ExpressAnalyst: a unified platform for RNA-seq analysis in non-model species

The increasing application of RNA-seq to study non-model species demands easy-to-use and efficient bioinformatics tools to help researchers quickly uncover biological and functional insights. We developed ExpressAnalyst (www.expressanalyst.ca), a web-based tool for processing, analyzing, and interpreting RNA-seq data from any eukaryotic species. ExpressAnalyst contains a series of modules that enable raw data processing and annotation of FASTQ files, and statistical and functional analysis of counts tables and gene lists. All modules are integrated with EcoOmicsDB, an ortholog database that enables comprehensive analysis for species without a reference transcriptome. By coupling ultra-fast read mapping algorithms with high-resolution ortholog databases through a user-friendly web interface, ExpressAnalyst enables researchers to obtain global expression profiles and gene-level insights from raw RNA-seq reads within 24 hours. Here, we present ExpressAnalyst and demonstrate its utility with a case study of RNA-seq data from multiple non-model salamander species, including two that do not have a reference transcriptome. Overall design: ExpressAnalyst contains recently updated version 2.0 of the Seq2Fun algorithm. To ensure that Seq2Fun 2.0 also reproduces results obtained using traditional approaches, we carried out two case studies using organisms with reference transcriptomes (American lobster and zebrafish). Here, we publish the lobster data. Stage I lobster larvae were exposed for 24hrs to four doses of WAF (10%, 19%, 37% and 72%) a positive control (1-methylnaphthalene, at 0.3 mg/L corresponding to the estimated concentration of EC20) or a negative control (0.22 µm filtered seawater). Due to the lack of effects reported on survival, molting and respiration after WAF exposures, only the highest dose of WAF (72% WAF) was considered for transcriptomics analysis. RNA extraction of whole larvae exposed to 72% WAF (n = 7), methylnaphthalene (n = 6) and filtered seawater (n = 6) was performed using Trizol. The transcriptomes were sequenced using Novaseq Illumina at 28M reads per library.