The nervous system is central to coordinating behavioural responses to
environmental change, likely including ocean acidification (OA).
However, a clear understanding of neurobiological responses to OA is
lacking, especially for marine invertebrates. We evaluated the
transcriptomic response of the central nervous system (CNS) and eyes of
the two-toned pygmy squid (Idiosepius pygmaeus) to OA conditions,
using a de novo transcriptome assembly created with long read
PacBio ISO-sequencing data. We then correlated patterns of gene
expression with CO2 treatment levels and OA-affected
behaviours in the same individuals. OA induced transcriptomic responses
within the nervous system related to various different types of
neurotransmission, neuroplasticity, immune function and oxidative
stress. These molecular changes may contribute to OA-induced behavioural
changes, as suggested by correlations between gene expression profiles,
CO2 treatment and OA-affected behaviours. This study
provides the first molecular insights into the neurobiological effects
of OA on a cephalopod and correlates molecular changes with whole animal
behavioural responses, helping to bridge the gap in our knowledge
between environmental change and animal responses.