Gallus gallus Raw sequence reads. Gallus gallus

Purpose: previous study identified that the late feathering (LF) chickens have slower innate immune factors expression rate compared with early feathering (EF) chickens, and the innate immune response in LF chickens are weaker than the EF chickens. To better understand the difference, we performed RNA-seq to analysis the lncRNA and mRNA expression profiles in ALV-J infected spleen between LF and EF chickensMethods:In this study, eight groups (in total 24 chickens), including 7 d.p.i (7-LF infection_3, 7-LF un-infection_3, 7-EF infection_3 and 7-EF un-infection_3) and 13 d.p.i (13-LF infection_3, 13-LF un-infection_3, 13-EF infection_3 and 13-EF un-infection_3). Total RNA was isolated by TRIzol following the manufacturer’s instruction. Illumina HiSeq 2500 platform was used for RNA-sequencing.Results: In total, 23,841 lncRNAs and 25,200 mRNAs were identified. KEGG analysis revealed that DE-lncRNAs were enriched in cytokine-cytokine receptor interaction and neuroactive ligand-receptor interaction at 7 d.p.i. The mRNA of Immune related of LF were enriched in Neuroactive ligand-receptor interaction, Toll-like receptor signaling pathway and Influenza A but no significantly. The mRNAs of EF were significantly enriched in TNF signaling pathway, Hepatitis B and HTLV-I infection.Conclusions: the LF chickens have slower innate immune factors expression rate compared with EF chickens, and the innate immune response in LF chickens are weaker than the EF chickens. We speculated that the host innate immune mediated by lncRNA caused such differences between SF and FF chicken lines. These results provide valuable insights into the game of host antiviral immune response and ALV-J infection.