Data from: De novo transcriptome assembly for the lobster Homarus americanus and characterization of differential gene expression across nervous system tissues
McGrath, Lara Lewis, Northeastern University
Vollmer, Steven V., Northeastern University
Kaluziak, Stefan T., Northeastern University
Ayers, Joseph, Northeastern University
Published Dec 22, 2016 on Dryad.
Cite this dataset
McGrath, Lara Lewis; Vollmer, Steven V.; Kaluziak, Stefan T.; Ayers, Joseph (2016). Data from: De novo transcriptome assembly for the lobster Homarus americanus and characterization of differential gene expression across nervous system tissues [Dataset]. Dryad. https://doi.org/10.5061/dryad.h617h
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.
Transcriptome assembly for American lobster Homarus americanus
Transcriptome 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.com
Read Counts for Homarus americanus transcriptome samples
Read 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.com
Protein 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.com
R 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.com