DOI: 10.5061/dryad.h617h
title: Data from: De novo transcriptome assembly for the lobster Homarus americanus and characterization of differential gene expression across nervous system tissues

description: 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.
description: Transcriptome assembly
 for American lobster Homarus americanusTranscriptome assembly
 for the American lobster, Homarus americanus. Assembly conducted in
 Trinity (version 8-14-2013) from 145 million single-end reads (Illumina
 HiSeq 2000) from mRNA extracted from nervous system, heart, and muscle
 tissues of Homarus americanus (2012). For additional information, please
 email Lara McGrath at lara.l.mcgrath [at] gmail.comHomarusamericanustranscriptome_LLM12-20-2015.faRead Counts for Homarus americanus transcriptome samplesRead counts from read mapping conducted in Bowtie (version 0.12.7) against de novo assembled Homarus americanus transcriptome. For identification of samples: U= untreated, P=proctolin-treated, M=muscle, B= brain, H= heart, A= abdominal ganglia, and number indicates individual lobster. For more information, email Lara McGrath at lara.l.mcgrath [at] gmail.comHomarusamericanustranscriptome_rawreadcounts_LLM12-20-2015.csvAnnotations for Homarus americanus transcriptomeProtein annotations from tBlast of de novo assembled Homarus americanus transcriptome against NCBI, and UniprotKB Swiss-Prot and TrEMBL databases. For more information, email Lara McGrath at lara.l.mcgrath [at] gmail.comHomarusamericanustranscriptome_annotations_LLM12-20-2015.csvCount Tables in RR script for counting differentially expressed and up- or down-regulated contigs for a given category. Useful for interpreting expression changes for multiple unique contigs within a category (i.e. multiple proteins of an ion channel). Written by Lara McGrath. For more information, email Lara McGrath at lara.l.mcgrath [at] gmail.comcounttables_LLM8-8-2015.R