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Background  The American lobster,  Homarus americanus , is an important species as an economically valuable fishery, a key member in marine ecosystems, and a well-studied model for central pattern generation, the neural networks that control rhythmic motor patterns. Despite multi-faceted scientific interest in this species, currently our genetic resources for the lobster are limited. In this study, we  de novo  assemble a transcriptome for  Homarus americanus  using central nervous system (CNS), muscle, and hybrid neurosecretory tissues and compare gene expression across these tissue types. In particular, we focus our analysis on genes relevant to central pattern generation and the identity of the neurons in a neural network, which is defined by combinations of genes distinguishing the neuronal behavior and phenotype, including ion channels, neurotransmitters, neuromodulators, receptors, transcription factors, and other gene products.    Results  Using samples from the central nervous system (brain, abdominal ganglia), abdominal muscle, and heart (cardiac ganglia, pericardial organs, muscle), we used RNA-Seq to characterize gene expression patterns across tissues types. We also compared control tissues with those challenged with the neuropeptide proctolin  in vivo . Our transcriptome generated 34,813 transcripts with known protein annotations. Of these, 5,000-10,000 of annotated transcripts were significantly differentially expressed (DE) across tissue types. We found 421 transcripts for ion channels and identified receptors and/or proteins for over 20 different neurotransmitters and neuromodulators. Results indicated tissue-specific expression of select neuromodulator (allostatin, myomodulin, octopamine, nitric oxide) and neurotransmitter (glutamate, acetylcholine) pathways. We also identify differential expression of ion channel families, including kainite family glutamate receptors, inward-rectifying K +  (IRK) channels, and transient receptor potential (TRP) A family channels, across central pattern generating tissues.    Conclusions  Our transcriptome-wide profiles of the rhythmic pattern generating abdominal and cardiac nervous systems in  Homarus americanus  reveal candidates for neuronal features that drive the production of motor output in these systems.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2373-3) contains supplementary material, which is available to authorized users.

De novo transcriptome assembly for the lobster Homarus americanus and characterization of differential gene expression across nervous system tissues