Improved resolution of reef-coral endosymbiont (Symbiodinium) species diversity, ecology, and evolution through psbA non-coding region genotyping.
Improved resolution of reef-coral endosymbiont (Symbiodinium) species diversity, ecology, and evolution through psbA non-coding region genotyping.
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DOI：
10.1371/journal.pone.0029013
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Thornhill DJ
中科院分区：
文献类型：
--
作者：
LaJeunesse TC;Thornhill DJ
核糖体DNA序列数据丰富的甲藻内共生体的珊瑚的众多研究，但多拷贝的性质和基因组内的rRNA基因和间隔区的变异混淆共生体的多样性和生态的解释。在一个有意义的生态和进化背景下，广泛的序列变异的一致意义将受益于额外的遗传标记的应用。质体psbA小环（psbAncr）的非编码区的序列被用来独立检查共生体的基因型和物种多样性，发现内和殖民地之间的夏威夷珊瑚礁属Montipora。通过直接测序在大多数样品中回收单个psbAncr单倍型（约80-90%），并且相同的内部转录间隔区2（ITS 2）类型的成员通过大量psbAncr序列差异与其他ITS 2类型在遗传学上区分开。对来自样品和克隆培养物的psbAncr的细菌克隆片段的重复测序常常恢复单个数值上常见的单倍型，伴随着罕见的、高度相似的序列变体。当克隆和基因组内变异的序列文物的因素，这些数据表明，大多数殖民地窝藏一个占主导地位的共生藻基因型。从这些相同样本中扩增的ITS 2 DNA的克隆和测序回收了数量丰富的变体（可以诊断不同的共生甲藻谱系），但也产生了大量包含PCR/克隆伪影与祖先和/或罕见变体相结合的序列，如果将其纳入系统发育重建，就会混淆对微小序列差异的解释。最后，psbAncr序列数据从广泛的采样共生藻多样性获得的各种珊瑚在整个印度-太平洋是一致的ITS谱系成员（定义的变性梯度凝胶电泳筛选），但表现出更大的序列分歧，并揭示了强大的地理结构，对应于主要的地理省。psbAncr数据提供的详细的遗传分辨率进一步澄清了共生甲藻的生态，进化和系统学。
Ribosomal DNA sequence data abounds from numerous studies on the dinoflagellate endosymbionts of corals, and yet the multi-copy nature and intragenomic variability of rRNA genes and spacers confound interpretations of symbiont diversity and ecology. Making consistent sense of extensive sequence variation in a meaningful ecological and evolutionary context would benefit from the application of additional genetic markers. Sequences of the non-coding region of the plastid psbA minicircle (psbAncr) were used to independently examine symbiont genotypic and species diversity found within and between colonies of Hawaiian reef corals in the genus Montipora. A single psbAncr haplotype was recovered in most samples through direct sequencing (∼80–90%) and members of the same internal transcribed spacer region 2 (ITS2) type were phylogenetically differentiated from other ITS2 types by substantial psbAncr sequence divergence. The repeated sequencing of bacterially-cloned fragments of psbAncr from samples and clonal cultures often recovered a single numerically common haplotype accompanied by rare, highly-similar, sequence variants. When sequence artifacts of cloning and intragenomic variation are factored out, these data indicate that most colonies harbored one dominant Symbiodinium genotype. The cloning and sequencing of ITS2 DNA amplified from these same samples recovered numerically abundant variants (that are diagnostic of distinct Symbiodinium lineages), but also generated a large amount of sequences comprising PCR/cloning artifacts combined with ancestral and/or rare variants that, if incorporated into phylogenetic reconstructions, confound how small sequence differences are interpreted. Finally, psbAncr sequence data from a broad sampling of Symbiodinium diversity obtained from various corals throughout the Indo-Pacific were concordant with ITS lineage membership (defined by denaturing gradient gel electrophoresis screening), yet exhibited substantially greater sequence divergence and revealed strong phylogeographic structure corresponding to major biogeographic provinces. The detailed genetic resolution provided by psbAncr data brings further clarity to the ecology, evolution, and systematics of symbiotic dinoflagellates.
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