Long Noncoding RNAs in Dogs: Comparative Insights Across Species and Breeds

Long noncoding RNAs (lncRNAs) have emerged as key regulators of gene expression, yet their annotation and functional characterization remain challenging, especially in nonclassical model organisms. In this review, we explore the landscape of lncRNAs in dogs (Canis lupus familiaris) and other species, highlighting recent advances in genome assemblies, transcriptomic resources, and computational tools for lncRNA discovery. We discuss the advantages of the canine system for studying genotype-phenotype relationships, including its rich breed diversity, well-characterized diseases, and simplified genetic architecture. We describe how both short- and long-read RNA-sequencing technologies, in combination with curated reference annotations from Ensembl and RefSeq, have enabled the detection of thousands of novel canine lncRNAs. However, we also point out discrepancies across assemblies and annotation strategies, which underscore the importance of integrating multi-omic data and refining computational pipelines. Using comparative genomics, we illustrate lncRNA conservation across dog breeds and species and review emerging examples of phenotype-associated or differentially expressed lncRNAs. Finally, we argue for a transition toward pangenome and pan-transcriptome approaches, which can better capture transcript diversity and structural variation across breeds. Such frameworks will be essential for the future functional annotation of lncRNAs and their application to both veterinary and human biomedical research.