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Background  Retinoic acid (RA) signaling controls many developmental processes in chordates, from early axis specification to late organogenesis. The functions of RA are chiefly mediated by a subfamily of nuclear hormone receptors, the retinoic acid receptors (RARs), that act as ligand-activated transcription factors. While RARs have been extensively studied in jawed vertebrates (that is, gnathostomes) and invertebrate chordates, very little is known about the repertoire and developmental roles of RARs in cyclostomes, which are extant jawless vertebrates. Here, we present the first extensive study of cyclostome RARs focusing on three different lamprey species: the European freshwater lamprey,  Lampetra fluviatilis , the sea lamprey,  Petromyzon marinus , and the Japanese lamprey,  Lethenteron japonicum .    Results  We identified four  rar  paralogs ( rar1 ,  rar2 ,  rar3 , and  rar4 ) in each of the three lamprey species, and phylogenetic analyses indicate a complex evolutionary history of lamprey  rar  genes including the origin of  rar1  and  rar4  by lineage-specific duplication after the lamprey-hagfish split. We further assessed their expression patterns during embryonic development by  in situ  hybridization. The results show that lamprey  rar  genes are generally characterized by dynamic and highly specific expression domains in different embryonic tissues. In particular, lamprey  rar  genes exhibit combinatorial expression domains in the anterior central nervous system (CNS) and the pharyngeal region.    Conclusions  Our results indicate that the genome of lampreys encodes at least four  rar  genes and suggest that the lamprey  rar  complement arose from vertebrate-specific whole genome duplications followed by a lamprey-specific duplication event. Moreover, we describe a combinatorial code of lamprey  rar  expression in both anterior CNS and pharynx resulting from dynamic and highly specific expression patterns during embryonic development. This ‘RAR code’ might function in regionalization and patterning of these two tissues by differentially modulating the expression of downstream effector genes during development.    Electronic supplementary material  The online version of this article (doi:10.1186/s13227-015-0016-4) contains supplementary material, which is available to authorized users.

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Evolution of retinoic acid receptors in chordates: insights from three lamprey species, Lampetra fluviatilis, Petromyzon marinus, and Lethenteron japonicum