A stage-resolved, proteome-supported co-expression atlas reveals coordinated expression remodeling at host entry in Haemonchus contortus.

Haemonchus contortus shifts from free-living larval stages on pasture to parasitic, blood-feeding stages in the host abomasum, but the coordinated gene programs that underlie this transition remain incompletely resolved. We aimed to construct a stage-resolved developmental co-expression atlas of H. contortus using public RNA-seq data and to integrate it with a 2025 developmental proteome atlas. We assembled 42 RNA-seq libraries spanning ten life-cycle stages from egg to adult and built a signed weighted gene co-expression network on 10,485 genes, which resolved 18 co-expression modules whose eigengenes followed an ordered developmental progression. Several modules were strongly associated with individual stages and showed functional enrichment matching that stage biology. Integration with the proteome atlas gave positive transcriptome-proteome concordance at every matched stage, supporting the modules at the protein level. A differential-expression contrast across the free-living to parasitic boundary identified 4286 genes that were differentially expressed between the two phases: free-living stages were associated with sensory and neuronal programs, whereas parasitic stages showed metabolic, gut and adult, and parasite-associated programs. These co-expression modules and stage-associated programs suggest coordinated stage-associated expression remodeling at host entry, although they do not by themselves demonstrate direct regulation. The atlas provides a reusable, systems-level framework for parasite developmental biology and a prioritized starting point for future functional studies in H. contortus and related nematodes.