Characterization of a single genomic locus encoding the clustered protocadherin receptor diversity in Xenopus tropicalis

Clustered protocadherins (cPcdhs) constitute the largest subgroup of the cadherin superfamily (Hulpiau & van Roy, 2009) and in mammals are grouped into clusters of alpha-, beta- and gamma-types. Tens of tandemly-arranged paralogous Pcdh genes of the protocadherin clusters generate a substantial diversity of receptor isoforms. cPcdhs are known to have important roles in neuronal development and genetic alterations of cPcdhs have been found to be associated with several neurological diseases. Here, we present a first characterization of cPcdhs in Xenopus tropicalis (X. tropicalis). We determined and annotated all cPcdh isoforms revealing that they are present in a single chromosomal locus. We validated a total of 96 isoforms, which we show are organized in three distinct clusters. The X. tropicalis cPcdh locus is composed of one alpha- and two distinct gamma-protocadherin clusters (pcdh-gamma1 and pcdh-gamma2). Bioinformatics analyses assisted by genomic BAC clone sequencing showed that the X. tropicalis alpha- and gamma-protocadherins are conserved at the cluster level, but unlike mammals, X. tropicalis does not contain a beta-protocadherin cluster. In contrast, the number of gamma-protocadherin isoforms has expanded possibly due to lineage-specific gene duplications. Interestingly, the number of X. tropicalis alpha-protocadherins is identical between X. tropicalis and mouse. Moreover, we find highly conserved as well as novel promoter elements potentially involved in regulating the cluster-specific expression of clustered protocadherin isoforms. This study provides important information for the understanding of the evolutionary history of cPcdh genes and future mechanistic studies. It provides an annotated X. tropicalis cPcdh genomic map and a first molecular characterization essential for functional and comparative studies