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

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

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.

Highlights

Corals and the ecosystems they construct have been among the most susceptible to climate change, but corals have been shown to exhibit variation in their responses to stress (Hughes et al 2018; Norstrom et al 2016)
One Acropora sp. sample, A08, falls outside of the main Acropora sp. grouping. The cause of this divergence is the difference in Internal Transcribed Spacer 2 (ITS2) diversity contained in this sample compared to the other samples of this host species, as can be seen in Fig. 3 aii
The multi-copy ITS2 sequence diversity harboured within every Symbiodiniaceae genome represents a wealth of information that is currently underutilised in many next-generation sequencing (NGS) analytical approaches

Summary

Introduction

Corals and the ecosystems they construct have been among the most susceptible to climate change, but corals have been shown to exhibit variation in their responses to stress (Hughes et al 2018; Norstrom et al 2016). Despite the multitude of markers available for assessing Symbiodiniaceae diversity, the Internal Transcribed Spacer 2 (ITS2) of the rRNA gene shows an uninterrupted popularity and remains the most commonly used marker (Cunning et al 2017; Fujise et al 2018; Pochon et al 2014; Smith et al 2017b; Varasteh et al 2017). This marker is multicopy in nature, which complicates its use. Without the use of additional genetic markers, differentiating among these sources of variation can be challenging (Thornhill et al 2007)

Methods

Results

Conclusion