File S1 - Investigation of De Novo Unique Differentially Expressed Genes Related to Evolution in Exercise Response during Domestication in Thoroughbred Race Horses

Contains the following. Table S1, List of unique DEGs in skeletal muscle and blood in six Thoroughbred horses before and after exercise RNA-seq data by de novo assembly (FDRST (FST cut-off value top 5% with empirical p-value1.73481 significant SNPs in Jeju domestic pony were selected. Table S6, List of basic stats such as the number of transcripts, components, and contig N50 value in RNA-seq whole reads and unmapped reads by trinity de novo assembly. Table S7, Number of annotated transcripts from RNA-seq unmapped reads by trinity de novo assembly. The number in the parentheses is the number of transcripts that were not included in the results of the reference-based analysis. Table S8, Basic information of 4 horses re-sequencing data. Table S9, RT-PCR primer information such as the gene symbol, direction and sequence. Figure S1, Summary of comparative analysis between de novo assemble and reference genome assemble from blood in six Thoroughbred horses before and after exercise RNA-seq data (Total 12 samples). a) The number of common transcripts of 12 samples between de novo assemble and reference genome assemble b) MDS plot of six Thoroughbred horses before and after exercise using de novo assemble. c) The number of DEGs between de novo assemble and reference genome assemble. d) Heat-map visualization of common DEGs between de novo assemble and reference genome assemble: rows represent DEGs from blood and columns represent assemble method from 6 horse samples (*First ‘B’ is for Blood and ‘M’ is for muscle. ‘F1’, ‘F2’, ‘F3’ and ‘S3’ are horse samples. Last ‘B’ is for ‘before exercise’ and ‘P’ is for ‘after exercise’). Figure S2, MDS plot of six Thoroughbred horses before and after exercise using reference genome assemble in RNA-seq. a) MDS plot of blood tissue in six Thoroughbred horse before and after exercise. b) MDS plot of skeletal muscle tissue in six Thoroughbred horse before and after exercise. (*First ‘B’ is for Blood and ‘M’ is for muscle. ‘F1’, ‘F2’, ‘F3’ and ‘S3’ are horse samples. Last ‘B’ is for ‘before exercise’ and ‘P’ is for ‘after exercise’). Figure S3, Hierarchical clustering of biological process GO terms associated with up-regulated DEGs in blood. The gene list of each GO term clustered using DAVID was compared to calculate the distance between the GO terms. For a distance value >0.5, GO terms were re-clustered, and GO term groups are shown as light-blue graduated blocks. The number of genes associated with the re-clustered GO term group is shown on the left side of the block. Figure S4, Hierarchical clustering of biological process GO terms associated with down-regulated DEGs in blood. The gene list of each GO term clustered using DAVID was compared to calculate the distance between the GO terms. For a distance value >0.5, GO terms were re-clustered, and GO term groups are shown as light-blue graduated blocks. The number of genes associated with the re-clustered GO term group is shown on the left side of the block. Figure S5, Hierarchical clustering of biological process GO terms associated with up-regulated DEGs in muscle. The gene list of each GO term clustered using DAVID was compared to calculate the distance between the GO terms. For a distance value >0.5, GO terms were re-clustered, and GO term groups are shown as light-blue graduated blocks. The number of genes associated with the re-clustered GO term group is shown on the left side of the block. Figure S6, Hierarchical clustering of biological process GO terms associated with down-regulated DEGs in muscle. The gene list of each GO term clustered using DAVID was compared to calculate the distance between the GO terms. For a distance value >0.5, GO terms were re-clustered, and GO term groups are shown as light-blue graduated blocks. The number of genes associated with the re-clustered GO term group is shown on the left side of the block. Figure S7, Histogram of conventional FST frequency between Thoroughbred and jeju pony. x-axis is conventional FST value, y-axis is gene frequency. Figure S8, qRT-PCR validation of de novo unique differentially expressed genes (DUDEGs) identified from the RNA-seq data set of Thoroughbred horses before and after exercise: a) RT-PCR of six DUDEG in horses before exercise and after exercise. b) qRT-PCR results depicted as Ct value was calculated using 2-ΔΔCt method. *: p-value (ZIP)