GeoSymbio: a hybrid, cloud‐based web application of global geospatial bioinformatics and ecoinformatics for Symbiodinium–host symbioses

Abstract

The genus Symbiodinium encompasses a group of unicellular, photosynthetic dinoflagellates that are found free living or in hospite with a wide range of marine invertebrate hosts including scleractinian corals. We present GeoSymbio, a hybrid web application that provides an online, easy to use and freely accessible interface for users to discover, explore and utilize global geospatial bioinformatic and ecoinformatic data on Symbiodinium-host symbioses. The novelty of this application lies in the combination of a variety of query and visualization tools, including dynamic searchable maps, data tables with filter and grouping functions, and interactive charts that summarize the data. Importantly, this application is hosted remotely or 'in the cloud' using Google Apps, and therefore does not require any specialty GIS, web programming or data programming expertise from the user. The current version of the application utilizes Symbiodinium data based on the ITS2 genetic marker from PCR-based techniques, including denaturing gradient gel electrophoresis, sequencing and cloning of specimens collected during 1982-2010. All data elements of the application are also downloadable as spatial files, tables and nucleic acid sequence files in common formats for desktop analysis. The application provides a unique tool set to facilitate research on the basic biology of Symbiodinium and expedite new insights into their ecology, biogeography and evolution in the face of a changing global climate. GeoSymbio can be accessed at https://sites.google.com/site/geosymbio/.

Differential coral bleaching—Contrasting the activity and response of enzymatic antioxidants in symbiotic partners under thermal stress

“…Successful amplifications were purified using ExoSAP-IT (Global Science) and sequenced in both directions by Macrogen Inc. (Seoul, South Korea). ITS genotypes were identified by comparison against the Geosymbio database (Franklin et al, 2012). Chlorophyll was extracted over 48 h in 1-2 mL N, Ndimethylformamide at 4°C in the dark.…”

The symbiotic life ofSymbiodiniumin the open ocean within a new species of calcifying ciliate (Tiarinasp.)

“…From station 72, we note that host genotypes 1 and 2 are associated with different but genetically close Symbiodinium types (3 nucleotide differences out of 795 bp of the 28S rDNA sequence), indicating a symbiont specificity within the same location. The earliest diverging clade A is found within several benthic hosts (for example, mollusks, corals, anemones and jellyfish) in temperate and tropical waters of the Atlantic, Pacific and Indian Oceans and Red Sea (Goulet et al, 2008;Franklin et al, 2012). Our results raise the question of whether the novel diversity of Symbiodinium associated with a planktonic ciliate in the open ocean can also live within benthic hosts from coastal waters.…”

“…did not match any previously described clade A sequence types, and instead represented 8 novel divergent subclade types (7 of which have ⩾ 2 nucleotide differences). Remarkably, this Symbiodinium diversity from a single host taxon is relatively high, and equivalent to the diversity described so far from ∼ 50 benthic host taxa in reef ecosystems worldwide (Franklin et al, 2012). The ITS2 diversity of Symbiodinium from Tiarina sp., like that of the 28S rRNA gene, is partly structured by geography, whereby sequences from the same Table S4 for the GenBank accession numbers).…”

“…Our results raise the question of whether the novel diversity of Symbiodinium associated with a planktonic ciliate in the open ocean can also live within benthic hosts from coastal waters. A complex genetic diversity composed of 15 common subclade types has been recognized in clade A with the highly resolutive ITS2 marker (LaJeunesse et al, 2001(LaJeunesse et al, , 2009Franklin et al, 2012;Lee et al, 2015). This marker was therefore used in this study to assign the new Symbiodinium sequences at the subclade level, and thus to provide a better understanding of the identity of the Tiarina symbiont and the specificity of the symbiotic partnership (LaJeunesse, 2001).…”

“…The ITS2 diversity of Symbiodinium from Tiarina sp., like that of the 28S rRNA gene, is partly structured by geography, whereby sequences from the same Table S4 for the GenBank accession numbers). Based on the GeoSymbio database (Franklin et al, 2012), the geographic origin and host spectrum for each Symbiodinium subclade are indicated by a color and a letter, respectively. All of the previously described subclade types (A1-A16 in squares) were found in benthic coastal hosts (∼50 host species).…”