Data from: Host specificity of Symbiodinium variants revealed by an ITS2 metahaplotype approach

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.针对广泛应用的内转录间隔区（Internal Transcribed Spacer, ITS）的分析，常因基因组内变异体（intragenomic variants, IGVs）的存在而受到干扰。在造礁珊瑚的藻类共生体虫黄藻属（Symbiodinium）中，研究人员多借助深度测序技术表征珊瑚体内的共生群落，但此类分析大多忽略了基因组内变异体。本研究认为，不同的ITS2序列可能代表基因组内变异体，而非独特的共生体类群；并提出可通过共生体的基因组内变异体比例组成——即其ITS2元单倍型——来区分共生体。我们将元单倍型分析方法应用于珊瑚Acropora downingi、Cyphastrea microphthalma与Playgyra daedalea的ITS2序列的最小熵分解（Minimum Entropy Decomposition, MED）分析，结果显示每种珊瑚内均存在单一物种特异性的虫黄藻C3变异体作为优势类群。我们通过psbA非编码区验证了这类物种特异性共生体的存在。本研究结果凸显了在ITS2分析中纳入基因组内变异体的重要性，并证实其可解析此前被忽视的生物学模式。