Coral reefs are in rapid decline on a global scale due to human activities and a changing climate. Shallow water reefs depend on the obligatory symbiosis between the habitat forming coral host and its algal symbiont from the genus Symbiodinium (zooxanthellae). This association is highly sensitive to thermal perturbations and temperatures as little as 1°C above the average summer maxima can cause the breakdown of this symbiosis, termed coral bleaching. Predicting the capacity of corals to survive the expected increase in seawater temperatures depends strongly on our understanding of the thermal tolerance of the symbiotic algae. Here we use molecular phylogenetic analysis of four genetic markers to describe Symbiodinium thermophilum, sp. nov. from the Persian/Arabian Gulf, a thermally tolerant coral symbiont. Phylogenetic inference using the non-coding region of the chloroplast psbA gene resolves S. thermophilum as a monophyletic lineage with large genetic distances from any other ITS2 C3 type found outside the Gulf. Through the characterisation of Symbiodinium associations of 6 species (5 genera) of Gulf corals, we demonstrate that S. thermophilum is the prevalent symbiont all year round in the world's hottest sea, the southern Persian/Arabian Gulf.

Multiple sequence alignment of psba(ncr) DNA sequences from Symbiodinium thermophilum and closely related Symbiodinium spp.This file is a multiple sequence alignment of partial chloroplast psbA non coding region genes from Symbiodinium thermophilum and other closely related species of Symbiodinium. It is in a FASTA format. The first 22 Symbiodinium sequences were obtained from algae within Porites spp. corals from the Persian/Arabian gulf. The host identity, specific collection location and host species for each sample are detailed in the supplementary materials of the associated paper. The alignment was implemented using ClustalW but heavily modified manually. Reference sequences are included in the alignment. These are available in Genbank as detailed in the associated paper.Dryad Submission alignment.fas