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

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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.