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

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，这些进化关系无法用形态学或初级序列数据来解决。具体来说，我们的研究目标是建立内含子-外显子结构作为原口动物系统发育的系统发育标记，并将我们新开发的标记应用于一组选定的原口动物，重点是环节动物分类群。我们将使用生物信息学方法来识别原口动物分类群中公开可用的基因组数据中的剪接体内含子位置，使用后口动物外群。我们对所谓的“近内含子对”（NIPs）特别感兴趣，这些内含子存在于不同基因组的同源基因的附近位置。由于两个内含子通常不会在同一基因组中如此紧密地共存，因此假设这些NIPs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被用于此目的。我们实验室的分子遗传学工作将加强计算工作。假定含有信息性内含子的基因同源物将被pcr扩增、克隆和测序。为了进行这项分析，我们有一组环节动物和其他浮游动物的标本。由于剪接体内含子通常含有反转录转座子或snorna，因此收集到的内含子数据随后可用于其他研究。因此，我们将能够通过计算识别这些元素，并探索它们作为系统发育标记的效用。

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.