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首页> 外文期刊>Harmful Algae >Secondary Structural Modeling Of The Second Internal Transcribed Spacer (its2) From Pfiesteria-like Dinoflagellates (dinophyceae)
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Secondary Structural Modeling Of The Second Internal Transcribed Spacer (its2) From Pfiesteria-like Dinoflagellates (dinophyceae)

机译：第二内部转录间隔物（its2）的第二个内部转录模型，从类似费非特氏菌的鞭毛虫（Dinophyceae）

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摘要

Pfiesteria piscicida is a harmful bloom-forming alga that has received a great deal of attention due to its potential association with large fish kills and neurological problems in humans. Since the discovery of Pfiesteria, several other Pfiesteria-like dinoflagellates (PLDs) have also been identified. Genetic identification and phylogenetic relationships among the PLDs commonly utilize sequence data from the genes and spacers of the ribosomal DNA (rDNA) operon. Of these, the internal transcribed spacers (ITSs) have been previously shown to fold into secondary structures that are critical for proper ribosomal processing. In this study, we modeled the secondary structure of the second internal transcribed spacer (ITS2) from 16 PLDs (as well as an outgroup taxon) using phylogenetic comparative methods and minimum free energy. The secondary structural models predicted for these dinoflagellates consisted of four paired helices separated by five unpaired regions, consistent with those reported from many eukaryotes. All of the structures were highly stable (△G= -66.1 to -122.3 kcal·mol at 37 ℃) and several structural characters were found to be conserved either across the PLDs or were specific to monophyletic subgroups, strengthening previously inferred phylogenetic relationships among taxa. Additionally, an 18 bp motif was identified in the PLDs whose position corresponds to a ribosomal processing site described from other eukaryotes. Potential applications of these ITS2 secondary structures include utility in strain and species identification, phylogenetic inference and serving as a tool for identifying and excluding rDNA pseudogenes when assessing biodiversity within the PLDs.
机译：Pfiesteria piscicida是一种有害的形成藻类的藻类，由于其与大型杀鱼和人类神经系统疾病的潜在联系而备受关注。自从发现非小孢子虫以来，还鉴定了其他几种非小孢子菌样鞭毛藻（PLD）。 PLD之间的遗传鉴定和系统发育关系通常利用来自核糖体DNA（rDNA）操纵子的基因和间隔区的序列数据。其中，内部转录的间隔子（ITS）先前已显示折叠成对于正确的核糖体加工至关重要的二级结构。在这项研究中，我们使用系统进化比较方法和最小的自由能，对来自16个PLD（以及外分类群）的第二个内部转录间隔子（ITS2）的二级结构进行了建模。对这些鞭毛鞭毛虫预测的二级结构模型由四个成对的螺旋组成，被五个不成对的区域隔开，这与许多真核生物报道的一致。所有结构都高度稳定（在37℃时△G = -66.1至-122.3 kcal·mol），并且发现几个结构特征在整个PLD中都是保守的或特定于单系亚群，从而加强了先前推断的类群之间的系统发生关系。 。另外，在PLD中鉴定出18bp的基序，其位置对应于从其他真核生物描述的核糖体加工位点。这些ITS2二级结构的潜在应用包括可用于菌株和物种鉴定，系统发育推断，并在评估PLD内的生物多样性时可作为鉴定和排除rDNA假基因的工具。

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