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

This study presents an updated genome annotation of Gallus gallus through a comprehensive multi-tissue transcriptome analysis aimed at enhancing the Functional Annotation of Animal Genomes (FAANG) efforts. Having generated RNA sequencing data from 20 different chicken tissues and cell types, this allowed for the identification of 110,930 transcript isoforms, including approximately 37,000 novel and unannotated transcripts. This expanded transcriptome resource comprises diverse biological systems, including digestive, immune, reproductive, and muscular tissues, significantly enhancing transcript diversity and functional annotation. Using advanced bioinformatics tools, we analyzed allele-specific expression (ASE) across these tissues, revealing 365,984 ASE single nucleotide polymorphisms (SNPs) and 11,530 unique ASE genes. Our findings elucidate the intricate landscape of gene expression patterns and allelic imbalances, providing insights into potential cis-regulatory mechanisms influencing traits relevant to poultry production and health. 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 complexity of the chicken genome and the necessity of continued genomic improvements. Collectively, this work contributes valuable resources for breeding strategies focused on disease resistance and productivity enhancement in chickens, addressing global agricultural challenges and the evolving needs of poultry science.