Paired-like subclass homeobox genes from the clitellate annelid Perionyx excavatus

The homeobox genes compose a large family of genes encoding for transcription factor proteins. A motif of 60 amino acids termed the homeodomain has been intensively studied in order to elucidate the molecular mechanism of the specification of body pattern during embryonic development, differentiation, and regeneration (Scott et al. 1989; Gehring et al. 1990). In the past decade, various classification systems have been proposed for the categorization of homeobox genes (Burglin 1994). These homeobox gene classes can be grouped into a few large superclasses, based on the results of molecular phylogenetic analyses. Homeodomain proteins are generally classified into 11 classes: Hox, NK, Paired, POU, LIM, TALE, SIX, Prox, Cut, ZFH, and HNF1 (Wada et al. 2003). The Paired class is subdivided into two subclasses, namely, the Paired-like subclass, including the Q50 and K50 genes, and the Pax-type subclass, which includes the S50 genes (Galliot et al. 1999). Annelids are a large and diverse taxon of marine, freshwater, and terrestrial worms. Traditionally regarded as comprising three distinct classes (polychaetes, oligochaetes, and leeches; Brusca and Brusca 1990), they are now thought to be paraphyletic with respect to Echiura, Pogonophora, and Sipuncula (McHugh 1997). Clitellata (uniting oligochaetes and leeches) is a major annelid grouping, accepted as monophyletic on the basis of both molecular and morphological criteria (Erseus