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Background  Transcription factors that determine retinal development seem to be conserved in different phyla throughout the animal kingdom. In most representatives, however, only a few of the involved transcription factors have been sampled and many animal groups remain understudied. In order to fill in the gaps for the chelicerate group of arthropods, we tested the expression pattern of the candidate genes involved in the eye development in the embryo of the wandering spider  Cupiennius salei . One main objective was to profile the molecular development of the eyes and to search for possible variation among eye subtype differentiation. A second aim was to form a basis for comparative studies in order to elucidate evolutionary pathways in eye development.    Results  We screened the spider embryonic transcriptome for retina determination gene candidates and discovered that all except one of the retinal determination genes have been duplicated. Gene expression analysis shows that the two orthologs of all the genes have different expression patterns. The genes are mainly expressed in the developing optic neuropiles of the eyes (lateral furrow, mushroom body, arcuate body) in earlier stages of development (160 to 220 h after egg laying). Later in development (180 to 280 h after egg laying), there is differential expression of the genes in disparate eye vesicles; for example,  Cs-otxa  is expressed only in posterior-lateral eye vesicles,  Cs-otxb ,  Cs-six1a , and  Cs-six3b  in all three secondary eye vesicles,  Cs-pax6a  only in principal eye vesicles,  Cs-six1b  in posterior-median, and posterior-lateral eye vesicles, and  Cs-six3a  in lateral and principal eye vesicles.    Conclusions  Principle eye development shows  pax6a  ( ey ) expression, suggesting  pax6  dependence, although secondary eyes develop independently of  pax6  genes and show differential expression of several retinal determination genes. Comparing this with the other arthropods suggests that  pax6 -dependent median eye development is a ground pattern of eye development in this group and that the ocelli of insects, the median eyes of chelicerates, and nauplius eyes can be homologised. The expression pattern of the investigated genes makes it possible to distinguish between secondary eyes and principal eyes. Differences of gene expression among the different lateral eyes indicate disparate function combined with genetic drift.    Electronic supplementary material  The online version of this article (doi:10.1186/s13227-015-0010-x) contains supplementary material, which is available to authorized users.

Differential expression of retinal determination genes in the principal and secondary eyes of Cupiennius salei Keyserling (1877)