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

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2373-3) contains supplementary material, which is available to authorized users.

Deep sequencing of transcriptomes from the nervous systems of two decapod crustaceans to characterize genes important for neural circuit function and modulation

“…No sequences were found in either species that represent the TRPC, TRPP, TRPL, or TRPN subfamilies. These results are consistent with found in a previously published transcriptome of H. americanus that identified 2 TRPA, one pyrexia, and two TRPM type channels [5]. We extend these results to include identification of the TRPV family of channels in both H. americanus and C. borealis .…”

“…The H. americanus metrics were C: 56.1 %, F: 16.4 %, and M: 27.5 % for the CLC Genomics assembly and C: 66.5 %, F: 13.4 %, and M: 20.1 % for the SeqMan NGen assembly. These results were compared against the arthropod transcriptome reference scores provided in the BUSCO supplementary materials, a recently published Homarus americanus nervous system transcriptome assembled using Trinity [5], and a recent transcriptome of the freshwater crayfish Astacus astacus [29]. Our results are comparable with the Astacus transcriptome in completeness and an apparent extension of the published Homarus americanus transcriptome [5].…”

“…b Horizontal stacked bar plots showing proportions of gene sets in BUSCO quality categories for the 4 different assemblies shown in panel A (CLC and SeqMan NGen, noted in bold ). A previously published nervous system transcriptome from H. americanus (denoted by *) is also provided for comparison [5]. Quality categories are as follows: i) Complete BUSCOs: genes that match a single gene in the BUSCO reference group; ii) Fragmented BUSCOs: genes only partially recovered with gene length exceeding alignment length cut-off; iii) Missing BUSCOs: non-recovered genes …”

“…These results were compared against the arthropod transcriptome reference scores provided in the BUSCO supplementary materials, a recently published Homarus americanus nervous system transcriptome assembled using Trinity [5], and a recent transcriptome of the freshwater crayfish Astacus astacus [29]. Our results are comparable with the Astacus transcriptome in completeness and an apparent extension of the published Homarus americanus transcriptome [5]. One possible explanation for the missing arthropod genes from our transcriptomes can be explained by the fact that our sequences were derived solely from nervous system tissue, while the references were built from arthropod genomic sequences.…”

“…As a microcrustacean, Daphnia is still a far cry from the large decapod crustaceans that are common models in neuroscience research, such as crabs, lobsters, crayfish and shrimp. Thus even with some very recent additions to decapod crustacean transcriptome data [4, 5], there is a strong need to add to our sequence knowledge of these species.…”