Enhance the annotation of long noncoding RNAs in the duck genome using multi-tissue transcriptome data

Long non-coding RNAs (lncRNAs), defined as RNA transcripts exceeding 200 nucleotides without protein-coding capacity, play pivotal regulatory roles in various biological processes. The duck is an economically important poultry species in China, and contributes significantly to meat and egg production. However, the current annotation of lncRNAs within the duck genome remains sparse, which limits a comprehensive understanding of their molecular regulatory mechanisms and biological functions. Based on 1,350 transcriptome datasets spanning multiple tissues, we systematically annotated 22,831 lncRNA loci within the ZJU1.0 duck reference genome, comprising 9,455 novel and 13,376 previously annotated lncRNAs. Structural analyses revealed that duck lncRNAs are characterized by significantly fewer exons, shorter transcript lengths, and lower expression levels compared to protein-coding genes (PCGs). Through construction of co-expression networks between lncRNAs and PCGs, we predicted potential regulatory functions of lncRNAs, highlighting their involvement in key biological pathways, including sarcomere, cytoskeleton in muscle cells and focal adhesion. In addition, we further identified tissue-specific lncRNAs, housekeeping lncRNAs, sex-biased lncRNAs, and cross-species conserved lncRNAs. This study establishes the most comprehensive lncRNA annotation resource to date for the duck genome, providing a crucial foundation for elucidating the roles of lncRNAs in biological processes and their genetic mechanisms in artificial selection.