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We conducted herein transcriptome sequencing of the ovine abomasal tissues using the Illumina HiSeq 4000 platform to segregate early and late H. contortus-infected sheep (7 and 50 days post-infected groups, respectively) from the control naive ones. A total of 548, 357 and 7 were substantially induced genes in 7 days post-infection versus uninfected-control group, 50 days post-infection versus 7 days post-infection (7 dpi), and 50 days post-infection (50 dpi) versus uninfected-control group, respectively. However, a total of 301, 355 and 11 were significantly repressed genes between 7 dpi versus uninfected-control group, 50 dpi versus 7 dpi, and 50 dpi versus uninfected-control group, correspondingly. This indicates that H. contortus infection induced a more potent activation of abomasal gene expression in the early stage of infection as compared to the late stage. Seven pathways were annotated by Kyoto …