An updated Gallus gallus genome annotation through multi-tissue transcriptome analysis

This study presents an updated Gallus gallus genome annotation through a comprehensive multi-tissue transcriptome analysis aimed at enhancing the Functional Annotation of Animal Genomes (FAANG) efforts. Generating RNA sequencing data from 20 different chicken tissues and cell types allowed for the identification of 110,930 transcript isoforms, including approximately 37,000 unannotated transcripts. This expanded resource significantly enhances transcript diversity and functional annotation. We analyzed allele-specific expression (ASE) across tissues, revealing 11,530 unique ASE genes. Our findings elucidate the intricate landscape of gene expression patterns and allelic imbalances. Notably, tissue-specific isoforms and differentially expressed genes, particularly in reproductive and muscle tissues, showcase their relevance for traits like fertility and meat quality. The identification of novel lncRNAs and protein-coding genes underscores the necessity of continued genomic improvements. This work contributes valuable resources for breeding strategies focused on disease resistance and productivity enhancement, addressing global agricultural challenges and the evolving needs of poultry science.