Transcriptional Signatures of Domestication Revealed by Meta-Analysis of Pig, Chicken, Wild Boar, and Red Junglefowl Gene Expression Data

Domesticated animals have undergone significant changes in their behavior, morphology, and physiological functions during domestication. To identify the changes in gene expression associated with domestication, we collected RNA-seq data of pigs, chickens, wild boars, and red junglefowl from public databases and performed a meta-analysis. Gene expression was quantified and the expression ratio between domesticated animals and their wild ancestors (DW-ratio) was calculated. Genes were classified as “upregulated,” “downregulated,” or “unchanged” based on their DW-ratio, and DW-score was calculated for each gene. Gene set enrichment analysis revealed that genes upregulated in pigs were related to defense from viral infection, whereas those upregulated in chickens were associated with aminoglycan and carbohydrate derivative catabolic processes. Genes commonly upregulated in pigs and chickens are involved in the immune response, olfactory learning, epigenetic regulation, cell division, and extracellular matrix. In contrast, genes upregulated in wild boar and red junglefowl are related to stress response, cell proliferation, cardiovascular function, neural regulation, and energy metabolism. These findings provide valuable insights into the genetic basis of the domestication process and highlight potential candidate genes for breeding applications.<br><b>Supplementary Table1 - Pig and Wild Boar Sample metadata</b><b>Supplementary Table2 - Chicken and Red Junglefowl sample metadata</b><b>Supplementary Table3 - TPM Data of Pig and Wild Boar</b><b>Supplementary Table4 - TPM Data of Chicken and Red Junglefowl</b><b>Supplementary Table5 - DW-Score Data for Gene Expression of Pig and Wild Boar</b><b>Supplementary Table6 - DW-Score Data for Gene Expression of Chicken and Red Junglefowl</b><b>Supplementary Table7 - Lists of upregulated genes in Pig</b><b>Supplementary Table8 - Lists of upregulated genes in Wild Boar</b><b>Supplementary Table9 - Result and lists of enrichment analysis of Pig</b><b>Supplementary Table10 - Result and lists of enrichment analysis of Wild Boar</b><b>Supplementary Table11 - Lists of upregulated genes in Chicken</b><b>Supplementary Table12 - Lists of upregulated genes in Red Junglefowl</b><b>Supplementary Table13 - Result and lists of enrichment analysis of chicken</b><b>Supplementary Table14 - Result and lists of enrichment analysis of Red Junglefowl</b><b>Supplementary Table15 - DW-Score data for pig and wild boar converted to human gene IDs</b><b>Supplementary Table16 - Lists of upregulated genes in Pig converted to human gene IDs</b><b>Supplementary Table17 - </b><b>Lists of upregulated genes in Wild Boar converted to human gene IDs</b>