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Background  Annelida is a morphologically diverse animal group that exhibits a remarkable variety in nervous system architecture (e.g., number and location of longitudinal cords, architecture of the brain). Despite this heterogeneity of neural arrangements, the molecular profiles related to central nervous system patterning seem to be conserved even between distantly related annelids. In particular, comparative molecular studies on brain and anterior neural region patterning genes have focused so far mainly on indirect-developing macrofaunal taxa. Therefore, analyses on microscopic, direct-developing annelids are important to attain a general picture of the evolutionary events underlying the vast diversity of annelid neuroanatomy.    Results  We have analyzed the expression domains of 11 evolutionarily conserved genes involved in brain and anterior neural patterning in adult females of the direct-developing meiofaunal annelid  Dinophilus gyrociliatus . The small, compact brain shows expression of  dimmed ,  foxg ,  goosecoid ,  homeobrain ,  nk2.1 ,  orthodenticle ,  orthopedia ,  pax6 ,  six3 / 6  and  synaptotagmin - 1 . Although most of the studied markers localize to specific brain areas, the genes  six3 / 6  and  synaptotagmin - 1  are expressed in nearly all perikarya of the brain. All genes except for  goosecoid ,  pax6  and  nk2.2  overlap in the anterior brain region, while the respective expression domains are more separated in the posterior brain.    Conclusions  Our findings reveal that the expression patterns of the genes  foxg ,  orthodenticle ,  orthopedia  and  six3 / 6  correlate with those described in  Platynereis dumerilii  larvae, and  homeobrain ,  nk2.1 ,  orthodenticle  and  synaptotagmin - 1  resemble the pattern of late larvae of  Capitella teleta . Although data on other annelids are limited, molecular similarities between adult  Dinophilus  and larval  Platynereis  and  Capitella  suggest an overall conservation of molecular mechanisms patterning the anterior neural regions, independent from developmental and ecological strategies, or of the size and configuration of the nervous system.    Electronic supplementary material  The online version of this article (doi:10.1186/s13227-016-0058-2) contains supplementary material, which is available to authorized users.

Molecular regionalization in the compact brain of the meiofaunal annelid Dinophilus gyrociliatus (Dinophilidae)