Spleen transcriptome analysis to identify genes and long noncoding RNAs in Leghorn and Fayoumi chicken during Newcastle disease.

Newcastle disease virus (NDV) causes Newcastle disease (ND) in a wide range of avian species. Leghorn and Fayoumi chicken breeds are known to differ in their responses to ND. This study aimed to analyse the spleen transcriptome, an important immune organ, to characterise genes and long noncoding RNAs (lncRNAs) associated with immune transcriptional response. Overall, we identified 5579 putative lncRNAs, including 3584 novel transcripts. Functional annotation revealed six differentially expressed genes (DEGs) associated with immune-related Gene Ontology terms and Reactome pathways. Subsequent co-expression analysis showed that these genes were co-expressed with 101 cis-lncRNAs. No immune-related DEGs were detected in the challenge-based analysis, whereas breed and timepoint-based analyses showed upregulation of immune DEGs and cis-lncRNAs predominantly in Fayoumi. These findings are consistent with our previous studies and indicate breed-dependent differences in immune-associated transcriptional regulation, even in the absence of detectable tissue-level viral transcripts. Collectively, this study identifies a limited set of immune-related genes and regulatory lncRNAs in the spleen that may contribute to differential host responses to NDV. Further functional studies are required to elucidate the regulatory mechanisms involving these lncRNAs.