Coleoid cephalopods like squids have a camera-type eye similar to vertebrates. 
On the other hand, Nautilus (Nautiloids) has a pinhole eye that lacks lens and 
cornea. Since pygmy squid and Nautilus are closely related species they are 
excellent model organisms to study eye evolution. Having being able to collect 
Nautilus embryos, we employed next-generation RNA sequencing using Nautilus and 
pygmy squid developing eyes. Their transcriptomes were compared and analyzed. 
Enrichment analysis of Gene Ontology revealed that contigs related to nucleic 
acid binding were largely up-regulated in squid, while the ones related to 
metabolic processes and extracellular matrix-related genes were up-regulated in 
Nautilus. These differences are most likely correlated with the complexity of 
tissue organization in these species. Moreover, when the analysis focused on the 
eye-related contigs several interesting patterns emerged. First, contigs from 
both species related to eye tissue differentiation and morphogenesis as well as 
to cilia showed best hits with their Human counterparts, while contigs related 
to rabdomeric photoreceptors showed the best hit with their Drosophila 
counterparts. This bolsters the idea that eye morphogenesis genes have been 
generally conserved in evolution, and compliments other studies showing that 
genes involved in photoreceptor differentiation clearly follow the 
diversification of invertebrate (rabdomeric) and vertebrate (ciliated) 
photoreceptors. Interestingly some contigs showed as good a hit with Drosophila 
and Human homologues in Nautilus and squid samples. One of them, capt/CAP1, is 
known to be preferentially expressed in Drosophila developing eye and in 
vertebrate lens. Importantly our analysis also provided evidence of gene 
duplication and diversification of their function in both species. One of these 
genes is the Neurofibromatosis 1 (NF1/Nf1), which in mice has been implicated in 
lens formation, suggesting a hitherto unsuspected role in the evolution of the 
lens in molluscs.