In-depth transcriptome analysis of the Hardin crayfish, Faxonius wrighti

Abstract

Freshwater crayfish are an ecological keystone species and flagship organisms for endangered aquatic habitats, yet they face population declines driven by anthropogenic activity. The Hardin crayfish (Faxonius wrighti), endemic to the middle Tennessee River basin, is particularly vulnerable due to habitat degradation from sedimentation, altered flow, and agricultural runoff. Establishing genomic resources for species of conservation concern, such as F. wrighti, is essential for understanding the molecular mechanisms underlying physiological responses to environmental stressors. In this study, RNA-Seq was performed on 11 F. wrighti individuals, using hepatopancreas, gill, and abdominal muscle tissues to generate a comprehensive, multi-tissue transcriptome. De novo assembly using Trinity yielded 91,808 unigenes, with 45.3 % annotated in major databases such as GO, KEGG, and NR. Differential gene expression analysis revealed strong tissue-specific expression, with stress-response pathways highly enriched in hepatopancreas and gill tissues. Notable among these were cytochrome P450 metabolism and Na⁺/K⁺-ATPase regulation, key pathways associated with responses to chemical stress and osmotic changes, respectively. This multi-tissue transcriptome represents the first genomic resource for the diverse genus Faxonius, offering a foundational resource for future studies of population-level adaptation and response to environmental stressors. More broadly, these findings also highlight the value of tissue-specific transcriptomics in non-model crayfish species and add to the limited genomic data available for endangered crayfish species.

Keywords: Crayfish; Freshwater; Gills; Hepatopancreas; RNA-Seq; Transcriptomics.