CREx: examples

here you can find some examples demonstrating the capabilities of CREx. for each example you can download the gene orders in the fasta format. so you can try it for yourself. first we demonstrate the ability to localize tdrls and second we demonstrate the usage for a larger data set of echinoderms gene orders. note that the examples show the original output from crex. we have only omited little details to simplify the presentation, e.g. the highlighting of the rearrangements in the family diagrams is enabled here by default, usually you have to trigger the highlighting by clicking on the corresponding rearrangements in the scenario (but you can try it here also).

the abbreviations of the gene names used in the examples and the example files are documented here

localisation of tdrls

Chauliodus sloani → Eurypharynx pelecanoides

in this example CREx identifies one tdrl (affecting the genes from atp8 to W (in chauliodus sloani)) and one transposition (of -Y and -C). the tdrl was described in Inoue et al. (2003) (click on the rearrangements listed in the scenario in order to highlight them). the tdrl is directed toward the eurypharynx pelecanoides gene order because the other direction needs three tdrls, as shown below. download fasta .

Chauliodus sloani → Eurypharynx pelecanoides Eurypharynx pelecanoides → Chauliodus sloani

Limulus polyphemus → Narceus annularus, Thyropygus sp

This example was described in detail in Lavrov et al. (2002). it is an example if "tandem duplication non-random loss", note that all negative genes are moved to the back by the rearrangement. Again the direction of the tdrl can be inferred with the parsimony criterion as the other direction needs two tdrl and a transposition. download fasta

Limulus polyphemus → Narceus annularus, Thyropygus sp

reconstruction of ancestral states

we have reconstructed the ancestral states for the known mitochondrial gene orders of the echinoderm species (except for the ophiorids) for a given phylogenetic tree (see Perseke et al. 2007). you can find the dataset here. The phylogenetic tree that we have used is depicted in the following - with the rearrangements annotated to the edges. the abbreviations are I: inversion, T: transposition, rT: reverse transposition, and TDRL: tandem duplication random loss. (the dots and numbers can be ignored here - they represent support valued for the phylogenetic analysis based on molecular data). how the rearrangements were assigned to the edges is described below.
Echinodermata tree
as you load the data set in CREx you can see immediately that there are a number of equal gene orders this is: now lets reconstruct the rearrangement history