Post-transcriptional modifications, such as mRNA editing, have the potential to diversify the proteome. Most animals do not show much mRNA editing that results in a codon change (recoding). However, squid (a member of the cephalopod taxa) were recently shown to have high levels of recoding, but it was not known if this translates into functional diversification of the proteome. Now, Liscovitch-Brauer et al. show that cephalopods diversify their neuronal proteome with RNA editing, and that this limits genome evolution.
A common form of RNA editing in animals is adenosine (A) deamination to inosine (I) by ADAR (adenosine deaminases acting on RNA) enzymes. The authors assessed recoding by using RNA sequencing (RNA-seq) data to assemble a transcriptome for several species, and then comparing this to known DNA and RNA sequences. Systematic mismatches were used to identify A-to-I RNA editing events. Four species of coleoid cephalopod (two species of octopus, a squid and a cuttlefish) were compared to more primitive species (a nautiloid and a mollusc). For the squid, octopus and cuttlefish species, 80,000–130,000 A-to-I editing events were obtained. By contrast, the few mismatches seen in the nautiloid and mollusc were attributed to background noise. The full genome for Octopus bimaculoides was also used to assess RNA editing, and showed a substantial overlap with A-to-I sites identified by the reference-genome-free approach.