Here we describe isolation and characterization of two zebrafish cDNAs, designated ph2alpha and ph2beta, which were identified as structural homologs of the Drosophila polyhomeotic, mouse Mph2, and human HPH2 genes, collectively termed the Polycomb group. The a and P transcripts shared a 1.9-kb sequence at their 3'-termini. alpha had an additional 1.6-kb sequence extending toward its 5'-terminus. Only a short 0.1-kb segment was unique to beta. Sequencing of a genomic clone corresponding to the two cDNAs indicated that the mRNAs were transcribed from a single gene locus by alternative promoters. Northern blots revealed expression of a transcripts during the segmentation period, while beta expression occurred at all developmental stages examined. Whole-mount in situ hybridizations with an a-specific probe and a probe recognizing both transcripts revealed distinct spatio-temporal expression patterns along developing somites. alpha transcripts were detected initially at the 7-8 somite stage; 13 transcripts appeared in the first somites. As segmentation proceeded, alpha and beta expression shifted position toward the tailbud in parallel with the formation of each somite. Within individual somites, the signal corresponding to a was strongest at the posterior border and weakest in the anterior region. Conversely, that corresponding to beta was strongest at the anterior border and weakest in the posterior region. The data support the idea that Ph2alpha and Ph2beta are involved in spatio-temporal generation of somites as well as in specification of antero-posterior regional differences within individual somites. (C) 2002 Elsevier Science (USA).