@article{736ad5ee8ea646c0b2d089dac759b8bf,
title = "SymPortal: A novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling",
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 {\textquoteleft}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.",
keywords = "ITS2, SymPortal, Symbiodiniaceae, molecular ecology, multicopy, phylogentics",
author = "Hume, {Benjamin C.C.} and Smith, {Edward G.} and Maren Ziegler and Warrington, {Hugh J.M.} and Burt, {John A.} and LaJeunesse, {Todd C.} and Joerg Wiedenmann and Voolstra, {Christian R.}",
note = "Funding Information: The SymPortal framework was conceived by B.C.C.H., C.R.V., J.W., E.G.S. and M.Z. The framework was built by B.C.C.H. with significant input from: C.R.V. and J.W. for funding and provision of computational resources; C.R.V., E.G.S., M.Z. and T.L.J. for developing analysis theory; E.G.S. and J.B. for providing example data sets; H.J.M.W. for informatic support; and C.R.V. for sourcing additional data to aid in development of the framework prior to public release. B.C.C.H. conducted data analyses and created the figures with significant input from C.R.V., M.Z. and E.G.S. B.C.C.H. and C.R.V. wrote the manuscript; all authors commented and approved the final manuscript. Funding Information: This work was supported by KAUST baseline funding to C.R.V., Red Sea Research Center funding (FCC/1/1973-22-01) to C.R.V. and B.C.C.H., Natural Environment Research Council Grant NE/K00641X/1 to J.W., and the European Research Council under the European Union's Seventh Framework Programme Grant FP7/2007-013/ERC Grant Agreement 311179 to J.W. The NYU Abu Dhabi Institute is acknowledged for funding coral sample collections. Alex Merci?re is thanked for his help in preparing Figure. Finally, three anonymous reviewers are thanked for their considerable contributions in improving the manuscript and the accessibility of the SymPortal framework in general. Funding Information: Natural Environment Research Council, Grant/Award Number: NE/K00641X/1; King Abdullah University of Science and Technology (KAUST), Grant/Award Number: Baseline funding; FP7 Ideas: European Research Council, Grant/Award Number: FP7/2007-013/ERC 311179 Funding Information: This work was supported by KAUST baseline funding to C.R.V., Red Sea Research Center funding (FCC/1/1973-22-01) to C.R.V. and B.C.C.H., Natural Environment Research Council Grant NE/ K00641X/1 to J.W., and the European Research Council under the European Union's Seventh Framework Programme Grant FP7/2007-013/ERC Grant Agreement 311179 to J.W. The NYU Abu Dhabi Institute is acknowledged for funding coral sample collections. Alex Merci{\`e}re is thanked for his help in preparing Figure 1. Finally, three anonymous reviewers are thanked for their considerable contributions in improving the manuscript and the accessibility of the SymPortal framework in general. Publisher Copyright: {\textcopyright} 2019 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.",
year = "2019",
month = jul,
doi = "10.1111/1755-0998.13004",
language = "English (US)",
volume = "19",
pages = "1063--1080",
journal = "Molecular Ecology Notes",
issn = "1755-098X",
publisher = "Wiley-Blackwell",
number = "4",
}