PMID- 24658125 OWN - NLM STAT- MEDLINE DCOM- 20150116 LR - 20220318 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 3 DP - 2014 TI - Investigation of de novo unique differentially expressed genes related to evolution in exercise response during domestication in Thoroughbred race horses. PG - e91418 LID - 10.1371/journal.pone.0091418 [doi] LID - e91418 AB - 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. FAU - Park, Woncheoul AU - Park W AD - Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea. FAU - Kim, Jaemin AU - Kim J AD - Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea. FAU - Kim, Hyeon Jeong AU - Kim HJ AD - C&K genomics, Seoul National University, Seoul, Republic of Korea. FAU - Choi, JaeYoung AU - Choi J AD - Department of Animal Science, College of Life Sciences, Pusan National University, Miryang, Republic of Korea. FAU - Park, Jeong-Woong AU - Park JW AD - Department of Animal Science, College of Life Sciences, Pusan National University, Miryang, Republic of Korea. FAU - Cho, Hyun-Woo AU - Cho HW AD - Department of Animal Science, College of Life Sciences, Pusan National University, Miryang, Republic of Korea. FAU - Kim, Byeong-Woo AU - Kim BW AD - Department of Animal Science, College of Life Sciences, Pusan National University, Miryang, Republic of Korea. FAU - Park, Myung Hum AU - Park MH AD - TNT Research, Anyang, Republic of Korea. FAU - Shin, Teak-Soon AU - Shin TS AD - Department of Animal Science, College of Life Sciences, Pusan National University, Miryang, Republic of Korea. FAU - Cho, Seong-Keun AU - Cho SK AD - Department of Animal Science, College of Life Sciences, Pusan National University, Miryang, Republic of Korea. FAU - Park, Jun-Kyu AU - Park JK AD - Leaders in Industry-university Cooperation, Pusan National University, Miryang, Republic of Korea. FAU - Kim, Heebal AU - Kim H AD - Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea; C&K genomics, Seoul National University, Seoul, Republic of Korea. FAU - Hwang, Jae Yeon AU - Hwang JY AD - Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea. FAU - Lee, Chang-Kyu AU - Lee CK AD - Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea. FAU - Lee, Hak-Kyo AU - Lee HK AD - Genomic Informatics Center, Hankyong National University, Anseong, Republic of Korea. FAU - Cho, Seoae AU - Cho S AD - C&K genomics, Seoul National University, Seoul, Republic of Korea. FAU - Cho, Byung-Wook AU - Cho BW AD - Department of Animal Science, College of Life Sciences, Pusan National University, Miryang, Republic of Korea. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140321 PL - United States TA - PLoS One JT - PloS one JID - 101285081 SB - IM MH - Animals MH - *Gene Expression Regulation MH - Genome MH - Genotype MH - Horses/*genetics/metabolism MH - *Physical Conditioning, Animal MH - Transcriptome PMC - PMC3962374 COIS- Competing Interests: MHP has the following financial competing interest: Paid employment in TNT Research Company Limited, Dongan-gu, Anyang-si, Republic of Korea. The rest of the authors have declared that no competing interests exist. This does not alter the authors' adherence to all the PLoS ONE policies on sharing data and materials. HK has the following financial competing interest: Paid employment in C&K Genomics company INC, C&K genomics Main Bldg. #514, SNU Research Park, Seoul National University Mt.4-2. SC has the following financial competing interest: CEO of C&K Genomics company INC, C&K genomics Main Bldg. #514, SNU Research Park, Seoul National University Mt.4-2. EDAT- 2014/03/25 06:00 MHDA- 2015/01/17 06:00 PMCR- 2014/03/21 CRDT- 2014/03/25 06:00 PHST- 2013/09/08 00:00 [received] PHST- 2014/02/11 00:00 [accepted] PHST- 2014/03/25 06:00 [entrez] PHST- 2014/03/25 06:00 [pubmed] PHST- 2015/01/17 06:00 [medline] PHST- 2014/03/21 00:00 [pmc-release] AID - PONE-D-13-36852 [pii] AID - 10.1371/journal.pone.0091418 [doi] PST - epublish SO - PLoS One. 2014 Mar 21;9(3):e91418. doi: 10.1371/journal.pone.0091418. eCollection 2014.