Fast evolving 18S rRNA sequences from Solenogastres (Mollusca) resist standard PCR amplification and give new insights into mollusk substitution rate heterogeneity.
Fast evolving 18S rRNA sequences from Solenogastres (Mollusca) resist standard PCR amplification and give new insights into mollusk substitution rate heterogeneity.
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DOI：
10.1186/1471-2148-10-70
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发表时间：
2010-03-09
影响因子：
3.4
通讯作者：
Lieb B
中科院分区：
文献类型：
--
作者：
Meyer A;Todt C;Mikkelsen NT;Lieb B
18S rRNA基因是最重要的分子标记之一，在分子系统发育分析和生物多样性筛选等方面有着广泛的应用。软体动物是动物界中的第二大门，软体动物在体型和生态适应方面表现出高度的多样性。虽然大量的18S数据可用于高等软体动物，但一些早期分支谱系的数据仍然有限。尽管在获得这些数据的一些部分成功，一些被认为是最“基础”的软体动物，这分类群仍然存在问题，由于污染的食物生物和一般的扩增困难。我们在这里报告的第一个真实的18S基因的三个长吻软体动物物种（软体动物），每个拥有独特的序列组成与地区显着丰富的鸟嘌呤和胞嘧啶。对于这些富含GC的区域，我们计算了强二级结构。所观察到的高分子内力阻碍了标准扩增，并且似乎增加了由来自潜在猎物生物的污染性外来DNA引起的嵌合序列的形成。在我们的分析中，通过使用RNA作为模板来避免污染。指示污染以前发表的长吻鳕序列。使用RNA特异性模型进行详细的系统发育分析，该模型解释了茎区的补偿性取代。极端的形态多样性的软体动物是反映在分子18S数据，并显示出升高的替代率主要在三个较高的类群：真正的帽贝（Patellogastropoda），Cephalopoda和Solenogastres。我们的系统发育树基于123个物种，包括所有软体动物类的代表，显示有限的分辨率在类的水平，但说明了由于共享偏见的序列组成形成的人工分组的陷阱。
The 18S rRNA gene is one of the most important molecular markers, used in diverse applications such as molecular phylogenetic analyses and biodiversity screening. The Mollusca is the second largest phylum within the animal kingdom and mollusks show an outstanding high diversity in body plans and ecological adaptations. Although an enormous amount of 18S data is available for higher mollusks, data on some early branching lineages are still limited. Despite of some partial success in obtaining these data from Solenogastres, by some regarded to be the most "basal" mollusks, this taxon still remained problematic due to contamination with food organisms and general amplification difficulties. We report here the first authentic 18S genes of three Solenogastres species (Mollusca), each possessing a unique sequence composition with regions conspicuously rich in guanine and cytosine. For these GC-rich regions we calculated strong secondary structures. The observed high intra-molecular forces hamper standard amplification and appear to increase formation of chimerical sequences caused by contaminating foreign DNAs from potential prey organisms. In our analyses, contamination was avoided by using RNA as a template. Indication for contamination of previously published Solenogastres sequences is presented. Detailed phylogenetic analyses were conducted using RNA specific models that account for compensatory substitutions in stem regions. The extreme morphological diversity of mollusks is mirrored in the molecular 18S data and shows elevated substitution rates mainly in three higher taxa: true limpets (Patellogastropoda), Cephalopoda and Solenogastres. Our phylogenetic tree based on 123 species, including representatives of all mollusk classes, shows limited resolution at the class level but illustrates the pitfalls of artificial groupings formed due to shared biased sequence composition.
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影响因子：
56.9
作者：
FIELD, KG;OLSEN, GJ;RAFF, RA
通讯作者：
RAFF, RA
影响因子：
14.8
作者：
Frey, Ulrich H.;Bachmann, Hagen S.;Siffert, Winfried
通讯作者：
Siffert, Winfried
影响因子：
2.4
作者：
Harasewych, MG;McArthur, AG
通讯作者：
McArthur, AG
影响因子：
3.9
作者：
Abouheif, E;Zardoya, R;Meyer, A
通讯作者：
Meyer, A
DOI：
10.1073/pnas.0602578103
发表时间：
2006-05-16
影响因子：
11.1
作者：
Giribet, Gonzalo;Okusu, Akiko;Nishiguchi, Michele K.
通讯作者：
Nishiguchi, Michele K.