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

Abstract

Previous studies of horse RNA-seq were performed by mapping sequence reads to the reference genome during transcriptome analysis. However in this study, we focused on two main ideas. First, differentially expressed genes (DEGs) were identified by de novo–based analysis (DBA) in RNA-seq data from six Thoroughbreds before and after exercise, here-after referred to as “de novo unique differentially expressed genes” (DUDEG). Second, by integrating both conventional DEGs and genes identified as being selected for during domestication of Thoroughbred and Jeju pony from whole genome re-sequencing (WGS) data, we give a new concept to the definition of DEG. We identified 1,034 and 567 DUDEGs in skeletal muscle and blood, respectively. DUDEGs in skeletal muscle were significantly related to exercise-induced stress biological process gene ontology (BP-GO) terms: ‘immune system process’; ‘response to stimulus’; and, ‘death’ and a KEGG pathways: ‘JAK-STAT signaling pathway’; ‘MAPK signaling pathway’; ‘regulation of actin cytoskeleton’; and, ‘p53 signaling pathway’. In addition, we found TIMELESS, EIF4A3 and ZNF592 in blood and CHMP4C and FOXO3 in skeletal muscle, to be in common between DUDEGs and selected genes identified by evolutionary statistics such as FST and Cross Population Extended Haplotype Homozygosity (XP-EHH). Moreover, in Thoroughbreds, three out of five genes (CHMP4C, EIF4A3 and FOXO3) related to exercise response showed relatively low nucleotide diversity compared to the Jeju pony. DUDEGs are not only conceptually new DEGs that cannot be attained from reference-based analysis (RBA) but also supports previous RBA results related to exercise in Thoroughbred. In summary, three exercise related genes which were selected for during domestication in the evolutionary history of Thoroughbred were identified as conceptually new DEGs in this study.

Genetic Susceptibility to Rhodococcus equi

“…Investigators have used RNA‐Seq to characterize the expression profile of genes critical to the differentiation and regulation of cells during embryogenesis,90 and to characterize the expression and inferred function of RNAs in the equine sperm transcriptome 89. Several studies also have used RNA‐Seq in horses to identify differentially expressed genes when comparing blood, muscle (obtained by biopsy), or both before and after exercise or racing 86, 87, 92. These studies have successfully identified pathways involved in stress during and while recovering from exercise.…”

“…Several studies have reported the application of RNA-Seq in horses in an attempt to identify differentially expressed genes. [86][87][88][89][90][91][92][93][94][95] To the authors' knowledge, the first report of RNA-Seq in horses was an effort to characterize the transcriptome and tissue-specific expression profiles from 8 equine tissues. 94 A subsequent study focused on characterizing gene expression by RNA-Seq in immunologically active tissues.…”

Developmental exposure to ethanol increases the neuronal vulnerability to oxygen–glucose deprivation in cerebellar granule cell cultures

“…A widely used systems biology technique to highlight biological processes is gene category over-representation analysis (Park et al, 2014). To perform this analysis genes are grouped into categories by a common biological property and then tested to find categories that are over-represented.…”

Reptile genomes open the frontier for comparative analysis of amniote development and regeneration

“…2B). There are many tools available for de novo transcriptome assembly and differential expression analysis of these transcriptomes (Davidson, Oshlack, 2014;Grabherr et al, 2011;Haas et al, 2013;Robertson et al, 2010;Schulz et al, 2012) In cases where the reference genome is of low quality, i.e., with misassemblies and large genomic deletions, genes of interest that are absent in the genome assembly can be present in the transcriptome (Park et al, 2014). Another possible approach is mapping assembled transcriptomes to a closely related reference genome, which has been utilized with non-human primates, across the mammalian clade, and the zebra finch and human genomes (Fig.…”