Genome structure characters as new markers for deep metazoan phylogeny, as exemplified for annelids.

基因组结构特征作为深层后生动物系统发育的新标记，例如环节动物。

• 批准号: 149103556
• 负责人: Dr. Stefanie Hartmann
• 金额: --
• 依托单位: Arbeitsgruppe Bioinformatik
• 依托单位国家: 德国
• 项目类别: Priority Programmes
• 财政年份: 2009
• 资助国家: 德国
• 起止时间: 2008-12-31 至 2012-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/149103556?language=en
• 关键词: Genome; structure; characters; new; markers

We aim to develop and apply a set of rare genomic changes as phylogenetic markers of major animal lineages, for which the evolutionary relationship could not be resolved with either morphological or primary sequence data. Specifically, the goal of our study is to establish intron-exon structure as a phylogenetic marker for protostome phylogeny, and to apply our newly developed markers to a selected set of protostomes, focusing on annelid taxa. We will use bioinformatic approaches to identify spliceosomal intron positions in genes of publicly available genome data of protostome taxa, using deuterostome outgroups. We are especially interested in so-called `near intron pairs' (NIPs), which are introns that exist in orthologous genes of different genomes at nearby positions. Because two introns generally do not co-exist this closely within the same genome, it is assumed that these NIPs represent the successive loss of an intron and the gain of another intron in a nearby position. Near intron pairs can therefore be used as reliable phylogenetic markers. Other spliceosomal introns have also been used for this purpose. The computational work will be augmented by molecular genetic work in our laboratory. Orthologs of genes with putatively informative introns will be PCR-amplified, cloned, and sequenced. For this analysis we have a set of annelid and other lophotrochozoan specimens available. The collected intron data can subsequently be used for additional studies, as spliceosomal introns often harbor retrotransposons or snoRNAs. We will therefore be able to computationally identify these elements and explore their utility as phylogenetic markers.

我们的目标是开发和应用一组罕见的基因组变化作为主要动物谱系的系统发育标记，对于这些动物谱系，不能用形态学或一级序列数据来解决进化关系。具体而言，我们的研究的目标是建立内含子-外显子结构作为原口动物的系统发育标记，并将我们新开发的标记应用于选定的一组原口动物，重点是环节动物类群。我们将使用生物信息学的方法，以确定剪接体内含子的位置在基因的公开可用的基因组数据的原口类类群，使用后口外群。我们特别感兴趣的是所谓的“近内含子对”（NIP），这是内含子存在于不同基因组的邻位基因中。由于两个内含子通常不会在同一基因组内如此紧密地共存，因此假设这些NIP代表一个内含子的连续丢失和附近位置的另一个内含子的获得。因此，近内含子对可以作为可靠的系统发育标记。其他剪接体内含子也用于此目的。我们实验室的分子遗传学工作将加强计算工作。将PCR扩增、克隆和测序具有pupirine信息内含子的基因的直向同源物。为了进行分析，我们有一套环节动物和其他钩轮动物标本。所收集的内含子数据随后可用于额外的研究，因为剪接体内含子通常含有反转录转座子或snoRNA。因此，我们将能够通过计算确定这些元素，并探索其效用作为系统发育标记。