title: Host specificity of Symbiodinium variants revealed by an ITS2 metahaplotype approach.
abstract: Analysis of the widely used ITS region is confounded by the presence of intragenomic variants (IGVs). In Symbiodinium, the algal symbionts of reef building corals, deep-sequencing analyses are used to characterise communities within corals, yet these analyses largely overlook IGVs. Here we consider that distinct ITS2 sequences could represent IGVs rather than distinct symbiont types and argue that symbionts can be distinguished by their proportional composition of IGVs, described as their ITS2 metahaplotype. Using our metahaplotype approach on Minimum Entropy Decomposition (MED) analysis of ITS2 sequences from the corals Acropora downingi, Cyphastrea microphthalma and Playgyra daedalea, we show the dominance of a single species-specific Symbiodinium C3 variant within each coral species. We confirm the presence of these species-specific symbionts using the psbA non-coding region. Our findings highlight the importance of accounting for IGVs in ITS2 analyses and demonstrate their capacity to resolve biological patterns that would otherwise be overlooked.
authors.affiliation: Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE.
authors.forename: Edward G
authors.initials: EG
authors.lastname: Smith
authors.affiliation: Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE.
authors.forename: Remi N
authors.initials: RN
authors.lastname: Ketchum
authors.affiliation: Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE.
authors.forename: John A
authors.initials: JA
authors.lastname: Burt
mesh_terms: D000818:Animals; D037421:Anthozoa / Q000502:physiology*; D057894:Coral Reefs; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D004141:Dinoflagellida / Q000235:genetics / Q000502:physiology*; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D058507:Host Specificity; D013045:Species Specificity; D013559:Symbiosis
chemical_list: D021903:DNA, Ribosomal Spacer