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 ...

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。在造礁珊瑚的共生藻类虫黄藻属（Symbiodinium）中，研究人员通常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，不同的内转录间隔区2（Internal Transcribed Spacer 2, ITS2）序列可能代表基因组内变异体，而非不同的共生菌类群，并提出可通过共生菌的基因组内变异体比例组成——即其ITS2元单倍型（metahaplotype）——来区分不同的共生菌。我们采用元单倍型分析方法，对采自鹿角珊瑚（Acropora downingi）、微脊珊瑚（Cyphastrea microphthalma）以及Playgyra daedalea的ITS2序列开展最小熵分解法（Minimum Entropy Decomposition, MED）分析，结果显示每个珊瑚物种内均存在单一物种特异性虫黄藻C3变异体的主导优势。我们通过psbA非编码区验证了这类物种特异性共生菌的存在。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，并证实了其……