Comparative transcriptomic and metagenomic analyses reveal key factors affecting the growth rate of Red Swamp Crayfish (Procambarus clarkii)

Even under highly-controlled growth conditions, sibling individuals of red swamp crayfish (Procambarus clarkii) frequently exhibit stunting. To elucidate the causes of stunting, we compared the hepatopancreas transcriptome and intestinal flora of sibling crayfish. Individual variations were investigated, and the association of gut bacterial community function with host transcriptome function was explored. A total of 60,637,958 single genes were assembled from 300,691,028 high-quality reads. When the expression patterns of crayfish hepatopancreas of various sizes were compared, 497 differentially expressed genes (P < 0.05) were discovered. KEGG database and GO functional annotation were conducted, revealing 32 enriched KEGG signaling pathways, with the most significant enrichment seen in genes associated with fatty acid production. We additionally found enrichment in other metabolism-related enzymes (AMS, Gls, and Lps) and immune-related enzymes (Lyz, SOD, and Ppo) when comparing rapidly growing individuals to slowly growing individuals. Furthermore, we discovered that Proteobacteria, Tenericutes, Actinomycetes, and Cyanobacteria bacteria were more prevalent in the microbiomes of rapidly growing individuals, implying that the crayfish microbiota is adapted to fast growth and may promote accelerated development by regulating the expression levels of metabolic genes. These results lay the foundation for future studies focused on the association between crayfish intestinal flora and growth rate.