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

BMC Genomics
Lara Lewis McGrathJoseph Ayers

Abstract

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. 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 i...Continue Reading

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Citations

Jun 3, 2016·Integrative and Comparative Biology·K F Clark, Spencer J Greenwood
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Datasets Mentioned

BETA
PRJNA297570

Methods Mentioned

BETA
RNA-Seq
PCR

Software Mentioned

GOseq
R package GOseq
tBlast
R package DESeq2
REVIGO
Blast
Trinity
TrEMBLE
Bowtie

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