SymPortal: a novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2\n profiling
AuthorsHume, B C C
Smith, E G
Warrington, H J M
Burt, J A
LaJeunesse, T C
Voolstra, Christian R.
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Marine Science Program
Red Sea Research Center (RSRC)
KAUST Grant NumberFCC/1/1973-22-01
Permanent link to this recordhttp://hdl.handle.net/10754/631056
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AbstractWe 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 characterise taxa within the family Symbiodiniaceae (formerly the genus Symbiodinium), the multi-copy nature of the marker complicates its use. Commonly, the intragenomic diversity resultant from this multi-copy 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 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, standardisation-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 a global Symbiodiniaceae diversity. This article is protected by copyright. All rights reserved.
CitationHume BCC, Smith EG, Ziegler M, Warrington HJM, Burt JA, et al. (2019) SymPortal: a novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2\n profiling. Molecular Ecology Resources. Available: http://dx.doi.org/10.1111/1755-0998.13004.
SponsorsThis work was supported by KAUST baseline funding to CRV, Red Sea Research Center funding (FCC/1/1973-22-01) to CRV and BCCH, 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, and the NYUAD Core Sequencing team are thanked for their support. Alex Mercière is thanked for his help in preparing Fig. 1. Finally, three anonymous reviewers are thanked for their considerable contributions in improving this manuscript and the accessibility of the SymPortal framework in general.
JournalMolecular Ecology Resources
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