430823
URI: http://eprints.soton.ac.uk/id/eprint/430823
ISSN: 1755-098X
PURE UUID: a13deb22-f1c4-4c01-aa36-3848b3a540a0
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Date deposited: 15 May 2019 16:30
Last modified: 16 Mar 2024 03:53
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Contributors
Author:
Benjamin C.C. Hume
Author:
Edward G. Smith
Author:
Maren Ziegler
Author:
Hugh J.M. Warrington
Author:
John A. Burt
Author:
Todd C. LaJeunesse
Author:
Christian R. Voolstra
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