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

BMC Genomics

Research Article

Stefan T. Kaluziak¹  Steven V. Vollmer¹  Joseph Ayers¹  Lara Lewis McGrath² 

[1] Northeastern University Marine Science Center, 430 Nahant Rd, 01908, Nahant, MA, USA;Northeastern University Marine Science Center, 430 Nahant Rd, 01908, Nahant, MA, USA;Current address: AstraZeneca, 35 Gatehouse Dr, 02451, Waltham, MA, USA;

关键词: Transcriptome;    RNA-Seq;    Gene expression;    CNS;    Nervous system;    Central pattern generation;    Locomotion;    Neuronal differentiation;    Lobster;    Homarus americanus;   

DOI  :  10.1186/s12864-016-2373-3

 received in 2015-08-14, accepted in 2016-01-06,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsUsing 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.ConclusionsOur 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.

【 授权许可】

CC BY   
© McGrath et al. 2016