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Background   Hox  genes are critical for patterning the bilaterian anterior-posterior axis. The evolution of their clustered genomic arrangement and ancestral function has been debated since their discovery. As acoels appear to represent the sister group to the remaining Bilateria (Nephrozoa), investigating  Hox  gene expression will provide an insight into the ancestral features of the  Hox  genes in metazoan evolution.    Results  We describe the expression of anterior, central and posterior class  Hox  genes and the  ParaHox  ortholog  Cdx  in the acoel  Convolutriloba longifissura . Expression of all three  Hox  genes begins contemporaneously after gastrulation and then resolves into staggered domains along the anterior-posterior axis, suggesting that the spatial coordination of  Hox  gene expression was present in the bilaterian ancestor. After early surface ectodermal expression, the anterior and central class genes are expressed in small domains of putative neural precursor cells co-expressing  ClSoxB1 , suggesting an evolutionary early function of  Hox  genes in patterning parts of the nervous system. In contrast, the expression of the posterior  Hox  gene is found in all three germ layers in a much broader posterior region of the embryo.    Conclusion  Our results suggest that the ancestral set of  Hox  genes was involved in the anterior-posterior patterning of the nervous system of the last common bilaterian ancestor and were later co-opted for patterning in diverse tissues in the bilaterian radiation. The lack of temporal colinearity of  Hox  expression in acoels may be due to a loss of genomic clustering in this clade or, alternatively, temporal colinearity may have arisen in conjunction with the expansion of the  Hox  cluster in the Nephrozoa.

Coordinated spatial and temporal expression of Hox genes during embryogenesis in the acoel Convolutriloba longifissura