De novo Assembly and Analysis of the Chilean Pencil Catfish Trichomycterus areolatus Transcriptome

Abstract

Trichomycterus areolatus is an endemic species of pencil catfish that inhabits the riffles and rapids of many freshwater ecosystems of Chile. Despite its unique adaptation to Chile's high gradient watersheds and therefore potential application in the investigation of ecosystem integrity and environmental contamination, relatively little is known regarding the molecular biology of this environmental sentinel. Here, we detail the assembly of the Trichomycterus areolatus transcriptome, a molecular resource for the study of this organism and its molecular response to the environment. RNA-Seq reads were obtained by next-generation sequencing with an Illumina® platform and processed using PRINSEQ. The transcriptome assembly was performed using TRINITY assembler. Transcriptome validation was performed by functional characterization with KOG, KEGG, and GO analyses. Additionally, differential expression analysis highlights sex-specific expression patterns, and a list of endocrine and oxidative stress related transcripts are included.

Muscle Transcriptome Sequencing Revealed Thermal Stress–Responsive Regulatory Genes in Farmed Rohu, Labeo rohita (Hamilton, 1822)

“…Thus, studies on molecular-level understanding of sh physiology in response to biotic and abiotic stressors are required. The advances in NGS technologies and computational tools have been helpful in the whole genome and transcriptome sequencing of several species for a better understanding of their biology and the changes that occur due to climate change (Chatchaiphan et al, 2017, Schulze et al, 2016. Several studies in teleost depicted that temperature affects sh physiology and they cope with that via adaptation (Akbarzadeh et al, 2018).…”

De novo transcriptome based on next-generation sequencing reveals candidate genes with sex-specific expression in Arapaima gigas (Schinz, 1822), an ancient Amazonian freshwater fish

“…Lu et al [ 83 ] reported over-expression of this gene in the brains of male catfish ( Pelteobagrus fulvidraco ), indicating that the differential expression of spaca4 in the two sexes may provide an informative tool for sexing juvenile arapaima. The spaca4 gene was also found to be up-regulated in analyses of the transcriptomes of two fish, Trichomycterus areolatus [ 84 ], based on whole-body samples, and Ictalurus punctatus [ 85 ], focusing on the testicles. While this gene is up-regulated in the males of many different organisms, it was also expressed in the liver libraries of both the male and female arapaima, which indicates that the lack of contigs in the skin of the females does not necessarily mean that the gene was not expressed in this tissue, but rather that there may have been a reduced level of recuperation of the reads from this library.…”

Editor’s Highlight: Organophosphate Diazinon Altered Quorum Sensing, Cell Motility, Stress Response, and Carbohydrate Metabolism of Gut Microbiome

“…Bioinformatics analysis of metatranscriptomics data. The raw fastq files of each animal were analyzed with our metatranscriptomic analysis workflow, built on several previous studies (Gaur et al, 2016;Haas et al, 2013;Livernois et al, 2016;Mora-Ortiz et al, 2016;Schulze et al, 2016). The process is briefly described as follows.…”