Non-lethal scute transcriptomics reveals biomarker candidates for environmental stress in Mexican Morelet’s crocodiles

We used RNA-seq on caudal scute biopsies from 43 Morelet’s crocodiles (Crocodylus moreletii) representing six wild populations and a captive reference group to characterize conserved and site-specific transcriptomic responses and derive candidate biomarkers for omics-based biomonitoring.

After mapping to the Alligator mississippiensis genome, 18,107 genes were retained for differential expression and weighted gene co-expression network analyses. Wild crocodiles showed a consistent shift along the first principal component, separating an extracellular matrix (ECM)/structural program from an epidermal-metabolic program. Intersect DEGs and scute modules up-regulated in all wild sites were enriched for ECM organization, ER stress, vesicle trafficking and adhesion pathways, whereas union DEGs captured site-specific alterations in lipid metabolism, ion transport, neuronal signaling and developmental processes, suggesting heterogeneous local stressors.