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Background  The Sapsaree ( Canis familiaris ) is a Korean native dog that is very friendly, protective, and loyal to its owner, and is registered as a natural monument in Korea (number: 368). To investigate large-scale gene expression profiles and identify the genes related to exercise-induced stress in the Sapsaree, we performed whole-transcriptome RNA sequencing and analyzed gene expression patterns before and after exercise performance.    Results  We identified 525 differentially expressed genes in ten dogs before and after exercise. Gene Ontology classification and KEGG pathway analysis revealed that the genes were mainly involved in metabolic processes, such as programmed cell death, protein metabolic process, phosphatidylinositol signaling system, and cation binding in cytoplasm. The ten Sapsarees could be divided into two groups based on the gene expression patterns before and after exercise. The two groups were significantly different in terms of their basic body type ( p ≤ 0.05 ). Seven representative genes with significantly different expression patterns before and after exercise between the two groups were chosen and characterized.    Conclusions  Body type had a significant effect on the patterns of differential gene expression induced by exercise. Whole-transcriptome sequencing is a useful method for investigating the biological characteristics of the Sapsaree and the large-scale genomic differences of canines in general.    Electronic supplementary material  The online version of this article (doi:10.1186/s40781-016-0097-1) contains supplementary material, which is available to authorized users.

Whole-transcriptome analyses of the Sapsaree, a Korean natural monument, before and after exercise-induced stress