mRNA editing analysis of Doryteuthis pealeii

Cephalopods are known for their large nervous systems, complex behaviors
and morphological innovations. To investigate the genomic underpinnings of
these features, we assembled the chromosomes of the Boston market squid
Doryteuthis (Loligo) pealeii and the California two-spot octopus, Octopus
bimaculoides, and compared them with those of the Hawaiian bobtail squid,
Euprymna scolopes. The genomes of the soft-bodied (coleoid) cephalopods
are highly rearranged relative to other extant molluscs, indicating an
intense, early burst of genome restructuring. The coleoid genomes feature
multi-megabase, tandem arrays of genes associated with brain development
and cephalopod-specific innovations. We find that another coleoid
hallmark, extensive A-to-I mRNA editing, displays two fundamentally
distinct patterns: one exclusive to the nervous system and concentrated in
genic sequences, the other widespread and directed toward repetitive
elements. We conclude that coleoid novelty is mediated in part by
substantial genome reorganization, gene family expansion, and
tissue-dependent mRNA editing.