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，这些进化关系无论是形态数据还是初级序列数据都无法解决。具体地说，我们的研究目标是建立内含子-外显子结构作为原口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，重点是环节动物类群。我们将使用生物信息学方法，利用后口外群，在公开可获得的原口类群基因组数据的基因中确定剪接体内含子位置。我们特别感兴趣的是所谓的‘近内含子对’(NIP)，它是存在于不同基因组的同源基因中的邻近位置的内含子。由于两个内含子通常不会如此紧密地共存于同一基因组中，因此假设这些NIP代表一个内含子的连续丢失和邻近位置上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。计算工作将通过我们实验室的分子遗传学工作得到加强。带有推测信息的内含子的基因的同源基因将被聚合酶链式反应扩增、克隆和测序。对于这项分析，我们有一套环节动物和其他轮虫标本可用。收集的内含子数据随后可用于其他研究，因为剪接体内含子通常含有反转录转座子或snoRNAs。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用途。

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.